From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 03:20:19 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 01:20:19 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. Message-ID: Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 04:01:46 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 02:01:46 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: References: Message-ID: Hi Carson, when I tried running genemark as below, I see the *.lst files (protein & nuc fasta) produced. But no gtf2 at all... And no gms.log files at all. Any ideas? /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p 0 -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -a Enmo_susu.11.fsa Thanks, Gowthaman ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org] Sent: Sunday, November 04, 2012 1:20 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Chunk failed at level 6 error.. Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 08:18:24 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:18:24 -0500 Subject: [maker-devel] Conensus gene model In-Reply-To: <1640.131.215.15.234.1351728273.squirrel@webmail.caltech.edu> Message-ID: The way models are generated, it really doesn't so much matter where the protein alignments came from. Basically the protein alignment is just creating a region of potential CDS. MAKER than gives that region as a hint to the gene predictors, but the gene predictors really make the call on how to finally structure the gene based on their training sets. You can short circuit this by using the protein2genome option as a separate run with only your primary proteins. MAKER will then try and turn those protein alignments directly into genes. Results from that run can sometimes be useful for generating training sets as well, or can be passed back into MAKER as pred_gff so MAKEr has the option to turn those into models as an alternative to the models produced by the ab initio predictors. --Carson On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: >Hi Jason, thanks for directions on generating training-set for augustus. >Also as alignment evidence if we are providing protein sequences from the >primary organism as well as other closely related species is there an >option to give the primary protein file precedence over others? >At the moment I have all the proteins(from primary organism as well as >related species) into a single file as protein option in maker_opts.ctl > >Thanks and regards, >Parul Kudtarkar > >> Paul - >> >> I think I've posted on this before here if you are asking how to go from >> SNAP training to Augustus training. >> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >> >> I do this type of training a lot - here some pointers. >> >> I often train by generating models using cegma on the genome and get >>these >> 400 or so good models as my training set. when I have EST or RNA-Seq I >> use PASA to generate the best set of annotations. >> >> For CEGMA - then I run this script that comes with MAKER: >> cegma2zff output.cegma.gff genome.fa >> >> Then I follow the SNAP directions >> >> fathom genome.ann genome.dna -categorize 1000 >> fathom uni.ann uni.dna -export 1000 -plus >> mkdir MYGENOME >> cd MYGENOME >> forge ../export.ann ../export.dna --OPTIONS >> cd ../MYGENOME >> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >> >> I then also make the augustus training data like this running in the >> directory that has the export.ann and export.dna files: >> perl gene_prediction/zff2augustus_gbk.pl > train.gb >> >> using this script: >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>ff2augustus_gbk.pl >> >> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>and >> best models from PASA and incorporate all these data in to my SNAP >> training set, and then export again back to gbk for the augustus >>training. >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>asatraining2zff.pl >> >> Then you just need to run the Augustus training (autoAugTrain.pl) on the >> train.gb file. >> >> Jason >> >> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar wrote: >> >>> Hello Carson and maker community, >>> >>> Thank you very much for your guidelines on using the maker-pipeline. >>> Yes, >>> green sea urchin genome that we are trying to annotate. >>> We are running the on scaffolds and most of these scaffolds are small >>>in >>> size(very first genome assembly). We would typically expect 20,000 >>>genes >>> in this genome. So we are running maker using EST and proteins from the >>> genome and out-groups to generate training dataset for SNAP and >>> Augustus. >>> Depending on the resulting predictions we may bootstrap the predicted >>> genes once again using EST and proteins. >>> >>> Do you have any further suggestions? Also could you point how to >>>convert >>> training set generated for SNAP to be used as training set for Augustus >>> as >>> well? Would maker give equal weightage to SNAP and Augustus predictions >>> for generating gene model? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> One thing you seem to be missing is protein evidence. >>>> >>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>> recommend adding all proteins from the Strongylocentrotus purpuratus >>> genome, then throw in another Deuterstome of your choice. Perhaps you >>> should also add a couple of outgroup organisms like Nematostella >>> vectensis >>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>> adding >>> to many protostome outgroups (i.e. C. elegans and Drosophila) because a >>> big part of their evolution is gene loss (so distant cnidaria often >>> match >>>> deuterstomes better than most protostomes do). >>>> >>>> You could take the maker results when protein data is included and use >>> it >>>> to retrain SNAP again. >>>> >>>> Even a 22 kb contig is still really short. Is this genome primarily >>> constituted by short contigs like this? I would recommend running >>>CEGMA >>> once on this genome to get an appropriate estimate of how recoverable >>> the >>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>> Cegma >>>> will give you an estimate for genome completeness as well as estimates >>> of >>>> what percentage of genes will be found in their entirety and what >>> percent >>>> will be partial genes. This is important to do if your genome is >>> fragmented as it will give you a reasonable expectation of what you can >>> expected to recover (as short contigs don't annotate very well - you >>> tend >>>> to loose a lot). >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>> >>>>> Hi Carson, >>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>as >>>>> 3 >>> exons EST alignments. Could you please recommend additional training. >>>We >>> are currently running maker on the entire contig set and eventually >>> merge >>>>> all the gff3 contig predictions. The using suggested >>>>>parameter/methods >>> we >>>>> would like to get a consensus gene-set with minimal false >>>>> positives/negatives. >>>>> Thanks, >>>>> Parul >>>>>> The contig in question is really too small to get much out of it >>>>>> (only 5 >>>>> kb). There was only one single exon EST alignments and a couple of >>> predictions with no evidence support. Anything smaller than 10 kb is >>> mostly useless for annotation purposes. You would really need a few >>> 100kb >>>>>> length or longer contigs to glean enough information for optimizing >>>>>> your >>>>> parameters. >>>>>> The general suggestions for any maker run are to use proteins from a >>>>> closely related organism or a couple of closely related organisms for >>>>> the >>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>> for >>>>> certain eukaryotes that have a bias for single exon transcripts (i.e. >>>>> some >>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>> initio >>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>> positives). >>>>>> Additional training would really depend on what your other contigs >>> look >>>>> like. Do you have any large contigs? I could look at one of those >>>>> and >>> give suggestions but the provided contig is just too short to glean >>> much. >>>>>> Thanks, >>>>>> Carson >>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>> Hello, >>>>>>> Please advice on the aforementioned query? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> ---------------------------- Original Message >>>>>>> ---------------------------- >>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>> From: "Parul Kudtarkar" >>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>> To: maker-devel at yandell-lab.org >>>>>>> >>>>>>>-------------------------------------------------------------------- >>>>>>>---- >>> -- >>>>> Hi, >>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>est,protein >>>>>>> and >>>>> contig file), agustus,genemarkE(we ran it outside maker and have gff3 >>>>>>> file >>>>>>> as input). The output that we get is combination of various >>>>>>> gene-predictors and evidences. I have attached sample result file. >>> What >>>>> would you recommend to get consensus result set? Bootstrapping the >>> resulting gff3 file (rerunning maker)? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 08:36:08 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:36:08 -0500 Subject: [maker-devel] Strange error at blastn step In-Reply-To: Message-ID: Sorry for the slow reply. I've been way for most of the last week. Could you do two more things before running another test. Update again to the latest development version, also set TMP to a non-NFS location like /tmp. Thanks, Carson From: Daniel Standage Date: Monday, 29 October, 2012 8:43 AM To: Carson Holt Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Strange error at blastn step I just ran svn update and tried again with the development version of Maker. Same long list of errors as in the last message. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Oct 29, 2012 at 9:39 AM, Daniel Standage wrote: > Carson, > > I was able to run the first svn update before the test job ran, but I didn't > get the message about this second update until after it has already executed > and failed. I got about 372 lines of such. > >> STATUS: Parsing control files... >> STATUS: Processing and indexing input FASTA files... >> STATUS: Setting up database for any GFF3 input... >> A data structure will be created for you at: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_datastore >> >> To access files for individual sequences use the datastore index: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_master_datastore_index.log >> >> STATUS: Now running MAKER... >> WARNING: Cannot find >scaffold_0, trying to re-index the fasta. >> stop here: scaffold_0 >> ERROR: Fasta index error >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 239. >> Process::MpiChunk::_prepare('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 73 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c808b0)', 'HASH(0x3c8ec40)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 79 >> Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x3c71f30)') >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 56 >> Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x3c80640)', 0, >> 'Process::MpiChunk') called at >> /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 627 >> --> rank=NA, hostname=c4 >> ERROR: Failed in tier preparation >> WARNING: You must always set a rank before running MpiTiers >> FATAL: argument `seq_id` does not exist in MpiTier object >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 86. >> >> Process::MpiChunk::_initialize_vars('Process::MpiChunk=HASH(0x3cc93d0)', >> 'HASH(0x3cc9400)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 47 >> Process::MpiChunk::new('Process::MpiChunk', 'HASH(0x3c80820)', 0, 0) >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 407 >> Process::MpiChunk::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f498)', 'HASH(0x3cc8f20)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 3811 >> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x3c8b300)', 'load', >> 'HASH(0x3c80820)', 0, 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 310 >> Process::MpiChunk::_loader('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0, 0, 'Process::MpiTiers=HASH(0x3c71f30)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 364 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f9c0)', 'HASH(0x3c8fb28)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 375 > > I'll try the next update and run the test again. I see a lot of references in > there to MPI, and just thought I would make it clear that although I am > running in a cluster environment, I am using the default serial version of > Maker, not the parallel MPI version. > > Also, after this failed, I tried changing the TMP directory so that it was > located on the same NFS mount as the scratch disk to which the output was > written. This did not seem to have any affect, and I saw the same issues with > the EST sequences unable to be found. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Fri, Oct 26, 2012 at 6:59 PM, Carson Holt wrote: >> >> >> From: Carson Holt >> Date: Friday, 26 October, 2012 6:10 PM >> To: Daniel Standage >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> I've been going over the indexing code using different scenarios and I may >> have isolated a candidate for what is causing this. Could you do one more >> 'svn update' inside the maker devel directory before running a test job? >> >> Thanks, >> Carson >> >> From: Daniel Standage >> Date: Friday, 26 October, 2012 2:29 PM >> To: Carson Holt >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> Got this from the compute node. Looks like native disk space to me. >> >> [dstandag at mason ~] df /tmp >> Filesystem 1K-blocks Used Available Use% Mounted on >> /dev/sda1 478573472 12319684 441943620 3% /tmp >> >> Installing a bundle of Perl prereqs for development version, will try that >> soon. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Fri, Oct 26, 2012 at 2:24 PM, Carson Holt wrote: >>> Ok. Try the developer release and see if it still happens. >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>> Date: Friday, 26 October, 2012 2:19 PM >>> >>> To: Carson Holt >>> Cc: "maker-devel at yandell-lab.org" >>> >>> Subject: Re: [maker-devel] Strange error at blastn step >>> >>> Unfortunately, the job is no longer running and as a result I cannot connect >>> to the compute nodes as I could while it was running. On the interactive >>> node, it looks like it's real disk, although it looks like there are some >>> tmpfs mounts. >>> >>> [dstandag at mason src] df /tmp >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> [dstandag at mason src] df >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> login_x86_64 16497564 3077352 13420212 19% / >>> tmpfs 16497564 0 16497564 0% /dev/shm >>> tmpfs 10240 0 10240 0% /var/tmp >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> AFS 9000000 0 9000000 0% /afs >>> bl-nas1:/vol/hd00 3435973856 1775658144 1660315712 52% /N/hd00 >>> bl-nas1:/vol/hd01 3435973856 1684116928 1751856928 50% /N/hd01 >>> bl-nas2:/vol/hd02 3435973856 1856598656 1579375200 55% /N/hd02 >>> bl-nas2:/vol/hd03 3435973856 2747626240 688347616 80% /N/hd03 >>> bl-nas1:/vol/hdln 81920 3424 78496 5% /N/u >>> bl-nas2:/vol/soft 1258291200 837003424 421287776 67% /N/soft >>> bl-nas1:/vol/logs 419430400 67163328 352267072 17% /N/logs >>> ... >>> ... >>> >>> I'll see if I can launch another short job and verify this on the compute >>> nodes. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Fri, Oct 26, 2012 at 2:14 PM, Carson Holt wrote: >>>> The command 'df /tmp' will tell you whether /tmp is a tmpfs mount >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Friday, 26 October, 2012 2:12 PM >>>> To: Carson Holt >>>> Cc: "maker-devel at yandell-lab.org" >>>> >>>> Subject: Re: [maker-devel] Strange error at blastn step >>>> >>>> It looks like /tmp is indeed being used: the files I played with were under >>>> /tmp/maker_1YQF9o. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Fri, Oct 26, 2012 at 2:09 PM, Carson Holt wrote: >>>>> Check to see where /tmp is located? Some clusters have it set up as a >>>>> tmpfs directory and I have had problems with fasta indexes running from >>>>> tmpfs mounts in the past. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Friday, 26 October, 2012 2:05 PM >>>>> To: Carson Holt >>>>> >>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>> >>>>> The maker working directory is in a cluster environment with shared >>>>> scratch space (I'm guessing NFS-mounted). I didn't change the temp >>>>> directory setting, so it should be the local default (/tmp). >>>>> >>>>> I'll give the dev version a shot. Thanks. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Fri, Oct 26, 2012 at 1:57 PM, Carson Holt wrote: >>>>>> Could you try this development version and tell me if the error still >>>>>> happens? >>>>>> >>>>>> Use this command to download --> >>>>>> <> >>>>>> >>>>>> Username: <> >>>>>> Password: <> >>>>>> >>>>>> Are you running in an NFS mounted directory or are you resetting TMP to a >>>>>> different location? >>>>>> >>>>>> Thanks, >>>>>> Carson >>>>>> >>>>>> >>>>>> From: Daniel Standage >>>>>> Date: Friday, 26 October, 2012 1:52 PM >>>>>> To: Maker Mailing List >>>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>>> >>>>>> I have since installed Maker on a different machine and tried it out. The >>>>>> test run completed successfully, but as I commenced with the full genome >>>>>> annotation, I have noticed the following error popping up frequently. >>>>>> >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.8.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-10 hits >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.9.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-6 hits >>>>>>> WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta. >>>>>>> stop here:comp59088_c1_seq7 >>>>>>> ERROR: Fasta index error >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while polishig ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 14 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_0 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> --Next Contig-- >>>>>>> >>>>>>> #--------------------------------------------------------------------- >>>>>>> Now starting the contig!! >>>>>>> SeqID: scaffold_1 >>>>>>> Length: 5805686 >>>>>>> #--------------------------------------------------------------------- >>>>>> >>>>>> My first thought based on the message is that blastdbcmd could not find >>>>>> the sequence in the database. I verified this was the case--I could not >>>>>> extract sequence comp59088_c1_seq7 from the database Maker had created >>>>>> under /tmp. However, after removing the index files and re-running >>>>>> makeblastdb with the -parse_seqids option set, blastdbcmd successfully >>>>>> extracted the sequence. >>>>>> >>>>>> I was initially happy with this finding, but upon closer inspection it >>>>>> looks like Maker does not use blastdbcmd to extract sequences, but rather >>>>>> its own internal code. Therefore I'm still not sure where the problem is >>>>>> and how I might fix it. Any insights? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> -- >>>>>> Daniel S. Standage >>>>>> Ph.D. Candidate >>>>>> Bioinformatics and Computational Biology Program >>>>>> Department of Genetics, Development, and Cell Biology >>>>>> Iowa State University >>>>>> >>>>>> >>>>>> >>>>>> On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage >>>>>> wrote: >>>>>>> Greetings! >>>>>>> >>>>>>> I am doing a test run of my Maker setup on a new machine, annotating a >>>>>>> pretty short contig (about 3kb). However, there seems to be a hiccup >>>>>>> during the blastn stage. This is the terminal message. >>>>>>> >>>>>>> #--------- command -------------# >>>>>>> Widget::blastn: >>>>>>> /share/home/01854/standage/local/bin/blastn -db >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Ef >>>>>>> asta.mpi.10.7 -query >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0 >>>>>>> -num_alignments 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend >>>>>>> 3 -word_size 15 -reward 1 -penalty -3 -gapopen 3 -dbsize 1000 -searchsp >>>>>>> 500000000 -num_threads 16 -lcase_masking -dust yes -soft_masking true >>>>>>> -show_gis -out >>>>>>> /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker >>>>>>> .output/maker.bogus_datastore/scaffold_866/theVoid.scaffold_866/scaffold >>>>>>> _866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrini >>>>>>> ty%2ETrimmomatic%2Efasta.mpi.10.7.blastn >>>>>>> #-------------------------------# >>>>>>> deleted:0 hits >>>>>>> ERROR: Could not obtain lock to format database >>>>>>> >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while doing blastn of ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 8 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_866 >>>>>>> >>>>>>> Several blastn steps appeared to have completed successfully to this one >>>>>>> failing. Any ideas what could be causing this? >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> -- >>>>>>> Daniel S. Standage >>>>>>> Ph.D. Candidate >>>>>>> Bioinformatics and Computational Biology Program >>>>>>> Department of Genetics, Development, and Cell Biology >>>>>>> Iowa State University >>>>>>> >>>>>> >>>>>> _______________________________________________ maker-devel mailing list >>>>>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinf >>>>>> o/maker-devel_yandell-lab.org >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 5 08:41:57 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:41:57 -0500 Subject: [maker-devel] gff3_preds2models script In-Reply-To: <3207.131.215.15.234.1350942378.squirrel@webmail.caltech.edu> Message-ID: The gff3_preds2models doesn't support the shared ID method for model assembly. You will need to create a parent match feature and child match_part features (each with a unique ID and Parent= attribute). You can find examples in the GFF3 specification here --> http://www.sequenceontology.org/gff3.shtml Thanks, Carson On 12-10-22 5:46 PM, "Parul Kudtarkar" wrote: >Hello, > >I want to add gene structure(gene/mRNA/exon) to gff3 file. I am using >gff3_preds2models for this purpose. However I get following error >**WARNING: No top level feature found for ID WHL22.100252 >I have attached the sample input gff3 file and the list of ids > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 09:08:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 10:08:36 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt , Maker Mailing List Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 09:14:18 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:14:18 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List < > maker-devel at yandell-lab.org> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PdomMaker9.e44232.bz2 Type: application/x-bzip2 Size: 5881 bytes Desc: not available URL: From parulk at caltech.edu Mon Nov 5 15:40:46 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 5 Nov 2012 13:40:46 -0800 (PST) Subject: [maker-devel] Conensus gene model In-Reply-To: References: Message-ID: <4116.131.215.15.234.1352151646.squirrel@webmail.caltech.edu> Dear Carson, Thanks you very much, this is helpful. > The way models are generated, it really doesn't so much matter where the > protein alignments came from. Basically the protein alignment is just > creating a region of potential CDS. MAKER than gives that region as a > hint to the gene predictors, but the gene predictors really make the call > on how to finally structure the gene based on their training sets. You > can short circuit this by using the protein2genome option as a separate > run with only your primary proteins. MAKER will then try and turn those > protein alignments directly into genes. Results from that run can > sometimes be useful for generating training sets as well, or can be passed > back into MAKER as pred_gff so MAKEr has the option to turn those into > models as an alternative to the models produced by the ab initio > predictors. > > --Carson > > > On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: > >>Hi Jason, thanks for directions on generating training-set for augustus. >>Also as alignment evidence if we are providing protein sequences from the >>primary organism as well as other closely related species is there an >>option to give the primary protein file precedence over others? >>At the moment I have all the proteins(from primary organism as well as >>related species) into a single file as protein option in maker_opts.ctl >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Paul - >>> >>> I think I've posted on this before here if you are asking how to go >>> from >>> SNAP training to Augustus training. >>> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >>> >>> I do this type of training a lot - here some pointers. >>> >>> I often train by generating models using cegma on the genome and get >>>these >>> 400 or so good models as my training set. when I have EST or RNA-Seq I >>> use PASA to generate the best set of annotations. >>> >>> For CEGMA - then I run this script that comes with MAKER: >>> cegma2zff output.cegma.gff genome.fa >>> >>> Then I follow the SNAP directions >>> >>> fathom genome.ann genome.dna -categorize 1000 >>> fathom uni.ann uni.dna -export 1000 -plus >>> mkdir MYGENOME >>> cd MYGENOME >>> forge ../export.ann ../export.dna --OPTIONS >>> cd ../MYGENOME >>> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >>> >>> I then also make the augustus training data like this running in the >>> directory that has the export.ann and export.dna files: >>> perl gene_prediction/zff2augustus_gbk.pl > train.gb >>> >>> using this script: >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>>ff2augustus_gbk.pl >>> >>> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>>and >>> best models from PASA and incorporate all these data in to my SNAP >>> training set, and then export again back to gbk for the augustus >>>training. >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>>asatraining2zff.pl >>> >>> Then you just need to run the Augustus training (autoAugTrain.pl) on >>> the >>> train.gb file. >>> >>> Jason >>> >>> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar >>> wrote: >>> >>>> Hello Carson and maker community, >>>> >>>> Thank you very much for your guidelines on using the maker-pipeline. >>>> Yes, >>>> green sea urchin genome that we are trying to annotate. >>>> We are running the on scaffolds and most of these scaffolds are small >>>>in >>>> size(very first genome assembly). We would typically expect 20,000 >>>>genes >>>> in this genome. So we are running maker using EST and proteins from >>>> the >>>> genome and out-groups to generate training dataset for SNAP and >>>> Augustus. >>>> Depending on the resulting predictions we may bootstrap the predicted >>>> genes once again using EST and proteins. >>>> >>>> Do you have any further suggestions? Also could you point how to >>>>convert >>>> training set generated for SNAP to be used as training set for >>>> Augustus >>>> as >>>> well? Would maker give equal weightage to SNAP and Augustus >>>> predictions >>>> for generating gene model? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> One thing you seem to be missing is protein evidence. >>>>> >>>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>>> recommend adding all proteins from the Strongylocentrotus purpuratus >>>> genome, then throw in another Deuterstome of your choice. Perhaps you >>>> should also add a couple of outgroup organisms like Nematostella >>>> vectensis >>>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>>> adding >>>> to many protostome outgroups (i.e. C. elegans and Drosophila) because >>>> a >>>> big part of their evolution is gene loss (so distant cnidaria often >>>> match >>>>> deuterstomes better than most protostomes do). >>>>> >>>>> You could take the maker results when protein data is included and >>>>> use >>>> it >>>>> to retrain SNAP again. >>>>> >>>>> Even a 22 kb contig is still really short. Is this genome primarily >>>> constituted by short contigs like this? I would recommend running >>>>CEGMA >>>> once on this genome to get an appropriate estimate of how recoverable >>>> the >>>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>>> Cegma >>>>> will give you an estimate for genome completeness as well as >>>>> estimates >>>> of >>>>> what percentage of genes will be found in their entirety and what >>>> percent >>>>> will be partial genes. This is important to do if your genome is >>>> fragmented as it will give you a reasonable expectation of what you >>>> can >>>> expected to recover (as short contigs don't annotate very well - you >>>> tend >>>>> to loose a lot). >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>> Hi Carson, >>>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>>as >>>>>> 3 >>>> exons EST alignments. Could you please recommend additional training. >>>>We >>>> are currently running maker on the entire contig set and eventually >>>> merge >>>>>> all the gff3 contig predictions. The using suggested >>>>>>parameter/methods >>>> we >>>>>> would like to get a consensus gene-set with minimal false >>>>>> positives/negatives. >>>>>> Thanks, >>>>>> Parul >>>>>>> The contig in question is really too small to get much out of it >>>>>>> (only 5 >>>>>> kb). There was only one single exon EST alignments and a couple of >>>> predictions with no evidence support. Anything smaller than 10 kb is >>>> mostly useless for annotation purposes. You would really need a few >>>> 100kb >>>>>>> length or longer contigs to glean enough information for optimizing >>>>>>> your >>>>>> parameters. >>>>>>> The general suggestions for any maker run are to use proteins from >>>>>>> a >>>>>> closely related organism or a couple of closely related organisms >>>>>> for >>>>>> the >>>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>>> for >>>>>> certain eukaryotes that have a bias for single exon transcripts >>>>>> (i.e. >>>>>> some >>>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>>> initio >>>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>>> positives). >>>>>>> Additional training would really depend on what your other contigs >>>> look >>>>>> like. Do you have any large contigs? I could look at one of those >>>>>> and >>>> give suggestions but the provided contig is just too short to glean >>>> much. >>>>>>> Thanks, >>>>>>> Carson >>>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>>> Hello, >>>>>>>> Please advice on the aforementioned query? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>>> From: "Parul Kudtarkar" >>>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>>> To: maker-devel at yandell-lab.org >>>>>>>> >>>>>>>>-------------------------------------------------------------------- >>>>>>>>---- >>>> -- >>>>>> Hi, >>>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>>est,protein >>>>>>>> and >>>>>> contig file), agustus,genemarkE(we ran it outside maker and have >>>>>> gff3 >>>>>>>> file >>>>>>>> as input). The output that we get is combination of various >>>>>>>> gene-predictors and evidences. I have attached sample result file. >>>> What >>>>>> would you recommend to get consensus result set? Bootstrapping the >>>> resulting gff3 file (rerunning maker)? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Wed Nov 7 08:00:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 09:00:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line for a > few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on > native disk space, and relaunched. I have attached the output of the job that > failed in <5 minutes. It looks pretty similar to the errors I got the last > time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 09:05:45 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:05:45 -0500 Subject: [maker-devel] Maker issues Message-ID: Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker.log Type: application/octet-stream Size: 48916 bytes Desc: not available URL: From daniel.standage at gmail.com Wed Nov 7 08:30:11 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 09:30:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > >> Thanks. Could you also run with the --debug flag set on the command line >> for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt , Maker Mailing List < >> maker-devel at yandell-lab.org> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory >> is on native disk space, and relaunched. I have attached the output of the >> job that failed in <5 minutes. It looks pretty similar to the errors I got >> the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 09:29:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 10:29:34 -0500 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: Message-ID: Sorry for the slow reply. I'm not on a long drive, but I am away this week. Could you send me the genemark hmm file and one of the contigs that fails. Thanks, Carson On 12-11-04 3:20 AM, "Gowthaman Ramasamy" wrote: >Hi Carson, >As it happens, I am sorry to bother you again on a weekend. Here is my >hoping that you are not on a long drive this time. > >I am running genemark prokaryote via maker on a genome with 36 >chromosomes. All but two finishes well. > >On those two, i am not able to find anything unusual. Following is the >error message i see. Could you please point to me what could be the >possible source of these errors. Thanks verymuch in advance... > >Widget::genemark: >/depot/perl-5.12.1/bin/perl >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gm >hmm_wrap -m >./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokar >yotic%2Emod_hmm%2Emod.genemark >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/query.fasta >#-------------------------------# >substr outside of string at >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMac >hine.pm line 223. > >FATAL ERROR >ERROR: Failed while preparing masked sequence and ab-inits!! > >ERROR: Chunk failed at level 6 >!! >FAILED CONTIG:Enmo_susu.05 > > >Thanks once again, >Gowthaman From daniel.standage at gmail.com Wed Nov 7 10:43:17 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 11:43:17 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed *loalize* to *localize* and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >> fasta indexer is broken. I have an open bug I am trying to resolve with >> the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >> >>> Thanks. Could you also run with the --debug flag set on the command line >>> for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List < >>> maker-devel at yandell-lab.org> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory >>> is on native disk space, and relaunched. I have attached the output of the >>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>> the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 10:46:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 11:46:31 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Looked good for a while, but came across this error. > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > > > > --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is > repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live >> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >> indexer is broken. I have an open bug I am trying to resolve with the >> Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> Thanks. Could you also run with the --debug flag set on the command line for >>> a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List >>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory is >>> on native disk space, and relaunched. I have attached the output of the job >>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>> last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Thu Nov 8 08:32:59 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 09:32:59 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > > It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to > *localize* and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >> and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>> fasta indexer is broken. I have an open bug I am trying to resolve with >>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List < >>>> maker-devel at yandell-lab.org> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>> errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Thu Nov 8 08:47:20 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Thu, 8 Nov 2012 14:47:20 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Hi Daniel, is it possible you have some proteins in your EST files? '------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw' Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [daniel.standage at gmail.com] Sent: Thursday, November 08, 2012 7:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From daniel.standage at gmail.com Thu Nov 8 09:48:52 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 10:48:52 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> References: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Message-ID: Based on Mark's suggestion, I took a look at the EST files. Luckily there is no protein sequence contamination. [dstandag at mason Transcriptome] grep -v '^>' Pdom.Trinity.Trimmomatic.fasta | grep -o . | sort | uniq -c 79400764 A 39834991 C 40702954 G 77980105 T [dstandag at mason Transcriptome] grep -v '^>' Pmet.Trinity.R.fasta | grep -o . | sort | uniq -c 18294708 A 9108213 C 9449127 G 17756470 T -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Thu, Nov 8, 2012 at 9:47 AM, Mark Yandell wrote: > Hi Daniel, > > is it possible you have some proteins in your EST files? > > '------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw' > > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [ > daniel.standage at gmail.com] > Sent: Thursday, November 08, 2012 7:32 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 09:02:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:02:21 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.make r.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold _7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffo ld_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58 983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 > --maxintron 10000 --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq37.for.716125-723330.0.fasta at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. ...as well as one occurrence of this error. > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869 > 077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sca > ffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar > --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7 > /theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm > :86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is >> repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl live >>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >>> indexer is broken. I have an open bug I am trying to resolve with the >>> Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> Thanks. Could you also run with the --debug flag set on the command line >>>> for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List >>>> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP directory is >>>> on native disk space, and relaunched. I have attached the output of the job >>>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>>> last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 09:13:38 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:13:38 -0500 Subject: [maker-devel] Query on genemark results In-Reply-To: Message-ID: The previous bug was a complete lack of GeneMark results in the GFF3, not just a lack of consensus models from GeneMark. It is possible to get no consensus models from GeneMark if they score poorly. Send me the GFF3 results of your larger contigs and I can review it and tell you if any models are being improperly categorized. Thanks, Carson On 12-10-28 1:50 PM, "kokwei" wrote: >Hi, > >I have the same problems as posted by Andr? Gomes on 10/4/10. I still >have the same problems even though using the current available version >of maker (maker 2.1 and maker 2.26 beta version). > >I have tried to do the gene prediction on eukaryotic genome using 3 >ab-initio gene predictors (SNAP, Augustus and GeneMark-ES) using Maker. >From the fasta_merge output, I have 3 separate files of gene models >($prefix.all.maker.augustus_masked.proteins.fasta, >$prefix.all.maker.snap_masked.proteins.fasta and >$prefix.all.maker.genemark.proteins.fasta) and one >$prefix.all.maker.proteins.fasta (I presume this should be the consensus >gene models from 3 predictors' results, right?). > > From the consensus gene models file, I don't see even one result from >genemark but all from snap/augustus only. Is that normal? >Also from the file naming and gene model label in final gff file, it's >showing that genemark is not masked like those of augustus and snap? Is >that true? Why only augustus and snap masked but not genemark? Please >assist and thanks for your helps. > >Kok Wei > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From mikael.durling at slu.se Tue Nov 13 07:57:36 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 13 Nov 2012 13:57:36 +0000 Subject: [maker-devel] NULs in master_datastore_index.log Message-ID: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Hello, In order to work around locking problems with SQLite, I tried running (latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason it seems maker does not detect the automounted volumes as being nfs mounted?). Running over NFSv4 makes SQLite happy, but then another problem popped up. It seems ds_utility.pm happens to write simultaneously to the datastore_index from several MPI ranks, which in my case results in stretches of NULs in the datastore file. This seems to result in maker trying to analyse the same contig simultaneously on two different MPI ranks. (I get rank failure notices on the output twice for the same rank, and maker complaining that the same GFF3 ID appears more than once). Any hints on how this can be handled? It appears as I should have installed and run maker on some other cluster without NFS mounted volumes to save myself a lot of hassles. Thanks in advance, Mikael From carsonhh at gmail.com Tue Nov 13 08:12:58 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 13 Nov 2012 09:12:58 -0500 Subject: [maker-devel] NULs in master_datastore_index.log In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Message-ID: Locks for not running contigs are a separate thing from the datastore index. They are handled by file locks in the directory for each contig. For the datastore index, it can be subject to race conditions if two processes happen to write an output string at the exact same time, but can be rebuilt in less than 2 min at the end of your job using the -dsindex flag. The failure notices you are getting might be because of the configuration of the NFS mount. MAKER will check the locks it creates several times while running a given contig to see if the lock was broken, and if it was then that contig will fail producing an error. This will happen before it does any activity that might conflict with the other active run of that contig by another process, so the process that broke the lock should continue without issue somewhere else, but you will get a trail of messages in the error log and maybe some ugliness in the datastore index. You can try altering the flags set for the NFS mount, or just set the retry count really high. You will have to run maker -dsindex once your MPI job finishes to get the datastore index log back in order on completion, but that only takes a couple of minutes to rebuild. --Carson On 12-11-13 8:57 AM, "Mikael Brandstr?m Durling" wrote: >Hello, > >In order to work around locking problems with SQLite, I tried running >(latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason >it seems maker does not detect the automounted volumes as being nfs >mounted?). Running over NFSv4 makes SQLite happy, but then another >problem popped up. It seems ds_utility.pm happens to write simultaneously >to the datastore_index from several MPI ranks, which in my case results >in stretches of NULs in the datastore file. This seems to result in maker >trying to analyse the same contig simultaneously on two different MPI >ranks. (I get rank failure notices on the output twice for the same rank, >and maker complaining that the same GFF3 ID appears more than once). > >Any hints on how this can be handled? > >It appears as I should have installed and run maker on some other cluster >without NFS mounted volumes to save myself a lot of hassles. > >Thanks in advance, >Mikael > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From es9 at sanger.ac.uk Thu Nov 15 04:20:56 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 10:20:56 +0000 Subject: [maker-devel] Augustus training within Maker Message-ID: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Hi, Could you please confirm something for me: If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. To achieve this, do I need to change anything in maker_opts.ctl or do I leave augustus_species= #Augustus gene prediction species model as is, or should it be edited for the 2nd run? Many thanks Eleanor -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From dsth at ebi.ac.uk Thu Nov 15 05:14:31 2012 From: dsth at ebi.ac.uk (Daniel Hughes) Date: Thu, 15 Nov 2012 11:14:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: heya, Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus > species config folder of gene parameters, then Augustus runs using this > data alone. > I understand that with a second Maker run Augustus retrains using the > BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I > leave > augustus_species= #Augustus gene prediction species model > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. dan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Thu Nov 15 05:34:09 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 11:34:09 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this Ele On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > heya, > > Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. > I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I leave > augustus_species= #Augustus gene prediction species model > > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. > > dan. > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 16 08:19:47 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 16 Nov 2012 09:19:47 -0500 Subject: [maker-devel] segmentation fault (core dumped) for maker running In-Reply-To: Message-ID: The correct file to update in Bioperl is /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm not Bioperl.pm, but technically you only have to fix whichever .pm file loads last. So if it's working then don't worry about it because one of the files fixed by the first command are loading after /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm. Thanks, Carson From: Hung Chih-Ming Date: Thursday, 15 November, 2012 2:02 AM To: Carson Holt Cc: Subject: segmentation fault (core dumped) for maker running Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ymwur1 at gmail.com Thu Nov 15 01:02:55 2012 From: ymwur1 at gmail.com (Hung Chih-Ming) Date: Thu, 15 Nov 2012 15:02:55 +0800 Subject: [maker-devel] segmentation fault (core dumped) for maker running Message-ID: Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Fri Nov 16 18:37:53 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri, 16 Nov 2012 17:37:53 -0700 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Message-ID: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Dan is correct about the workings of the hint based communication between MAKER and the gene predictors - and just to clarify further. MAKER never 're-trains' Augustus or any of the other gene predictors. Many people will retrain the gene predictors between iterative MAKER runs, but this is a manual (and for Augustus non-trivial) step. B On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this > > Ele > > > On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > >> heya, >> >> Could you please confirm something for me: >> >> If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. >> I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. >> >> To achieve this, do I need to change anything in maker_opts.ctl or do I leave >> augustus_species= #Augustus gene prediction species model >> >> >> AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. >> >> dan. >> >> >> > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Sat Nov 17 04:42:31 2012 From: es9 at sanger.ac.uk (es9) Date: Sat, 17 Nov 2012 10:42:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Message-ID: Thank you to you both for clarifying this ... I was get a smidge confused and reading previous posts I can see the answer had already been asked and replied to. Next time I will cruise the archives before posting! Regards, Eleanor > Dan is correct about the workings of the hint based communication > between MAKER and the gene predictors - and just to clarify further. > MAKER never 're-trains' Augustus or any of the other gene predictors. > Many people will retrain the gene predictors between iterative MAKER > runs, but this is a manual (and for Augustus non-trivial) step. > > B > > On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > >> Aha - that makes sense, so with every run Augustus is run with the >> BLAST hints available, thanks for clarifying this >> >> Ele >> >> On 15 Nov 2012, at 11:14, Daniel Hughes wrote: >> >>> heya, >>> >>>> Could you please confirm something for me: >>>> >>>> If with the first Maker run you provide the location of the >>>> Augustus species config folder of gene parameters, then Augustus >>>> runs using this data alone. >>>> I understand that with a second Maker run Augustus retrains >>>> using the BLAST evidence from the 1st run. >>>> >>>> To achieve this, do I need to change anything in maker_opts.ctl >>>> or do I leave >>>> augustus_species= #Augustus gene prediction species model >>> >>> AFAIK maker runs augustus, blast etc., as sort of raw compute >>> stages in the earlier tier_types, the results of these stages e.g. >>> protein alignments etc., are then 'synthesised' into 'hints' >>> (early tier_type 3) that are provided to ab initio predicters >>> capable of taking external 'hints' - such as augustus - that are >>> used to generate the final models (after further adjustmnets wrt., >>> utrs etc.). that is to say i think what you mean by first and >>> second maker runs are actually internal usage of ab initios that >>> occur at different stages of any single maker run and you should >>> be shielded from this. >>> >>> dan. >> >> -- The Wellcome Trust Sanger Institute is operated by Genome >> Research Limited, a charity registered in England with number >> 1021457 and a company registered in England with number 2742969, >> whose registered office is 215 Euston Road, London, NW1 2BE. >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com [1] >> > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > Links: > ------ > [1] mailto:maker-devel at box290.bluehost.com -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From parulk at caltech.edu Tue Nov 20 17:35:34 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:35:34 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction Message-ID: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Hello, I am running SNAP, Augustus and genemark(genemarkE results were calculated externally and gff3 file was provided to option pred_gff). However the resulting gff3 source field does not mention if the prediction were derived from SNAP, Augustus or genemark. I have attached the configuration file. Also is there any option where were could have priority for SNAP predictions? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4630 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 20 17:39:42 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:39:42 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> References: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Message-ID: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Hello, Just found that for Scaffold of larger size it does explicitly specify the prediction source. Thanks, Parul > Hello, > > I am running SNAP, Augustus and genemark(genemarkE results were calculated > externally and gff3 file was provided to option pred_gff). However the > resulting gff3 source field does not mention if the prediction were > derived from SNAP, Augustus or genemark. I have attached the > configuration file. Also is there any option where were could have > priority for SNAP predictions? > > Thanks and regards, > Parul Kudtarkar > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From barry.utah at gmail.com Tue Nov 20 21:21:47 2012 From: barry.utah at gmail.com (Barry Moore) Date: Tue, 20 Nov 2012 20:21:47 -0700 Subject: [maker-devel] email about Maker In-Reply-To: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> References: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> Message-ID: Hi Jorge, These would be two different proteins identified on the same scaffold. The numbers don't have any meaning other than that the genes are numbered sequentially and so these two genes would be adjacent to each other. If you have access to the GFF3 file produced by Maker for this genome you should see those two IDs with adjacent but different coordinates as well. B On Nov 19, 2012, at 10:48 AM, Jorge Ibarra wrote: > Dear Dr Moore > > I have a quick question about Maker and I'd appreciate if you could answer that to me. I downloaded two protein sequences predicted by Maker with the following indentifiers: > > >maker_scaffold_7-snap-gene-1.23-mRNA-1 Glucosylceramidase > >maker_scaffold_7-snap-gene-1.24-mRNA-1 Glucosylceramidase > > The only thing that varies in the two sequences identifiers are the number 1.23 and 1.24, and I was wondering what this numbers mean. Their sequence are also really similar (96%). > > I wonder if these sequences represent two genes in the same scaffold (scaffold_7) or if they are two slightly different predictions of the same gene. > > So my question is what do those numbers (1.23 and 1.24) represent in Maker? > > Thank you. > > Jorge Ibarra > PhD student Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 08:25:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 09:25:36 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Message-ID: Is it possible that you just picked a contig that didn't have any pred_gff entries for snap and augustus the first time? The predictions you pass through should be of type match/match_part and will have the source as pred_gff:snap or pred_gff:augustus. Could you check and let me know or send me an example of entries from a contig you passed through and the results you are seeing? No. there is no priority given to one prediction over the other. They are choses based on evidence overlap similarity. Thanks, Carson On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >Hello, > >Just found that for Scaffold of larger size it does explicitly specify the >prediction source. > >Thanks, >Parul > >> Hello, >> >> I am running SNAP, Augustus and genemark(genemarkE results were >>calculated >> externally and gff3 file was provided to option pred_gff). However the >> resulting gff3 source field does not mention if the prediction were >> derived from SNAP, Augustus or genemark. I have attached the >> configuration file. Also is there any option where were could have >> priority for SNAP predictions? >> >> Thanks and regards, >> Parul Kudtarkar >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From benayoun at stanford.edu Wed Nov 21 12:45:55 2012 From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=) Date: Wed, 21 Nov 2012 10:45:55 -0800 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Message-ID: Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department *BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 14:58:05 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 15:58:05 -0500 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? In-Reply-To: Message-ID: There are many ways of doing this. You can run everything separately and then copy all GFF3 files into a common folder and use the gff3_merge script that comes with maker to combine them. Alternatively you can run maker with the -g and -base options. This allows you to specify a new genome on the command line and the base name of the directory to write to. Using those flags you can swap in a different contig file while maintaining the same output directory for your job as a whole. Just run maker at the end of the run using the original fasta and the -dsindex flag, to sync the datastore index file so it is complete if you do this option. To split out contigs of interest you can also use the fasta_tool that comes with maker and use the -grep_header or ?select flags to indicate which contigs to retrieve. --Carson From: B?r?nice Benayoun Date: Wednesday, 21 November, 2012 1:45 PM To: Cc: Dario Riccardo Valenzano Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 21 15:15:00 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 21 Nov 2012 13:15:00 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Dear Carson, That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb which is very small). I have attached a Scaffold of 1.5kb with no predictions and another Scaffold of 28kb. It is of course expected that we would not get any gene-prediction for small size Scaffolds. For next maker run would you recommend bootstrap to reduce false positives? Thanks and regards, Parul Kudtarkar > Is it possible that you just picked a contig that didn't have any pred_gff > entries for snap and augustus the first time? The predictions you pass > through should be of type match/match_part and will have the source as > pred_gff:snap or pred_gff:augustus. Could you check and let me know or > send me an example of entries from a contig you passed through and the > results you are seeing? > > No. there is no priority given to one prediction over the other. They are > choses based on evidence overlap similarity. > > Thanks, > Carson > > > > > On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: > >>Hello, >> >>Just found that for Scaffold of larger size it does explicitly specify >> the >>prediction source. >> >>Thanks, >>Parul >> >>> Hello, >>> >>> I am running SNAP, Augustus and genemark(genemarkE results were >>>calculated >>> externally and gff3 file was provided to option pred_gff). However the >>> resulting gff3 source field does not mention if the prediction were >>> derived from SNAP, Augustus or genemark. I have attached the >>> configuration file. Also is there any option where were could have >>> priority for SNAP predictions? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold118825.gff Type: application/octet-stream Size: 1718 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold20.gff Type: application/octet-stream Size: 377513 bytes Desc: not available URL: From carsonhh at gmail.com Sun Nov 25 16:55:32 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 17:55:32 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Message-ID: I see both augustus and snap derived predictions (match/match_part) with augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that were derived from these predictions. There are no predictions from genemark. Is that what you were expecting? If not could you specify how it varies. With respect to bootstrapping, it really depends how well trained your gene predictors are. In general only one round of bootstrapping may be necessary after newly training a gene predictor. Thanks, Carson On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >Dear Carson, > >That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >which is very small). I have attached a Scaffold of 1.5kb with no >predictions and another Scaffold of 28kb. It is of course expected that we >would not get any gene-prediction for small size Scaffolds. > >For next maker run would you recommend bootstrap to reduce false >positives? > >Thanks and regards, >Parul Kudtarkar > >> Is it possible that you just picked a contig that didn't have any >>pred_gff >> entries for snap and augustus the first time? The predictions you pass >> through should be of type match/match_part and will have the source as >> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >> send me an example of entries from a contig you passed through and the >> results you are seeing? >> >> No. there is no priority given to one prediction over the other. They >>are >> choses based on evidence overlap similarity. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >> >>>Hello, >>> >>>Just found that for Scaffold of larger size it does explicitly specify >>> the >>>prediction source. >>> >>>Thanks, >>>Parul >>> >>>> Hello, >>>> >>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>calculated >>>> externally and gff3 file was provided to option pred_gff). However the >>>> resulting gff3 source field does not mention if the prediction were >>>> derived from SNAP, Augustus or genemark. I have attached the >>>> configuration file. Also is there any option where were could have >>>> priority for SNAP predictions? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Sun Nov 25 22:10:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 23:10:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more detail > to the errors in the development version if you do an 'svn update'. Then you > will know the system specific reason why close or opened failed. For the > other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1 > 869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, > there are some intermittent issues. I've seen a couple occurrences of the > following error... > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq101.for.716125-721460.0.fasta -t >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 >> --maxintron 10000 --showcigar --percent 20 > >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq37.for.716125-723330.0.fasta at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > > ...as well as one occurrence of this error. > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker >> .output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.186 >> 9077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >> affold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >> --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_ >> 7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.p >> m:86 >> STACK: Widget::exonerate::est2genome::assemble >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:82 >> STACK: polisher::exonerate::est::polish >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:44 >> STACK: GI::to_polisher >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:166>> 3 >> STACK: Process::MpiChunk::run >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling uri_escape at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling File::Path::mkpath at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> >>> >>> >>> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to >> localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps and >>> is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl live >>>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command line >>>>> for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List >>>>> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP directory >>>>> is on native disk space, and relaunched. I have attached the output of the >>>>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>>>> the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Sun Nov 25 22:56:31 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 26 Nov 2012 04:56:31 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> good detective work there Carson! Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] Sent: Sunday, November 25, 2012 9:10 PM To: Daniel Standage Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage > Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From cjfields at illinois.edu Sun Nov 25 23:33:52 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 05:33:52 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { if ( $str =~ m/U/i ) { $alphabet = 'rna'; } else { $alphabet = 'dna'; } } else { $alphabet = 'protein'; } Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. chris On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > good detective work there Carson! > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] > Sent: Sunday, November 25, 2012 9:10 PM > To: Daniel Standage > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. > That is why you get --> > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > > You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. > > Thanks, > Carson > > > > From: Daniel Standage > > Date: Friday, 23 November, 2012 3:06 PM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Thanks for your reply, and sorry for my delayed response. > > I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 > STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 > STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: > 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: > Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From daniel.standage at gmail.com Mon Nov 26 05:08:56 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 26 Nov 2012 06:08:56 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thanks for the responses from everybody! The genomic sequence I am annotating is coming directly from AllPaths-LG, which I've noticed retains as much ambiguity as possible--thus the seldom seen ambiguity nucleotides which in this case seem to outnumber the resolved nucleotides. On one hand, I would hate to lose all the information these ambiguity characters provide by replacing them with Ns, but on the other hand if most tools treat them as such, then it might not make much of a difference. Another option I guess would be to replace ambiguity nucleotides by the most likely explicit nucleotide based solely on sequence composition. This would retain more information than an N, and would at least partially correct. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 26, 2012 at 12:33 AM, Fields, Christopher J < cjfields at illinois.edu> wrote: > This is coming from BioPerl trying to guess the alphabet if one is not > provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just > committed, in fact). It's probably best to explicitly set this when > possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell > wrote: > > > good detective work there Carson! > > > > > > Mark Yandell > > Professor of Human Genetics > > H.A. & Edna Benning Presidential Endowed Chair > > Eccles Institute of Human Genetics > > University of Utah > > 15 North 2030 East, Room 2100 > > Salt Lake City, UT 84112-5330 > > ph:801-587-7707 > > > > ________________________________________ > > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [ > carsonhh at gmail.com] > > Sent: Sunday, November 25, 2012 9:10 PM > > To: Daniel Standage > > Cc: Maker Mailing List > > Subject: Re: [maker-devel] Maker issues > > > > I think the problem is in the sequence of your scaffold. I pulled this > out of the exonerate alignment --> > > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > > > Notice the letters W, K, R, M, etc. While these are technically legal > nucleotides, many external programs, and in this case BioPerl doesn't > handle them well. > > That is why you get --> > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > > > You might want to replace them in your input fasta with the letter 'N' > so they are treated as masked. You will have to delete the mpi_blastdb > directory to let maker rebuild the fasta indexes and you will probably have > to set clean_try=1 in the control files so that MAKER deletes old result > files that contain those characters on the retry. The other error may be > just a snowball effect from the first error, so you should see of it still > happens after fixing the input fasta file. > > > > Thanks, > > Carson > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Friday, 23 November, 2012 3:06 PM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Thanks for your reply, and sorry for my delayed response. > > > > I have attached the first file you requested, but the other two do not > exist. I have attached a listing of the files in that directory. Let me > know if you need anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > > > thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Thursday, 8 November, 2012 9:32 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_23 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_23 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > ...as well as one occurrence of this error. > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > > > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > > q93.est_exonerate.0 > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > > ----------------------------------------------------------- > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_7 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_7 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > I'll let you know if I see anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Typo now fixed on my end too ;-) > > > > Thanks, > > Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Wednesday, 7 November, 2012 11:43 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Looked good for a while, but came across this error. > > > > total clusters:20 now processing 0 > > flattening EST clusters > > doing tblastx of alt-ESTs > > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > > --> rank=NA, hostname=c4 > > ERROR: Failed while doing tblastx of alt-ESTs > > ERROR: Chunk failed at level:4, tier_type:2 > > FAILED CONTIG:scaffold_58 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_58 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > > > --Next Contig-- > > > > It seems pretty clear that there is a typo in GI.pm. I changed loalize > to localize and relaunched. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < > daniel.standage at gmail.com> wrote: > > Done. > > > > Test job has successfully cleared the preliminary Fasta indexing steps > and is repeat masking. I'll let you know if there are any problems. Thanks! > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > > > Thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:14 AM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Debug output attached (bzip2 compressed). > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > > > --Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:05 AM > > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > > Subject: Maker issues > > > > Carson, > > > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > > > > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Nov 26 10:53:59 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 26 Nov 2012 16:53:59 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thank you for the commit to Bioperl. I'll can also manipulate the alphabet value in the object hash right before calling the revcomp method, it's not the most elegant solution but the seq object creation is insulated from my control so I can't set it there --> Bio::Search::HSP::HSPI.pm line 578 I would still recommend losing the ambiguous bases though as they will very likely still cause problems in some downstream application. Thanks, Carson On 12-11-26 12:33 AM, "Fields, Christopher J" wrote: >This is coming from BioPerl trying to guess the alphabet if one is not >provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > >Easy enough to fix to allow for additional ambiguous nucleotides (just >committed, in fact). It's probably best to explicitly set this when >possible, though; it is a guess, after all. > >chris > >On Nov 25, 2012, at 10:56 PM, Mark Yandell >wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>[carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this >>out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal >>nucleotides, many external programs, and in this case BioPerl doesn't >>handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' >>so they are treated as masked. You will have to delete the mpi_blastdb >>directory to let maker rebuild the fasta indexes and you will probably >>have to set clean_try=1 in the control files so that MAKER deletes old >>result files that contain those characters on the retry. The other >>error may be just a snowball effect from the first error, so you should >>see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage >>> >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not >>exist. I have attached a listing of the files in that directory. Let me >>know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>> wrote: >> The first error is an IO error with your system. I've added some more >>detail to the errors in the development version if you do an 'svn >>update'. Then you will know the system specific reason why close or >>opened failed. For the other error, could you send me this file --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/sc >>affold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta >> >> And this one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. >>However, there are some intermittent issues. I've seen a couple >>occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta -t >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq37.for.716125-723330.0.fasta at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pd >> >>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for >>.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> >>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastor >>e/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>--showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> >>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaff >>old_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_in >>fo.pm:86 >> STACK: Widget::exonerate::est2genome::assemble >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:82 >> STACK: polisher::exonerate::est::polish >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:44 >> STACK: GI::to_polisher >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:1663 >> STACK: Process::MpiChunk::run >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:335 >> STACK: Process::MpiChunk::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:351 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>> wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >>> >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>> wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >>and is repeat masking. I'll let you know if there are any problems. >>Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>> wrote: >> 1.006902 Bio::Root::Version >>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>It's fasta indexer is broken. I have an open bug I am trying to resolve >>with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>> wrote: >> Thanks. Could you also run with the --debug flag set on the command >>line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker >>Mailing List >>> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP >>directory is on native disk space, and relaunched. I have attached the >>output of the job that failed in <5 minutes. It looks pretty similar to >>the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From parulk at caltech.edu Mon Nov 26 13:21:23 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 11:21:23 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Hello Carson, Thanks for the feedback.Genemark was run outside maker and the resulting gff3 file was provided as option to pred_gff. What would the source in the gff3 of maker result state of the predictions where made from pred_gff? Thanks and regards, Parul Kudtarkar > I see both augustus and snap derived predictions (match/match_part) with > augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that > were derived from these predictions. There are no predictions from > genemark. Is that what you were expecting? If not could you specify how > it varies. > > With respect to bootstrapping, it really depends how well trained your > gene predictors are. In general only one round of bootstrapping may be > necessary after newly training a gene predictor. > > Thanks, > Carson > > > > On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: > >>Dear Carson, >> >>That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >>which is very small). I have attached a Scaffold of 1.5kb with no >>predictions and another Scaffold of 28kb. It is of course expected that >> we >>would not get any gene-prediction for small size Scaffolds. >> >>For next maker run would you recommend bootstrap to reduce false >>positives? >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Is it possible that you just picked a contig that didn't have any >>>pred_gff >>> entries for snap and augustus the first time? The predictions you pass >>> through should be of type match/match_part and will have the source as >>> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >>> send me an example of entries from a contig you passed through and the >>> results you are seeing? >>> >>> No. there is no priority given to one prediction over the other. They >>>are >>> choses based on evidence overlap similarity. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>> >>>>Hello, >>>> >>>>Just found that for Scaffold of larger size it does explicitly specify >>>> the >>>>prediction source. >>>> >>>>Thanks, >>>>Parul >>>> >>>>> Hello, >>>>> >>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>calculated >>>>> externally and gff3 file was provided to option pred_gff). However >>>>> the >>>>> resulting gff3 source field does not mention if the prediction were >>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>> configuration file. Also is there any option where were could have >>>>> priority for SNAP predictions? >>>>> >>>>> Thanks and regards, >>>>> Parul Kudtarkar >>>>> >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From jason.stajich at gmail.com Mon Nov 26 15:32:42 2012 From: jason.stajich at gmail.com (Jason Stajich) Date: Mon, 26 Nov 2012 13:32:42 -0800 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: right - you can explicitly set the alphabet to 'dna' when building a sequence object but I don't know if this down in MAKER code that is tripping up? Jason On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" wrote: > This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage > >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: >> The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta >> >> And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 >> STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 >> STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 >> STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 >> STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage > >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: >> 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: >> Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker Mailing List > >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Jason Stajich jason.stajich at gmail.com jason at bioperl.org From parulk at caltech.edu Mon Nov 26 15:35:48 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 13:35:48 -0800 (PST) Subject: [maker-devel] AED score Message-ID: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Dear Maker community, For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K genes however I am getting 8 times the expected gene count indicating too many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes how to go about this? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Mon Nov 26 15:37:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:37:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The sequence object is being created well down into BioPerl (outside of my control), but I think I can explicitly set the alphabet to 'dna' by modifying the existing object just before calling the revcomp method to get around that. Thanks, Carson On 12-11-26 4:32 PM, "Jason Stajich" wrote: >right - you can explicitly set the alphabet to 'dna' when building a >sequence object but I don't know if this down in MAKER code that is >tripping up? > >Jason >On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" > wrote: > >> This is coming from BioPerl trying to guess the alphabet if one is not >>provided. The specific spot: >> >> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >> if ( $str =~ m/U/i ) { >> $alphabet = 'rna'; >> } else { >> $alphabet = 'dna'; >> } >> } else { >> $alphabet = 'protein'; >> } >> >> Easy enough to fix to allow for additional ambiguous nucleotides (just >>committed, in fact). It's probably best to explicitly set this when >>possible, though; it is a guess, after all. >> >> chris >> >> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>wrote: >> >>> good detective work there Carson! >>> >>> >>> Mark Yandell >>> Professor of Human Genetics >>> H.A. & Edna Benning Presidential Endowed Chair >>> Eccles Institute of Human Genetics >>> University of Utah >>> 15 North 2030 East, Room 2100 >>> Salt Lake City, UT 84112-5330 >>> ph:801-587-7707 >>> >>> ________________________________________ >>> From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>[carsonhh at gmail.com] >>> Sent: Sunday, November 25, 2012 9:10 PM >>> To: Daniel Standage >>> Cc: Maker Mailing List >>> Subject: Re: [maker-devel] Maker issues >>> >>> I think the problem is in the sequence of your scaffold. I pulled >>>this out of the exonerate alignment --> >>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>> >>> Notice the letters W, K, R, M, etc. While these are technically legal >>>nucleotides, many external programs, and in this case BioPerl doesn't >>>handle them well. >>> That is why you get --> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> >>> You might want to replace them in your input fasta with the letter 'N' >>>so they are treated as masked. You will have to delete the mpi_blastdb >>>directory to let maker rebuild the fasta indexes and you will probably >>>have to set clean_try=1 in the control files so that MAKER deletes old >>>result files that contain those characters on the retry. The other >>>error may be just a snowball effect from the first error, so you should >>>see of it still happens after fixing the input fasta file. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Friday, 23 November, 2012 3:06 PM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Thanks for your reply, and sorry for my delayed response. >>> >>> I have attached the first file you requested, but the other two do not >>>exist. I have attached a listing of the files in that directory. Let me >>>know if you need anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> wrote: >>> The first error is an IO error with your system. I've added some more >>>detail to the errors in the development version if you do an 'svn >>>update'. Then you will know the system specific reason why close or >>>opened failed. For the other error, could you send me this file --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>> >>> This one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta >>> >>> And this one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta >>> >>> thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Thursday, 8 November, 2012 9:32 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Scaling up to whole-genome annotation, things seem to be going well. >>>However, there are some intermittent issues. I've seen a couple >>>occurrences of the following error... >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> couldn't close >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>60. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_23 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_23 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> ...as well as one occurrence of this error. >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pd >>> >>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>> >>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>--showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>> >>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>> q93.est_exonerate.0 >>> #-------------------------------# >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>> STACK: Bio::PrimarySeqI::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>> STACK: Bio::LocatableSeq::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>nfo.pm:86 >>> STACK: Widget::exonerate::est2genome::assemble >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:686 >>> STACK: Widget::exonerate::est2genome::parse >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:961 >>> STACK: polisher::exonerate::est::e_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:82 >>> STACK: polisher::exonerate::est::polish >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:44 >>> STACK: GI::to_polisher >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>> STACK: GI::polish_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>> STACK: Process::MpiChunk::_go >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:1663 >>> STACK: Process::MpiChunk::run >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:335 >>> STACK: Process::MpiChunk::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:351 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_7 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_7 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> I'll let you know if I see anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> wrote: >>> Thanks. Typo now fixed on my end too ;-) >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Wednesday, 7 November, 2012 11:43 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Looked good for a while, but came across this error. >>> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> >>> --Next Contig-- >>> >>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>to localize and relaunched. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>>and is repeat masking. I'll let you know if there are any problems. >>>Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> wrote: >>> 1.006902 Bio::Root::Version >>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>It's fasta indexer is broken. I have an open bug I am trying to >>>resolve with the Bioperl developers, but for now use the CPAN version >>>of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> wrote: >>> Thanks. Could you also run with the --debug flag set on the command >>>line for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt >, Maker >>>Mailing List >>>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP >>>directory is on native disk space, and relaunched. I have attached the >>>output of the job that failed in <5 minutes. It looks pretty similar to >>>the errors I got the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >Jason Stajich >jason.stajich at gmail.com >jason at bioperl.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 15:46:48 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:46:48 -0500 Subject: [maker-devel] AED score In-Reply-To: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Message-ID: AED score with 1 are the ones you don't want. 0 is best and 1 is worst as it is a distance metric. You can use the AED_threshold parameter to require better matching to the evidence by setting it closer to 0. You can also try to increase protein homology evidence as some of your calls may be split genes due to lack of evidence linking them. --Carson On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >Dear Maker community, > >For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect 20-30K >genes however I am getting 8 times the expected gene count indicating too >many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if yes how >to go about this? > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 15:48:18 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:48:18 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Message-ID: They should show up as genemark or pred_gff:genemark. Could you verify that the input file from genemark indeed contained predictions that should have been on this contig as not all contigs may have calls from genemark? --Carson On 12-11-26 2:21 PM, "Parul Kudtarkar" wrote: >Hello Carson, > >Thanks for the feedback.Genemark was run outside maker and the resulting >gff3 file was provided as option to pred_gff. What would the source in the >gff3 of maker result state of the predictions where made from pred_gff? > >Thanks and regards, >Parul Kudtarkar > >> I see both augustus and snap derived predictions (match/match_part) with >> augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that >> were derived from these predictions. There are no predictions from >> genemark. Is that what you were expecting? If not could you specify how >> it varies. >> >> With respect to bootstrapping, it really depends how well trained your >> gene predictors are. In general only one round of bootstrapping may be >> necessary after newly training a gene predictor. >> >> Thanks, >> Carson >> >> >> >> On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson, >>> >>>That is correct. There were no pred_gff for smaller size >>>Scaffolds(~1.5kb >>>which is very small). I have attached a Scaffold of 1.5kb with no >>>predictions and another Scaffold of 28kb. It is of course expected that >>> we >>>would not get any gene-prediction for small size Scaffolds. >>> >>>For next maker run would you recommend bootstrap to reduce false >>>positives? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>> Is it possible that you just picked a contig that didn't have any >>>>pred_gff >>>> entries for snap and augustus the first time? The predictions you >>>>pass >>>> through should be of type match/match_part and will have the source as >>>> pred_gff:snap or pred_gff:augustus. Could you check and let me know >>>>or >>>> send me an example of entries from a contig you passed through and the >>>> results you are seeing? >>>> >>>> No. there is no priority given to one prediction over the other. They >>>>are >>>> choses based on evidence overlap similarity. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Hello, >>>>> >>>>>Just found that for Scaffold of larger size it does explicitly specify >>>>> the >>>>>prediction source. >>>>> >>>>>Thanks, >>>>>Parul >>>>> >>>>>> Hello, >>>>>> >>>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>>calculated >>>>>> externally and gff3 file was provided to option pred_gff). However >>>>>> the >>>>>> resulting gff3 source field does not mention if the prediction were >>>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>>> configuration file. Also is there any option where were could have >>>>>> priority for SNAP predictions? >>>>>> >>>>>> Thanks and regards, >>>>>> Parul Kudtarkar >>>>>> >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > From cjfields at illinois.edu Mon Nov 26 15:55:04 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 21:55:04 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> That makes sense. The change I made should also allow these sequences to 'just work', but this would of course require a BioPerl update. We could also make that change within BioPerl if needed if we know where it might be; it seems in this case a returned sequence should be 'dna' if the application is exonerate. chris On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > The sequence object is being created well down into BioPerl (outside of my > control), but I think I can explicitly set the alphabet to 'dna' by > modifying the existing object just before calling the revcomp method to > get around that. > > Thanks, > Carson > > > On 12-11-26 4:32 PM, "Jason Stajich" wrote: > >> right - you can explicitly set the alphabet to 'dna' when building a >> sequence object but I don't know if this down in MAKER code that is >> tripping up? >> >> Jason >> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >> wrote: >> >>> This is coming from BioPerl trying to guess the alphabet if one is not >>> provided. The specific spot: >>> >>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>> if ( $str =~ m/U/i ) { >>> $alphabet = 'rna'; >>> } else { >>> $alphabet = 'dna'; >>> } >>> } else { >>> $alphabet = 'protein'; >>> } >>> >>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>> committed, in fact). It's probably best to explicitly set this when >>> possible, though; it is a guess, after all. >>> >>> chris >>> >>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>> wrote: >>> >>>> good detective work there Carson! >>>> >>>> >>>> Mark Yandell >>>> Professor of Human Genetics >>>> H.A. & Edna Benning Presidential Endowed Chair >>>> Eccles Institute of Human Genetics >>>> University of Utah >>>> 15 North 2030 East, Room 2100 >>>> Salt Lake City, UT 84112-5330 >>>> ph:801-587-7707 >>>> >>>> ________________________________________ >>>> From: maker-devel-bounces at yandell-lab.org >>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>> [carsonhh at gmail.com] >>>> Sent: Sunday, November 25, 2012 9:10 PM >>>> To: Daniel Standage >>>> Cc: Maker Mailing List >>>> Subject: Re: [maker-devel] Maker issues >>>> >>>> I think the problem is in the sequence of your scaffold. I pulled >>>> this out of the exonerate alignment --> >>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>> >>>> Notice the letters W, K, R, M, etc. While these are technically legal >>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>> handle them well. >>>> That is why you get --> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> >>>> You might want to replace them in your input fasta with the letter 'N' >>>> so they are treated as masked. You will have to delete the mpi_blastdb >>>> directory to let maker rebuild the fasta indexes and you will probably >>>> have to set clean_try=1 in the control files so that MAKER deletes old >>>> result files that contain those characters on the retry. The other >>>> error may be just a snowball effect from the first error, so you should >>>> see of it still happens after fixing the input fasta file. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Friday, 23 November, 2012 3:06 PM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Thanks for your reply, and sorry for my delayed response. >>>> >>>> I have attached the first file you requested, but the other two do not >>>> exist. I have attached a listing of the files in that directory. Let me >>>> know if you need anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> > wrote: >>>> The first error is an IO error with your system. I've added some more >>>> detail to the errors in the development version if you do an 'svn >>>> update'. Then you will know the system specific reason why close or >>>> opened failed. For the other error, could you send me this file --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>> >>>> This one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta >>>> >>>> And this one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>> >>>> thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Thursday, 8 November, 2012 9:32 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Scaling up to whole-genome annotation, things seem to be going well. >>>> However, there are some intermittent issues. I've seen a couple >>>> occurrences of the following error... >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> couldn't close >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>> 60. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> ...as well as one occurrence of this error. >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pd >>>> >>>> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>> >>>> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>> --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>> >>>> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>> q93.est_exonerate.0 >>>> #-------------------------------# >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>> STACK: Bio::PrimarySeqI::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>>> STACK: Bio::LocatableSeq::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>> nfo.pm:86 >>>> STACK: Widget::exonerate::est2genome::assemble >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:686 >>>> STACK: Widget::exonerate::est2genome::parse >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:961 >>>> STACK: polisher::exonerate::est::e_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:82 >>>> STACK: polisher::exonerate::est::polish >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:44 >>>> STACK: GI::to_polisher >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>> STACK: GI::polish_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>> STACK: Process::MpiChunk::_go >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:1663 >>>> STACK: Process::MpiChunk::run >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:335 >>>> STACK: Process::MpiChunk::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:351 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> I'll let you know if I see anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> > wrote: >>>> Thanks. Typo now fixed on my end too ;-) >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Looked good for a while, but came across this error. >>>> >>>> total clusters:20 now processing 0 >>>> flattening EST clusters >>>> doing tblastx of alt-ESTs >>>> Undefined subroutine &GI::loalize_file called at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while doing tblastx of alt-ESTs >>>> ERROR: Chunk failed at level:4, tier_type:2 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> >>>> --Next Contig-- >>>> >>>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>> to localize and relaunched. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> > wrote: >>>> Done. >>>> >>>> Test job has successfully cleared the preliminary Fasta indexing steps >>>> and is repeat masking. I'll let you know if there are any problems. >>>> Thanks! >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> > wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>> It's fasta indexer is broken. I have an open bug I am trying to >>>> resolve with the Bioperl developers, but for now use the CPAN version >>>> of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> > wrote: >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt >, Maker >>>> Mailing List >>>> > >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to >>>> the errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > From carsonhh at gmail.com Mon Nov 26 16:07:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 17:07:46 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> Message-ID: The seq object is being create in Bio::Search::HSP::HSPI.pm line 578 which itself is several layers deep into BioPerl after creation of a Bio::Search::Hit object. I think explicitly setting the alphabet would require modifications to a number of modules that create hits from Bio::SearchIO so that the alphabet gets stored early on, but that seems like a lot of work and could break any number of things along the way. The current change should allow BioPerl to guess right. After all the upstream code did explicitly call revcomp, so it obviously thinks that the sequence can be reverse complimented, so BioPerl is now just verifying that the alphabet matches legal characters, even if it is an unlikely match. --Carson On 12-11-26 4:55 PM, "Fields, Christopher J" wrote: >That makes sense. The change I made should also allow these sequences to >'just work', but this would of course require a BioPerl update. > >We could also make that change within BioPerl if needed if we know where >it might be; it seems in this case a returned sequence should be 'dna' if >the application is exonerate. > >chris > >On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > >> The sequence object is being created well down into BioPerl (outside of >>my >> control), but I think I can explicitly set the alphabet to 'dna' by >> modifying the existing object just before calling the revcomp method to >> get around that. >> >> Thanks, >> Carson >> >> >> On 12-11-26 4:32 PM, "Jason Stajich" wrote: >> >>> right - you can explicitly set the alphabet to 'dna' when building a >>> sequence object but I don't know if this down in MAKER code that is >>> tripping up? >>> >>> Jason >>> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >>> wrote: >>> >>>> This is coming from BioPerl trying to guess the alphabet if one is not >>>> provided. The specific spot: >>>> >>>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>>> if ( $str =~ m/U/i ) { >>>> $alphabet = 'rna'; >>>> } else { >>>> $alphabet = 'dna'; >>>> } >>>> } else { >>>> $alphabet = 'protein'; >>>> } >>>> >>>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>>> committed, in fact). It's probably best to explicitly set this when >>>> possible, though; it is a guess, after all. >>>> >>>> chris >>>> >>>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>>> >>>> wrote: >>>> >>>>> good detective work there Carson! >>>>> >>>>> >>>>> Mark Yandell >>>>> Professor of Human Genetics >>>>> H.A. & Edna Benning Presidential Endowed Chair >>>>> Eccles Institute of Human Genetics >>>>> University of Utah >>>>> 15 North 2030 East, Room 2100 >>>>> Salt Lake City, UT 84112-5330 >>>>> ph:801-587-7707 >>>>> >>>>> ________________________________________ >>>>> From: maker-devel-bounces at yandell-lab.org >>>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>>> [carsonhh at gmail.com] >>>>> Sent: Sunday, November 25, 2012 9:10 PM >>>>> To: Daniel Standage >>>>> Cc: Maker Mailing List >>>>> Subject: Re: [maker-devel] Maker issues >>>>> >>>>> I think the problem is in the sequence of your scaffold. I pulled >>>>> this out of the exonerate alignment --> >>>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>>> >>>>> Notice the letters W, K, R, M, etc. While these are technically >>>>>legal >>>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>>> handle them well. >>>>> That is why you get --> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> >>>>> You might want to replace them in your input fasta with the letter >>>>>'N' >>>>> so they are treated as masked. You will have to delete the >>>>>mpi_blastdb >>>>> directory to let maker rebuild the fasta indexes and you will >>>>>probably >>>>> have to set clean_try=1 in the control files so that MAKER deletes >>>>>old >>>>> result files that contain those characters on the retry. The other >>>>> error may be just a snowball effect from the first error, so you >>>>>should >>>>> see of it still happens after fixing the input fasta file. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Friday, 23 November, 2012 3:06 PM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Thanks for your reply, and sorry for my delayed response. >>>>> >>>>> I have attached the first file you requested, but the other two do >>>>>not >>>>> exist. I have attached a listing of the files in that directory. Let >>>>>me >>>>> know if you need anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>>> > wrote: >>>>> The first error is an IO error with your system. I've added some >>>>>more >>>>> detail to the errors in the development version if you do an 'svn >>>>> update'. Then you will know the system specific reason why close or >>>>> opened failed. For the other error, could you send me this file --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_ >>>>>7/ >>>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>>> >>>>> This one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta >>>>> >>>>> And this one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>>> >>>>> thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Thursday, 8 November, 2012 9:32 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Scaling up to whole-genome annotation, things seem to be going well. >>>>> However, there are some intermittent issues. I've seen a couple >>>>> occurrences of the following error... >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> couldn't close >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm >>>>>line >>>>> 60. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> ...as well as one occurrence of this error. >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> maker.output/maker.pd >>>>> >>>>> >>>>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93. >>>>>fo >>>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>>> >>>>> >>>>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datas >>>>>to >>>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>>> --showcigar --percent 20 > >>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>>> >>>>> >>>>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >>>>>af >>>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>>> q93.est_exonerate.0 >>>>> #-------------------------------# >>>>> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> STACK: Error::throw >>>>> STACK: Bio::Root::Root::throw >>>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>>> STACK: Bio::PrimarySeqI::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:38 >>>>>1 >>>>> STACK: Bio::LocatableSeq::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:5 >>>>>77 >>>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice >>>>>_i >>>>> nfo.pm:86 >>>>> STACK: Widget::exonerate::est2genome::assemble >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:686 >>>>> STACK: Widget::exonerate::est2genome::parse >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:961 >>>>> STACK: polisher::exonerate::est::e_exonerate >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:82 >>>>> STACK: polisher::exonerate::est::polish >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:44 >>>>> STACK: GI::to_polisher >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>>> STACK: GI::polish_exonerate >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>>> STACK: Process::MpiChunk::_go >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:1663 >>>>> STACK: Process::MpiChunk::run >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:335 >>>>> STACK: Process::MpiChunk::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:351 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>>> ----------------------------------------------------------- >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> I'll let you know if I see anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Typo now fixed on my end too ;-) >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Looked good for a while, but came across this error. >>>>> >>>>> total clusters:20 now processing 0 >>>>> flattening EST clusters >>>>> doing tblastx of alt-ESTs >>>>> Undefined subroutine &GI::loalize_file called at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>2648. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while doing tblastx of alt-ESTs >>>>> ERROR: Chunk failed at level:4, tier_type:2 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> >>>>> --Next Contig-- >>>>> >>>>> It seems pretty clear that there is a typo in GI.pm. I changed >>>>>loalize >>>>> to localize and relaunched. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>>> > wrote: >>>>> Done. >>>>> >>>>> Test job has successfully cleared the preliminary Fasta indexing >>>>>steps >>>>> and is repeat masking. I'll let you know if there are any problems. >>>>> Thanks! >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>>> > wrote: >>>>> 1.006902 Bio::Root::Version >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.p >>>>>m >>>>> >>>>> One thing I noticed, in the debug output is that you are using >>>>>Bioperl >>>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>>> It's fasta indexer is broken. I have an open bug I am trying to >>>>> resolve with the Bioperl developers, but for now use the CPAN version >>>>> of Bioperl. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:14 AM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Debug output attached (bzip2 compressed). >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt >, >>>>>Maker >>>>> Mailing List >>>>> > >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached >>>>>the >>>>> output of the job that failed in <5 minutes. It looks pretty similar >>>>>to >>>>> the errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> maker-devel mailing list >>>>> maker-devel at box290.bluehost.com >>>>> >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > From parulk at caltech.edu Mon Nov 26 16:15:58 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 14:15:58 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <2223.131.215.15.234.1353968158.squirrel@webmail.caltech.edu> Dear Carson, Thanks, I retrain/rerun using better AED score to filter false negatives. > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From daniel.standage at gmail.com Fri Nov 23 14:06:34 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Fri, 23 Nov 2012 15:06:34 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> >> It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to >> *localize* and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < >> daniel.standage at gmail.com> wrote: >> >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>> and is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List < >>>>> maker-devel at yandell-lab.org> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached the >>>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>>> errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... 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-rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303233.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303234.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303235.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038212.gnl%7CAmel_4%2E5%7CGB40495-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB40142-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB53378-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038224.gnl%7CAmel_4%2E5%7CGB43258-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:19 scaffold_23.1037324-1038248.gnl%7CAmel_4%2E5%7CGB48486-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 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Nov 8 06:55 scaffold_23.11767-15264.gnl%7CDmel_r5%2E47%7CFBpp0079114.p_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:20 scaffold_23.1177210-1187515.comp55832_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 06:57 scaffold_23.118600-121630.comp56223_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:05 scaffold_23.119493-121535.gnl%7CAmel_4%2E5%7CGB42515-PA.p_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0080719.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0085457.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:24 scaffold_23.11.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 33K Nov 8 06:28 scaffold_23.11.drosophila.rb.out -rw-r--r-- 1 dstandag biol 469K Nov 8 12:05 scaffold_23.11.final.section -rw-r--r-- 1 dstandag biol 198K Nov 8 11:19 scaffold_23.11.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 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-rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:25 scaffold_23.1239438-1240065.comp58697_c2_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:25 scaffold_23.1240020-1240577.comp51041_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:58 scaffold_23.125651-126606.comp51692_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:57 scaffold_23.126190-129712.comp51692_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:58 scaffold_23.126190-129712.comp51692_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:05 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dstandag biol 5.4K Nov 8 07:05 scaffold_23.129450-131047.gnl%7CAmel_4%2E5%7CGB47192-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 11:35 scaffold_23.1296927-1297434.gnl%7CAmel_4%2E5%7CGB43383-PA.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:29 scaffold_23.12.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 24K Nov 8 06:29 scaffold_23.12.drosophila.rb.out -rw-r--r-- 1 dstandag biol 343K Nov 8 12:05 scaffold_23.12.final.section -rw-r--r-- 1 dstandag biol 119K Nov 8 11:24 scaffold_23.12.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 104K Nov 8 11:28 scaffold_23.12.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 41K Nov 8 07:09 scaffold_23.1-2.raw.section -rw-r--r-- 1 dstandag biol 344K Nov 8 11:29 scaffold_23.12.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:29 scaffold_23.12.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1307615-1308418.comp1419599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 26K Nov 8 11:35 scaffold_23.1308043-1330696.gnl%7CAmel_4%2E5%7CGB48919-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1308162-1309528.comp44341_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302629.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302630.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302631.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1330258.gnl%7CDmel_r5%2E47%7CFBpp0302633.p_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:30 scaffold_23.1309128-1310251.comp26811_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 11:30 scaffold_23.1309844-1319042.comp55832_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:58 scaffold_23.131077-131586.comp59045_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 132K Nov 8 11:40 scaffold_23.13-14.raw.section -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1316714-1317272.comp1218705_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:59 scaffold_23.131685-132925.comp58909_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:59 scaffold_23.131685-134704.comp58909_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 8.3K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 11:30 scaffold_23.1318842-1326844.comp55832_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 11:30 scaffold_23.1318842-1329152.comp55832_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 11:30 scaffold_23.1318842-1331426.comp55832_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 06:58 scaffold_23.132429-133368.comp59433_c2_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1325517-1326265.comp1845494_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:59 scaffold_23.132575-133077.comp59433_c2_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 06:59 scaffold_23.132639-133189.comp59433_c2_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:58 scaffold_23.132947-134704.comp58909_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:59 scaffold_23.132947-134801.comp58909_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 11:30 scaffold_23.1331331-1332259.comp40535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:59 scaffold_23.133194-134178.comp58909_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 11:30 scaffold_23.1331948-1333303.comp32761_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1333133-1334007.comp56864_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1333600-1334315.comp56864_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 11:30 scaffold_23.1333918-1335419.comp56864_c3_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1335705.comp56864_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1337728.comp56864_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:35 scaffold_23.1334768-1337724.gnl%7CAmel_4%2E5%7CGB48917-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:05 scaffold_23.133512-135390.gnl%7CAmel_4%2E5%7CGB45366-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1335366-1335970.comp1729875_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:30 scaffold_23.1336887-1337499.comp1746631_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:00 scaffold_23.133757-134452.comp58909_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1340213-1340817.comp3166415_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1341145-1341745.comp2137934_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1341790-1342546.comp2308491_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:58 scaffold_23.134716-136043.comp58909_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:30 scaffold_23.1351224-1351773.comp56864_c3_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1351855-1352444.comp49157_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:30 scaffold_23.1352403-1353237.comp50400_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 11:30 scaffold_23.1352824-1354274.comp50400_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1353863-1354457.comp32051_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:30 scaffold_23.1354103-1354916.comp32051_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 11:30 scaffold_23.1354495-1355883.comp28788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:30 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scaffold_23.1361370-1362023.comp63024_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1361962-1362628.comp56945_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 11:30 scaffold_23.1362208-1364017.comp56945_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1363621-1364241.comp56945_c15_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1363824-1364656.comp56945_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:30 scaffold_23.1364241-1365534.comp56945_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 11:30 scaffold_23.1365475-1366354.comp58627_c6_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1365475-1367018.comp58627_c6_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 11:30 scaffold_23.1366668-1368555.comp58344_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1369001-1370345.comp57731_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1369932-1370651.comp57731_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.137055-137860.comp53917_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1370982-1372429.comp58968_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 scaffold_23.1372006-1372825.comp56955_c2_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 11:30 scaffold_23.1373883-1375967.comp53188_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:00 scaffold_23.137439-138464.comp53917_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1376023-1376568.comp58089_c12_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:35 scaffold_23.1389507.1410090.0.comp58089_c6_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 scaffold_23.1389801-1390543.comp47217_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 07:00 scaffold_23.138981-140060.comp58679_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1389854-1390711.comp47217_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 11:36 scaffold_23.1390291-1390966.comp47217_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 11:36 scaffold_23.1390743-1392000.comp58289_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1391945-1392597.comp58289_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 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-rw-r--r-- 1 dstandag biol 5.4K Nov 8 11:36 scaffold_23.1397553-1399112.comp58089_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.139809-140616.comp39902_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1398718-1399314.comp58089_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1398899-1399721.comp58089_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:36 scaffold_23.1399307-1400290.comp58089_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 11:36 scaffold_23.1399900-1400941.comp58089_c17_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 58K Nov 8 11:35 scaffold_23.13.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 34K Nov 8 06:30 scaffold_23.13.drosophila.rb.out -rw-r--r-- 1 dstandag biol 1.5M Nov 8 12:05 scaffold_23.13.final.section -rw-r--r-- 1 dstandag biol 364K Nov 8 11:29 scaffold_23.13.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 430K Nov 8 11:33 scaffold_23.13.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 1.4M Nov 8 11:35 scaffold_23.13.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:30 scaffold_23.13.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1400609-1401459.comp55139_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1401269-1402022.comp55139_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1401609-1402216.comp55139_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:36 scaffold_23.1402425-1403729.comp53666_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:00 scaffold_23.140332-144653.comp32064_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1403482-1404578.comp48783_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1404302-1405136.comp56313_c10_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1404714-1405577.comp56313_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1404752-1405577.comp56313_c9_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1405378-1406432.comp58905_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406035-1406617.comp58905_c6_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406210-1406799.comp57287_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 11:36 scaffold_23.1406210-1408214.comp57287_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409289.comp57287_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409306.comp57287_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1408987-1409890.comp55527_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:36 scaffold_23.1409724-1410684.comp53099_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410284-1410885.comp53099_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1410463-1411098.comp53099_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410682-1411329.comp53099_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411082-1411787.comp53099_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:40 scaffold_23.1411196-1420373.gnl%7CAmel_4%2E5%7CGB48913-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1411769-1412299.comp53730_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411806-1412343.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 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2.1K Nov 8 11:46 scaffold_23.1628188-1628869.comp53690_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1628995-1629629.comp1757695_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:46 scaffold_23.1629447-1630245.comp2225268_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:51 scaffold_23.1630078-1640599.gnl%7CAmel_4%2E5%7CGB48912-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1633935-1634941.comp469996_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1634612-1635227.comp1032535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:46 scaffold_23.1634842-1635615.comp9891_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:46 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06:46 scaffold_23.47976-52664.comp57565_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481059-481744.comp5788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:15 scaffold_23.481631-482286.comp31314_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481869-482552.comp1406842_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K 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-rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:22 scaffold_23.4.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503515-504045.comp57130_c2_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503604-504201.comp59180_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:20 scaffold_23.503604-504204.comp59180_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.503604-504276.comp59180_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:20 scaffold_23.503604-504336.comp59180_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:20 scaffold_23.503654-504201.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:20 scaffold_23.503654-504350.comp59180_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503699-504221.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 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2.2K Nov 8 07:20 scaffold_23.570506-571138.comp58475_c5_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:47 scaffold_23.57128-61415.comp57935_c3_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 07:20 scaffold_23.577559-578709.comp58715_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 07:20 scaffold_23.577559-578885.comp58715_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.578520-579331.comp17262_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:20 scaffold_23.579634-580662.comp19872_c0_seq1.est_exonerate -rw-r--r-- 1 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dstandag biol 4.5K Nov 8 07:20 scaffold_23.588308-588965.comp58681_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:20 scaffold_23.588513-589494.comp58681_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:21 scaffold_23.588513-589516.comp58681_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:26 scaffold_23.589528-590438.comp56568_c1_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 07:26 scaffold_23.590043-590860.comp56568_c1_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:26 scaffold_23.590182-590860.comp56568_c1_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CAmel_4%2E5%7CGB42672-PA.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0291239.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0293789.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 08:01 scaffold_23.590687-592189.gnl%7CDmel_r5%2E47%7CFBpp0071071.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0081035.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303794.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303795.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303796.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590885-592138.gnl%7CAmel_4%2E5%7CGB44981-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590894-591937.gnl%7CAmel_4%2E5%7CGB44980-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590909-591693.gnl%7CDmel_r5%2E47%7CFBpp0083755.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:26 scaffold_23.591776-592368.comp42067_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.592659-593271.comp59308_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.592659-593380.comp59308_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:26 scaffold_23.592965-593648.comp48548_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.593120-593648.comp48548_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:26 scaffold_23.593237-593841.comp59308_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.594070-594730.comp1421803_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:26 scaffold_23.599941-600713.comp58738_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 47K Nov 8 07:25 scaffold_23.5.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 49K Nov 8 06:22 scaffold_23.5.drosophila.rb.out -rw-r--r-- 1 dstandag biol 917K Nov 8 12:05 scaffold_23.5.final.section -rw-r--r-- 1 dstandag biol 730K Nov 8 07:19 scaffold_23.5.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 416K Nov 8 07:23 scaffold_23.5.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 976K Nov 8 07:25 scaffold_23.5.raw.section -rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:23 scaffold_23.5.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.600393-600917.comp59155_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:26 scaffold_23.600937-601763.comp1225959_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 08:01 scaffold_23.604967-608877.gnl%7CAmel_4%2E5%7CGB43104-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.606823-608989.comp51953_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:26 scaffold_23.608733-612437.comp56721_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:27 scaffold_23.608733-612437.comp56721_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609085-612369.gnl%7CAmel_4%2E5%7CGB54556-PA.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0070184.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303734.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303735.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0071164.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0304872.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.61000-61642.comp57935_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:01 scaffold_23.612645-614365.gnl%7CAmel_4%2E5%7CGB43132-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.612828-614317.gnl%7CDmel_r5%2E47%7CFBpp0074633.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.613400-614111.gnl%7CDmel_r5%2E47%7CFBpp0075906.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:26 scaffold_23.614151-614876.comp1433111_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:27 scaffold_23.614490-616677.comp62542_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615220-616300.gnl%7CDmel_r5%2E47%7CFBpp0080690.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615229-616300.gnl%7CAmel_4%2E5%7CGB48404-PA.p_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 07:30 scaffold_23.616573-622123.comp53298_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 06:55 scaffold_23.61662-63231.gnl%7CAmel_4%2E5%7CGB47823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:01 scaffold_23.617032-621897.gnl%7CAmel_4%2E5%7CGB43186-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.617361-621707.gnl%7CDmel_r5%2E47%7CFBpp0078372.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 06:49 scaffold_23.62025-63600.comp57576_c4_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 scaffold_23.62037-63192.gnl%7CDmel_r5%2E47%7CFBpp0070204.p_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 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-rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:27 scaffold_23.622010-624802.comp57205_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 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dstandag biol 9.8K Nov 8 07:27 scaffold_23.622010-625026.comp57205_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:30 scaffold_23.622010-625026.comp57205_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:28 scaffold_23.622010-625026.comp57205_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:30 scaffold_23.622010-625178.comp57205_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:27 scaffold_23.622010-625178.comp57205_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 scaffold_23.622010-625178.comp57205_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 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-rw-r--r-- 1 dstandag biol 6.9K Nov 8 08:01 scaffold_23.635723-637373.gnl%7CDmel_r5%2E47%7CFBpp0082101.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:30 scaffold_23.637770-638562.comp42460_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:30 scaffold_23.638373-640543.comp40473_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649502.gnl%7CAmel_4%2E5%7CGB43214-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649511.gnl%7CDmel_r5%2E47%7CFBpp0292225.p_exonerate -rw-r--r-- 1 dstandag biol 27K Nov 8 08:01 scaffold_23.638434-649538.gnl%7CAmel_4%2E5%7CGB45049-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.638434-649601.gnl%7CDmel_r5%2E47%7CFBpp0288420.p_exonerate -rw-r--r-- 1 dstandag biol 55K Nov 8 08:01 scaffold_23.638434-650174.gnl%7CAmel_4%2E5%7CGB49952-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638437-649103.gnl%7CAmel_4%2E5%7CGB42359-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638440-647567.gnl%7CAmel_4%2E5%7CGB55144-PA.p_exonerate -rw-r--r-- 1 dstandag biol 28K Nov 8 08:01 scaffold_23.638440-649430.gnl%7CDmel_r5%2E47%7CFBpp0293284.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638443-649532.gnl%7CAmel_4%2E5%7CGB42373-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.63987-64717.comp59376_c14_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 07:30 scaffold_23.640205-641458.comp934535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.641067-641742.comp17454_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 08:01 scaffold_23.641259-642288.gnl%7CAmel_4%2E5%7CGB41007-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K Nov 8 07:30 scaffold_23.641345-642764.comp17454_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:30 scaffold_23.642369-643170.comp1226599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.642760-643453.comp3200316_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.64294-84968.comp42086_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:01 scaffold_23.645509-646340.gnl%7CAmel_4%2E5%7CGB49823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.647483-648154.comp3284778_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:55 scaffold_23.649-1243.gnl%7CDmel_r5%2E47%7CFBpp0290776.p_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:01 scaffold_23.649971-651261.gnl%7CAmel_4%2E5%7CGB49951-PA.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:30 scaffold_23.651850-655866.comp56215_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 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Nov 8 08:02 scaffold_23.659787-662130.gnl%7CDmel_r5%2E47%7CFBpp0293463.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075012.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075013.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0073292.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:02 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0290751.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0304481.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659802-662082.gnl%7CDmel_r5%2E47%7CFBpp0075772.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659802-662088.gnl%7CDmel_r5%2E47%7CFBpp0293948.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662097.gnl%7CAmel_4%2E5%7CGB47477-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662121.gnl%7CAmel_4%2E5%7CGB41363-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662139.gnl%7CAmel_4%2E5%7CGB43707-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662290.gnl%7CAmel_4%2E5%7CGB51586-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662299.gnl%7CAmel_4%2E5%7CGB49425-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0089153.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0290826.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304233.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304234.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0305596.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659808-662094.gnl%7CAmel_4%2E5%7CGB52193-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CAmel_4%2E5%7CGB47284-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0076890.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0085042.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB44431-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB49047-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083843.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083906.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659817-662079.gnl%7CAmel_4%2E5%7CGB46102-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0073585.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0082346.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0305521.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:31 scaffold_23.664598-665339.comp57441_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.664951-665488.comp59321_c5_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 06:55 scaffold_23.66506-67079.gnl%7CAmel_4%2E5%7CGB47837-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088318.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088319.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088320.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089257.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089258.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0288398.p_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:31 scaffold_23.665135-665802.comp285497_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 07:31 scaffold_23.665399-666883.comp53689_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.666469-667197.comp53689_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.667162-667951.comp52180_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:31 scaffold_23.667162-671428.comp52180_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 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dstandag biol 3.3K Nov 8 07:31 scaffold_23.667978-669042.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 07:31 scaffold_23.668017-669001.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 07:31 scaffold_23.668059-668959.comp59180_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.668936-669683.comp382769_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.66912-67979.comp5946_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:31 scaffold_23.669726-671764.comp52180_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 06:49 scaffold_23.67030-67979.comp5946_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:31 scaffold_23.671029-677447.comp52180_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.671054-671764.comp52180_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.671886-672575.comp57527_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671901-672561.comp57527_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672538.comp57527_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672575.comp57527_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41577-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41578-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB46989-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB50263-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.672098-672598.comp59502_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:31 scaffold_23.672970-673610.comp59089_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 07:31 scaffold_23.673324-674422.comp53293_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:31 scaffold_23.673999-677447.comp52180_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076415.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076416.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302862.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302863.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302864.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0081016.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0304068.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.675963-676551.comp408860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:31 scaffold_23.677207-677898.comp772804_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 06:49 scaffold_23.67721-68472.comp350940_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.677525-678233.comp53322_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 scaffold_23.677908-678920.comp53322_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:31 scaffold_23.677908-679249.comp53322_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.9K Nov 8 07:31 scaffold_23.678839-682919.comp32442_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:31 scaffold_23.679979-680866.comp36035_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 07:31 scaffold_23.679979-681267.comp36035_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.1M Nov 8 11:03 scaffold_23.6-7.raw.section -rw-r--r-- 1 dstandag biol 1.8K Nov 8 07:31 scaffold_23.680259-680866.comp36035_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.680259-681267.comp36035_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 08:02 scaffold_23.680843-682232.gnl%7CAmel_4%2E5%7CGB50275-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 08:02 scaffold_23.680846-682172.gnl%7CDmel_r5%2E47%7CFBpp0070979.p_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:50 scaffold_23.682524-683916.comp33074_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:44 scaffold_23.683503-684184.comp59066_c0_seq140.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:46 scaffold_23.683503-688813.comp59066_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:35 scaffold_23.683503-688813.comp59066_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:53 scaffold_23.683503-688813.comp59066_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:50 scaffold_23.683503-688813.comp59066_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:33 scaffold_23.683503-688813.comp59066_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:55 scaffold_23.683503-688813.comp59066_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:37 scaffold_23.683503-688813.comp59066_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:36 scaffold_23.683503-688813.comp59066_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:44 scaffold_23.683503-688813.comp59066_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683763-688813.comp59066_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683882-688813.comp59066_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:36 scaffold_23.683882-688813.comp59066_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:48 scaffold_23.683882-688813.comp59066_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:51 scaffold_23.683882-688813.comp59066_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:56 scaffold_23.683882-688813.comp59066_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:47 scaffold_23.683882-688813.comp59066_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:32 scaffold_23.683882-688813.comp59066_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:42 scaffold_23.683882-688813.comp59066_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:49 scaffold_23.683882-688813.comp59066_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:50 scaffold_23.683882-688813.comp59066_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:35 scaffold_23.683988-688813.comp59066_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:32 scaffold_23.684333-688813.comp59066_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:49 scaffold_23.684333-688813.comp59066_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:51 scaffold_23.684333-688813.comp59066_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:52 scaffold_23.684333-688813.comp59066_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:54 scaffold_23.684333-688813.comp59066_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:33 scaffold_23.684333-688813.comp59066_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:44 scaffold_23.684333-688813.comp59066_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:39 scaffold_23.684333-688813.comp59066_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:43 scaffold_23.684333-688975.comp59066_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:53 scaffold_23.684333-688975.comp59066_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:45 scaffold_23.684333-688975.comp59066_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:55 scaffold_23.684333-688975.comp59066_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721817.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721839.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 12K Nov 8 07:56 scaffold_23.684971-688813.comp59066_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.684971-688813.comp59066_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.684971-688813.comp59066_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:42 scaffold_23.684971-688813.comp59066_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:37 scaffold_23.684971-688975.comp59066_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:41 scaffold_23.684971-688975.comp59066_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.684975-688813.comp59066_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:39 scaffold_23.684975-688813.comp59066_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.684975-688813.comp59066_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.684975-688813.comp59066_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:45 scaffold_23.684975-688975.comp59066_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:53 scaffold_23.684975-688975.comp59066_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq2%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 12K Nov 8 07:38 scaffold_23.685264-688813.comp59066_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.685264-688813.comp59066_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.685264-688813.comp59066_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685264-688813.comp59066_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685264-688813.comp59066_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:52 scaffold_23.685264-688813.comp59066_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:32 scaffold_23.685264-688813.comp59066_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685264-688813.comp59066_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:37 scaffold_23.685264-688975.comp59066_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.685264-688975.comp59066_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685264-688975.comp59066_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685334-688813.comp59066_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685334-688813.comp59066_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685334-688813.comp59066_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:48 scaffold_23.685334-688813.comp59066_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685334-688813.comp59066_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:49 scaffold_23.685334-688813.comp59066_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685334-688975.comp59066_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:46 scaffold_23.685334-688975.comp59066_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.685334-688975.comp59066_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.68540-69483.comp433_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 11:02 scaffold_23.685479.720745.0.gnl%7CAmel_4%2E5%7CGB49172-PA%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072421%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072422%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0290562%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304412%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304413%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304414%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 11K Nov 8 07:44 scaffold_23.685588-688813.comp59066_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685588-688813.comp59066_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:33 scaffold_23.685588-688813.comp59066_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:51 scaffold_23.685588-688813.comp59066_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:32 scaffold_23.685588-688813.comp59066_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:49 scaffold_23.685588-688813.comp59066_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:52 scaffold_23.685801-688813.comp59066_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:41 scaffold_23.685801-688813.comp59066_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:44 scaffold_23.685801-688813.comp59066_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:42 scaffold_23.685801-688813.comp59066_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:46 scaffold_23.685801-688813.comp59066_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:54 scaffold_23.685801-688813.comp59066_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:51 scaffold_23.685801-688813.comp59066_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:45 scaffold_23.685801-688975.comp59066_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:42 scaffold_23.685801-688975.comp59066_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:32 scaffold_23.685801-688975.comp59066_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:37 scaffold_23.685801-688975.comp59066_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:38 scaffold_23.686019-688813.comp59066_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:37 scaffold_23.686019-688813.comp59066_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 07:52 scaffold_23.686019-688813.comp59066_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:42 scaffold_23.686019-688813.comp59066_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:45 scaffold_23.686019-688975.comp59066_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:56 scaffold_23.686019-688975.comp59066_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:32 scaffold_23.686019-688975.comp59066_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:55 scaffold_23.686019-688975.comp59066_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:52 scaffold_23.686019-688975.comp59066_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:43 scaffold_23.686506-688813.comp59066_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686506-688813.comp59066_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:48 scaffold_23.686506-688813.comp59066_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:38 scaffold_23.686506-688813.comp59066_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:54 scaffold_23.686506-688813.comp59066_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:34 scaffold_23.686506-688813.comp59066_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:44 scaffold_23.686506-688813.comp59066_c0_seq135.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:35 scaffold_23.686506-688975.comp59066_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:51 scaffold_23.686506-688975.comp59066_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:43 scaffold_23.686506-688975.comp59066_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:38 scaffold_23.686506-688975.comp59066_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:51 scaffold_23.686591-688813.comp59066_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686591-688813.comp59066_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:44 scaffold_23.686591-688813.comp59066_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:32 scaffold_23.686591-688813.comp59066_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:41 scaffold_23.686591-688813.comp59066_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:54 scaffold_23.686591-688975.comp59066_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:39 scaffold_23.686591-688975.comp59066_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:56 scaffold_23.686591-688975.comp59066_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:40 scaffold_23.686591-688975.comp59066_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:46 scaffold_23.686591-688975.comp59066_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:45 scaffold_23.686591-688975.comp59066_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:49 scaffold_23.686979-688813.comp59066_c0_seq136.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:51 scaffold_23.686979-688813.comp59066_c0_seq139.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:39 scaffold_23.686979-688975.comp59066_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:51 scaffold_23.686979-688975.comp59066_c0_seq137.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:54 scaffold_23.686979-688975.comp59066_c0_seq138.est_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 07:56 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scaffold_23.690234-691062.comp58228_c7_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 06:49 scaffold_23.69062-69744.comp433_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 08:03 scaffold_23.692420-694948.comp51249_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 08:03 scaffold_23.694556-695181.comp839860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 scaffold_23.695279-710945.gnl%7CAmel_4%2E5%7CGB49172-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072421.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072422.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0290562.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304412.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304413.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 08:03 scaffold_23.696083-696661.comp59447_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 08:03 scaffold_23.696083-696714.comp59447_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 08:03 scaffold_23.696083-696748.comp59447_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:03 scaffold_23.696083-696759.comp59447_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 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dstandag biol 957K Nov 8 08:01 scaffold_23.6.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 30K Nov 8 06:23 scaffold_23.6.drosophila.rb.out -rw-r--r-- 1 dstandag biol 4.8M Nov 8 12:05 scaffold_23.6.final.section -rw-r--r-- 1 dstandag biol 2.7M Nov 8 07:25 scaffold_23.6.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 1.2M Nov 8 07:59 scaffold_23.6.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 5.5M Nov 8 08:02 scaffold_23.6.raw.section -rw-r--r-- 1 dstandag biol 562K Nov 8 06:24 scaffold_23.6.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.70076-70676.comp16610_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0089425.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0290563.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0304411.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.70266-70881.comp1005591_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.71180-72221.comp36225_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:03 scaffold_23.712367-714691.gnl%7CAmel_4%2E5%7CGB49161-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 08:03 scaffold_23.712520-713560.comp54814_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:03 scaffold_23.712520-713766.comp54814_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 scaffold_23.712609-713560.comp54814_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.712609-713766.comp54814_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:50 scaffold_23.716125-720215.comp58983_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:04 scaffold_23.716125-720215.comp58983_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:47 scaffold_23.716125-720215.comp58983_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:46 scaffold_23.716125-720215.comp58983_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:45 scaffold_23.716125-720215.comp58983_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:51 scaffold_23.716125-720215.comp58983_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720215.comp58983_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.716125-720215.comp58983_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:06 scaffold_23.716125-720215.comp58983_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:53 scaffold_23.716125-720628.comp58983_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:03 scaffold_23.716125-720628.comp58983_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-720628.comp58983_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:48 scaffold_23.716125-720628.comp58983_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:51 scaffold_23.716125-720628.comp58983_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:06 scaffold_23.716125-720628.comp58983_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720628.comp58983_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720628.comp58983_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720628.comp58983_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:50 scaffold_23.716125-720628.comp58983_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:05 scaffold_23.716125-720628.comp58983_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721166.comp58983_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:07 scaffold_23.716125-721166.comp58983_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:03 scaffold_23.716125-721166.comp58983_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:05 scaffold_23.716125-721166.comp58983_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:51 scaffold_23.716125-721166.comp58983_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:08 scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:46 scaffold_23.716125-721460.comp58983_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721460.comp58983_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:45 scaffold_23.716125-721460.comp58983_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:53 scaffold_23.716125-721460.comp58983_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-721460.comp58983_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:48 scaffold_23.716125-721460.comp58983_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:44 scaffold_23.716125-721460.comp58983_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:52 scaffold_23.716125-721460.comp58983_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-721720.comp58983_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:46 scaffold_23.716125-721720.comp58983_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:45 scaffold_23.716125-721720.comp58983_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 08:06 scaffold_23.716125-721720.comp58983_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:48 scaffold_23.716125-721720.comp58983_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:47 scaffold_23.716125-721720.comp58983_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:53 scaffold_23.716125-721720.comp58983_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:45 scaffold_23.716125-722098.comp58983_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:48 scaffold_23.716125-722098.comp58983_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:53 scaffold_23.716125-722098.comp58983_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:50 scaffold_23.716125-722098.comp58983_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:05 scaffold_23.716125-722098.comp58983_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-722098.comp58983_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:47 scaffold_23.716125-722098.comp58983_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-722098.comp58983_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:46 scaffold_23.716125-722428.comp58983_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:08 scaffold_23.716125-722428.comp58983_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:49 scaffold_23.716125-722428.comp58983_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:53 scaffold_23.716125-722428.comp58983_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:06 scaffold_23.716125-722428.comp58983_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:05 scaffold_23.716125-722428.comp58983_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:47 scaffold_23.716125-722428.comp58983_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-722428.comp58983_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 08:04 scaffold_23.716125-722428.comp58983_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:50 scaffold_23.716125-722757.comp58983_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:05 scaffold_23.716125-722757.comp58983_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:52 scaffold_23.716125-722757.comp58983_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722757.comp58983_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:47 scaffold_23.716125-723330.comp58983_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:05 scaffold_23.716125-723330.comp58983_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:04 scaffold_23.716125-723330.comp58983_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:44 scaffold_23.716125-723330.comp58983_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:51 scaffold_23.716125-723330.comp58983_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:48 scaffold_23.716125-723330.comp58983_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:07 scaffold_23.716125-723330.comp58983_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:45 scaffold_23.716125-723330.comp58983_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 10:47 scaffold_23.716125-725421.comp58983_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:46 scaffold_23.716125-725421.comp58983_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:05 scaffold_23.716125-725421.comp58983_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:04 scaffold_23.716125-725421.comp58983_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:45 scaffold_23.716125-725421.comp58983_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:49 scaffold_23.716125-725421.comp58983_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:49 scaffold_23.716125-728040.comp58983_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:48 scaffold_23.716125-728040.comp58983_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:47 scaffold_23.716125-728040.comp58983_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:06 scaffold_23.716125-728040.comp58983_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:04 scaffold_23.716125-728040.comp58983_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 06:55 scaffold_23.7171-17933.gnl%7CAmel_4%2E5%7CGB46618-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070125.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070126.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070127.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070128.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291468.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291469.p_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 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dstandag biol 3.2K Nov 8 10:53 scaffold_23.728443-729727.comp45774_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.729783-730395.comp2904457_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 10:53 scaffold_23.730057-730704.comp1503238_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:49 scaffold_23.73016-73676.comp16138_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 scaffold_23.731277-731906.comp1893859_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.733065-733673.comp3350191_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.73345-73945.comp16138_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 10:53 scaffold_23.734599-735763.comp1287295_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.73525-74446.comp9823_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 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-rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0290962.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303730.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303731.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:03 scaffold_23.748248-752313.gnl%7CAmel_4%2E5%7CGB49163-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:49 scaffold_23.75148-75896.comp276986_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:56 scaffold_23.751890-761021.comp49210_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:55 scaffold_23.751890-761021.comp49210_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:54 scaffold_23.751890-761021.comp49210_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:03 scaffold_23.752357-755378.gnl%7CAmel_4%2E5%7CGB49169-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K 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11:03 scaffold_23.772644-773319.gnl%7CDmel_r5%2E47%7CFBpp0075479.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773322.gnl%7CAmel_4%2E5%7CGB48430-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773325.gnl%7CDmel_r5%2E47%7CFBpp0077688.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773328.gnl%7CDmel_r5%2E47%7CFBpp0071844.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773349.gnl%7CAmel_4%2E5%7CGB40139-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772647-773280.gnl%7CDmel_r5%2E47%7CFBpp0072463.p_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 06:49 scaffold_23.77438-78155.comp13284_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 10:57 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Name: scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 Type: application/octet-stream Size: 4811 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 27 16:39:18 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:39:18 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Hello Carson, Just to confirm, Is there a script that would filter gene models at specific AED score. Alternatively if I were to do this within maker with regards to parameters in maker_opts.ctl file I would have to provide my predicted genes gff3 file to model_gff and set AED_threshold at desired threshold? Thanks and regards, Parul Kudtarkar > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From parulk at caltech.edu Tue Nov 27 16:41:12 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:41:12 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Message-ID: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From dence at genetics.utah.edu Tue Nov 27 16:55:49 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 27 Nov 2012 22:55:49 +0000 Subject: [maker-devel] AED score In-Reply-To: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: Hi Parul, I think the way you described (with the maker_opts.ctl file) is how you want to proceed. You still need to give the genome too. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] Sent: Tuesday, November 27, 2012 3:41 PM To: Parul Kudtarkar Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] AED score Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Tue Nov 27 16:59:22 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:59:22 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: <3841.131.215.15.234.1354057162.squirrel@webmail.caltech.edu> Thanks for quick response Daniel, I'll do it through maker. > Hi Parul, > > I think the way you described (with the maker_opts.ctl file) is how you > want to proceed. You still need to give the genome too. > > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar > [parulk at caltech.edu] > Sent: Tuesday, November 27, 2012 3:41 PM > To: Parul Kudtarkar > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] AED score > > Also, are there any other parameters that are required when filtering > based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >> parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>> may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>> 20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>> how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From kapeelc at gmail.com Tue Nov 27 19:23:12 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Tue, 27 Nov 2012 18:23:12 -0700 Subject: [maker-devel] Maker error message Message-ID: Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Nov 27 19:38:33 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 01:38:33 +0000 Subject: [maker-devel] Maker error message In-Reply-To: References: Message-ID: Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Nov 27 21:39:56 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 27 Nov 2012 22:39:56 -0500 Subject: [maker-devel] AED score In-Reply-To: Message-ID: Use the AED_threshold option in the maker_opts.ctl file if you just want to restrict final gene models to close matches directly within maker. On the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset for SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. Thanks, Carson On 12-11-27 5:55 PM, "Daniel Ence" wrote: >Hi Parul, > >I think the way you described (with the maker_opts.ctl file) is how you >want to proceed. You still need to give the genome too. > >Daniel > > >Daniel Ence >Graduate Student >Eccles Institute of Human Genetics >University of Utah >15 North 2030 East, Room 2100 >Salt Lake City, UT 84112-5330 >________________________________________ >From: maker-devel-bounces at yandell-lab.org >[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >Sent: Tuesday, November 27, 2012 3:41 PM >To: Parul Kudtarkar >Cc: maker-devel at yandell-lab.org >Subject: Re: [maker-devel] AED score > >Also, are there any other parameters that are required when filtering >based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >>parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>>may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>>20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>>how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From dence at genetics.utah.edu Wed Nov 28 13:25:22 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 19:25:22 +0000 Subject: [maker-devel] Maker error message In-Reply-To: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Hi Kapeel,? Please keep this discussion on the maker-devel group, so we can get everyone's input to help resolve this issue with maker.? Can you sen me the maker_opts file that you were using? The options that might be relevant include the libraries you were giving repeatrunner and repeatmasker. Thanks, Daniel? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: kapeelc at gmail.com [kapeelc at gmail.com] Sent: Wednesday, November 28, 2012 11:39 AM To: Daniel Ence Subject: Re: Maker error message Hi Daniel, Here is the output around the error: j_size:94 current j:76 j_size:94 current j:77 j_size:94 current j:78 j_size:94 current j:79 j_size:94 current j:80 j_size:94 current j:81 j_size:94 current j:82 j_size:94 current j:83 j_size:94 current j:84 j_size:94 current j:85 j_size:94 current j:86 j_size:94 current j:87 j_size:94 current j:88 j_size:94 current j:89 j_size:94 current j:90 j_size:94 current j:91 j_size:94 current j:92 j_size:94 current j:93 ...finished clustering. re reading repeat masker report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out re reading blast report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner deleted:1 hits in cluster::shadow_cluster... DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 --Next Contig-- Processing run.log file... Maker is now finished!!! For RepeatMasker I am using wublast as the search engine. The run log had this: LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 DIED RANK 0 DIED COUNT 2 Is there way to skip the the failed chunk and move forward?? Thanks Kapeel Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Quoted from: http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html From kapeelc at gmail.com Wed Nov 28 14:15:13 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Wed, 28 Nov 2012 13:15:13 -0700 Subject: [maker-devel] Maker error message In-Reply-To: References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get > everyone's input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that > might be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out > re reading blast report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're > running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html > -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4830 bytes Desc: not available URL: From carsonhh at gmail.com Thu Nov 29 08:22:42 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:22:42 -0500 Subject: [maker-devel] AED score In-Reply-To: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Message-ID: There are certain characteristics that are apparent in this contig. First it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many of them to align spuriously which produces very short gene models that are more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial bias to get back very short and incomplete models. How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as well as get an estimate of fragmentation as one of the statistics produced is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), and if they are distantly related to other annotated species few proteins may align to the contigs because the introns in the alignments tend to be so long and exons so short that it pushes down the significance scores too much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. Thanks, Carson On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >Dear Carson and Daniel, > >Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 >genes with AED score less than 0.75. However there were no genes predicted >in the output file(see attached file Scaffold1_out). I have also attached >the maker_opts.ctl. Could you please advice on this. > >Thanks and regards, >Parul Kudtarkar > >> Use the AED_threshold option in the maker_opts.ctl file if you just want >> to restrict final gene models to close matches directly within maker. >>On >> the other hand, if you are trying to build a dataset for training gene >> predictors, use the maker2zff script for generating a filtered dataset >>for >> SNAP training. There are a number of filters available. Just call the >> script once without parameters to see the options. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >> >>>Hi Parul, >>> >>>I think the way you described (with the maker_opts.ctl file) is how you >>>want to proceed. You still need to give the genome too. >>> >>>Daniel >>> >>> >>>Daniel Ence >>>Graduate Student >>>Eccles Institute of Human Genetics >>>University of Utah >>>15 North 2030 East, Room 2100 >>>Salt Lake City, UT 84112-5330 >>>________________________________________ >>>From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>>[parulk at caltech.edu] >>>Sent: Tuesday, November 27, 2012 3:41 PM >>>To: Parul Kudtarkar >>>Cc: maker-devel at yandell-lab.org >>>Subject: Re: [maker-devel] AED score >>> >>>Also, are there any other parameters that are required when filtering >>>based on AED score? >>> >>>> Hello Carson, >>>> >>>> Just to confirm, Is there a script that would filter gene models at >>>> specific AED score. >>>> Alternatively if I were to do this within maker with regards to >>>>parameters >>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>> file to model_gff and set AED_threshold at desired threshold? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>>> worst >>>>> as >>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>> require better matching to the evidence by setting it closer to 0. >>>>>You >>>>> can >>>>> also try to increase protein homology evidence as some of your calls >>>>>may >>>>> be split genes due to lack of evidence linking them. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>>Dear Maker community, >>>>>> >>>>>>For gene-prediction I get training data-set from evidence based >>>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>>predictions, followed by boot-strapping. I would typically expect >>>>>>20-30K >>>>>>genes however I am getting 8 times the expected gene count indicating >>>>>> too >>>>>>many false positives. Is there a way to further refine these >>>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>>how >>>>>>to go about this? >>>>>> >>>>>>Thanks and regards, >>>>>>Parul Kudtarkar >>>>>> >>>>>>-- >>>>>>Scientific Programmer >>>>>>Center for Computational Regulatory Genomics >>>>>>Beckman Institute, >>>>>>California Institute of Technology >>>>>>http://www.spbase.org >>>>>> >>>>>> >>>>>>_______________________________________________ >>>>>>maker-devel mailing list >>>>>>maker-devel at box290.bluehost.com >>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o >>>>>>rg >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 08:52:25 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:52:25 -0500 Subject: [maker-devel] Maker error message In-Reply-To: Message-ID: There should normally be more error message than that. The module used to capture the error returns the string "Died" without an end line character when there is a problem capturing the STDERR of the failure (and I see that phrase here), so could you run this again and see if it produces a different message the second time. Also I'm going to send you instructions on download the development version of MAKER in a separate message (off list). It is easier for me to make changes and have you test them immediately that way. Also there are already some bug fixes in the devel version so it's good to rule those out. Thanks, Carson From: Kapeel Chougule Date: Wednesday, 28 November, 2012 3:15 PM To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Maker error message Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get everyone's > input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that might > be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific > .out > re reading blast report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2 > Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 28 15:40:51 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 28 Nov 2012 13:40:51 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Dear Carson and Daniel, Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 genes with AED score less than 0.75. However there were no genes predicted in the output file(see attached file Scaffold1_out). I have also attached the maker_opts.ctl. Could you please advice on this. Thanks and regards, Parul Kudtarkar > Use the AED_threshold option in the maker_opts.ctl file if you just want > to restrict final gene models to close matches directly within maker. On > the other hand, if you are trying to build a dataset for training gene > predictors, use the maker2zff script for generating a filtered dataset for > SNAP training. There are a number of filters available. Just call the > script once without parameters to see the options. > > Thanks, > Carson > > > > > On 12-11-27 5:55 PM, "Daniel Ence" wrote: > >>Hi Parul, >> >>I think the way you described (with the maker_opts.ctl file) is how you >>want to proceed. You still need to give the genome too. >> >>Daniel >> >> >>Daniel Ence >>Graduate Student >>Eccles Institute of Human Genetics >>University of Utah >>15 North 2030 East, Room 2100 >>Salt Lake City, UT 84112-5330 >>________________________________________ >>From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>[parulk at caltech.edu] >>Sent: Tuesday, November 27, 2012 3:41 PM >>To: Parul Kudtarkar >>Cc: maker-devel at yandell-lab.org >>Subject: Re: [maker-devel] AED score >> >>Also, are there any other parameters that are required when filtering >>based on AED score? >> >>> Hello Carson, >>> >>> Just to confirm, Is there a script that would filter gene models at >>> specific AED score. >>> Alternatively if I were to do this within maker with regards to >>>parameters >>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>> file to model_gff and set AED_threshold at desired threshold? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>> worst >>>> as >>>> it is a distance metric. You can use the AED_threshold parameter to >>>> require better matching to the evidence by setting it closer to 0. You >>>> can >>>> also try to increase protein homology evidence as some of your calls >>>>may >>>> be split genes due to lack of evidence linking them. >>>> >>>> --Carson >>>> >>>> >>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Dear Maker community, >>>>> >>>>>For gene-prediction I get training data-set from evidence based >>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>predictions, followed by boot-strapping. I would typically expect >>>>>20-30K >>>>>genes however I am getting 8 times the expected gene count indicating >>>>> too >>>>>many false positives. Is there a way to further refine these >>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>how >>>>>to go about this? >>>>> >>>>>Thanks and regards, >>>>>Parul Kudtarkar >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1.gff Type: application/octet-stream Size: 594161 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1_out.gff Type: application/octet-stream Size: 371507 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4560 bytes Desc: not available URL: From mikael.durling at slu.se Thu Nov 29 10:20:10 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Thu, 29 Nov 2012 16:20:10 +0000 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids Message-ID: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Hello all, I'm running Maker (2.26 / r956 from svn) with a previous run in the input as maker_gff. However, the maker mpi ranks quit stop one after another with the following error messages. prepare section files Gathering GFF3 input into hits - chunk:3 ERROR: Non-unique top level ID for While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. --> rank=4, hostname=my-mgrid2 ERROR: Failed while prepare section files ERROR: Chunk failed at level:12, tier_type:2 FAILED CONTIG:scf_89936 In the end no ranks are running, but maker doesn't quit. Checking the maker_gff input, I do find duplicated ids, as this sample: scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.082870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.082870 but not for the scaffold found in the error message above. Are those two errors unrelated? If I run maker without providing a maker_gff the run works fine. Any input on this issue would be appreciated as I would like the reannotation to work in order to carry forward human readable names. cheers, Mikael ------------------------------------- Mikael Brandstr?m Durling, PhD Assistant Professor Sveriges lantbruksuniversitet Swedish University of Agricultural Sciences Uppsala BioCenter Dept of Forest Mycology and Plant Pathology Box 7026, 75007 Uppsala Visiting address: Almas All? 5 Telefon: 018-671503 mikael.durling at slu.se, www.slu.se/mykopat From carsonhh at gmail.com Thu Nov 29 10:23:39 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 11:23:39 -0500 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Message-ID: You can get the fixed version by doing svn update inside the maker directory. I will be changing the download version to 2.27 on yandell0lab.org, probably this weekend. Thanks, Carson On 12-11-29 11:20 AM, "Mikael Brandstr?m Durling" wrote: >Hello all, > >I'm running Maker (2.26 / r956 from svn) with a previous run in the input >as maker_gff. However, the maker mpi ranks quit stop one after another >with the following error messages. > >prepare section files >Gathering GFF3 input into hits - chunk:3 >ERROR: Non-unique top level ID for >While this is technically legal in GFF3, it usually >indicates a poorly fomatted GFF3 file (perhaps you >tried to merge two GFF3 files without accounting for >unique IDs). MAKER will not handle these correctly. > >--> rank=4, hostname=my-mgrid2 >ERROR: Failed while prepare section files >ERROR: Chunk failed at level:12, tier_type:2 >FAILED CONTIG:scf_89936 > >In the end no ranks are running, but maker doesn't quit. > >Checking the maker_gff input, I do find duplicated ids, as this sample: > >scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158 >:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 >scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.0 >82870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.08287 >0 > >but not for the scaffold found in the error message above. Are those two >errors unrelated? > >If I run maker without providing a maker_gff the run works fine. > >Any input on this issue would be appreciated as I would like the >reannotation to work in order to carry forward human readable names. > >cheers, >Mikael > > > > >------------------------------------- >Mikael Brandstr?m Durling, PhD >Assistant Professor > >Sveriges lantbruksuniversitet >Swedish University of Agricultural Sciences > >Uppsala BioCenter >Dept of Forest Mycology and Plant Pathology >Box 7026, 75007 Uppsala >Visiting address: Almas All? 5 >Telefon: 018-671503 >mikael.durling at slu.se, www.slu.se/mykopat > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Thu Nov 29 18:31:40 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Thu, 29 Nov 2012 16:31:40 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Thanks for the guidance Carson, total contig size is 330,611 with N50 of 39.17kb. I agree we have short ESTs. So this is the possible reason when filtering based on AED score 0.75 there are no gene models predicted despite the model_gff file has few genes with scores less than 0.75? Thanks and regards, Parul Kudtarkar > There are certain characteristics that are apparent in this contig. First > it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many > of them to align spuriously which produces very short gene models that are > more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add > more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models > almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial > bias to get back very short and incomplete models. > > How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as > well as get an estimate of fragmentation as one of the statistics produced > is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter > and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. > > If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), > and if they are distantly related to other annotated species few proteins > may align to the contigs because the introns in the alignments tend to be > so long and exons so short that it pushes down the significance scores too > much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. > > Thanks, > Carson > > > > On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: > >>Dear Carson and Daniel, >>Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >> 5 >>genes with AED score less than 0.75. However there were no genes >> predicted >>in the output file(see attached file Scaffold1_out). I have also attached >>the maker_opts.ctl. Could you please advice on this. >>Thanks and regards, >>Parul Kudtarkar >>> Use the AED_threshold option in the maker_opts.ctl file if you just want >>> to restrict final gene models to close matches directly within maker. >>>On >>> the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset >>>for >>> SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. >>> Thanks, >>> Carson >>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>Hi Parul, >>>>I think the way you described (with the maker_opts.ctl file) is how you >>>>want to proceed. You still need to give the genome too. >>>>Daniel >>>>Daniel Ence >>>>Graduate Student >>>>Eccles Institute of Human Genetics >>>>University of Utah >>>>15 North 2030 East, Room 2100 >>>>Salt Lake City, UT 84112-5330 >>>>________________________________________ >>>>From: maker-devel-bounces at yandell-lab.org >>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] >>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>To: Parul Kudtarkar >>>>Cc: maker-devel at yandell-lab.org >>>>Subject: Re: [maker-devel] AED score >>>>Also, are there any other parameters that are required when filtering based on AED score? >>>>> Hello Carson, >>>>> Just to confirm, Is there a script that would filter gene models at specific AED score. >>>>> Alternatively if I were to do this within maker with regards to >>>>>parameters >>>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>>> file to model_gff and set AED_threshold at desired threshold? Thanks and regards, >>>>> Parul Kudtarkar >>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>>>>> as >>>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>You >>>>>> can >>>>>> also try to increase protein homology evidence as some of your calls >>>>>>may >>>>>> be split genes due to lack of evidence linking them. >>>>>> --Carson >>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>Dear Maker community, >>>>>>>For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K >>>>>>>genes however I am getting 8 times the expected gene count >>>>>>> indicating >>>>>>> too >>>>>>>many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes >>>>>>>how >>>>>>>to go about this? >>>>>>>Thanks and regards, >>>>>>>Parul Kudtarkar >>>>>>>-- >>>>>>>Scientific Programmer >>>>>>>Center for Computational Regulatory Genomics >>>>>>>Beckman Institute, >>>>>>>California Institute of Technology >>>>>>>http://www.spbase.org >>>>>>>_______________________________________________ >>>>>>>maker-devel mailing list >>>>>>>maker-devel at box290.bluehost.com >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o rg >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org _______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 19:39:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 20:39:31 -0500 Subject: [maker-devel] AED score In-Reply-To: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Message-ID: Wow 330,000 is a lot. a large portion of genes are likely to be partial at best. You should seriously consider using mRNAseq to capture those by using maker's est_gff option to pass in results from cufflinks or trinity. Also I wouldn't even try to annotate contigs less than 10kb in size, just have maker skip them by setting the min_contig filter in the maker_opts.ctl file. Thanks, Carson On 12-11-29 7:31 PM, "Parul Kudtarkar" wrote: >Thanks for the guidance Carson, total contig size is 330,611 with N50 of >39.17kb. I agree we have short ESTs. So this is the possible reason when >filtering based on AED score 0.75 there are no gene models predicted >despite the model_gff file has few genes with scores less than 0.75? > >Thanks and regards, >Parul Kudtarkar > >> There are certain characteristics that are apparent in this contig. >First >> it seems to be repeat rich with a very low gene density. You also have >very short ESTs, and because of the lengths you are probably getting >many >> of them to align spuriously which produces very short gene models that >are >> more than likely false positives or at the very least just a piece of a >gene. I would turn off est2genome as a predictor for this reason unless >you can get longer EST assemblies (i.e. From mRNAseq). Your protein >alignments also seem to be few and far between. You probably need to >add >> more proteins from a couple of related species, and you might consider >using protein2genome rather than est2genome as a predictor if you are >still working to generate a training set. Also est2genome produced >models >> almost always have an AED score near 0 so mixing est2genome with the >AED_threshold with such limited protein support does create an >artificial >> bias to get back very short and incomplete models. >> >> How many contigs do you have in total and what is the N50 value for the >assembly? If you have a large number of very short contigs, you will get >very inflated gene counts because you get genes split across contigs and >many contigs tend t be subtle rearrangements of other contigs just >assembled in a slightly different way (so you can get bits and pieces of >the same genes just rearranged). This scenario is another confounding >factor if using the est2genome predictor with short ESTs. I would >recommend running CEGMA to get an estimate for the genome completeness >as >> well as get an estimate of fragmentation as one of the statistics >produced >> is a percent of genes that are found complete (end to end) vs those that >are partial. CEGMA identifies house keeping genes that tend to be >shorter >> and less intron rich than other genes in the genome, so if CEGMA gives a >high partial percentage and a low complete percentage, then this pattern >can be expected to be even more exaggerated for other genes in the >genome. >> >> If your genome is highly fragmented or proteins do not align well then >there are other strategies. For example, some vertebrate genomes end up >having extremely fragmented assemblies (on the order of 100,000 >contigs), >> and if they are distantly related to other annotated species few >proteins >> may align to the contigs because the introns in the alignments tend to >be >> so long and exons so short that it pushes down the significance scores >too >> much. In those cases heavy mRNAseq seems to be the best if not only way >to get enough evidence to stitch gene models together. >> >> Thanks, >> Carson >> >> >> >> On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson and Daniel, >>>Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >>> 5 >>>genes with AED score less than 0.75. However there were no genes >>> predicted >>>in the output file(see attached file Scaffold1_out). I have also >attached >>>the maker_opts.ctl. Could you please advice on this. >>>Thanks and regards, >>>Parul Kudtarkar >>>> Use the AED_threshold option in the maker_opts.ctl file if you just >>>>want >>>> to restrict final gene models to close matches directly within maker. >>>>On >>>> the other hand, if you are trying to build a dataset for training gene >predictors, use the maker2zff script for generating a filtered dataset >>>>for >>>> SNAP training. There are a number of filters available. Just call the >script once without parameters to see the options. >>>> Thanks, >>>> Carson >>>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>>Hi Parul, >>>>>I think the way you described (with the maker_opts.ctl file) is how >you >>>>>want to proceed. You still need to give the genome too. >>>>>Daniel >>>>>Daniel Ence >>>>>Graduate Student >>>>>Eccles Institute of Human Genetics >>>>>University of Utah >>>>>15 North 2030 East, Room 2100 >>>>>Salt Lake City, UT 84112-5330 >>>>>________________________________________ >>>>>From: maker-devel-bounces at yandell-lab.org >>>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >>>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>>To: Parul Kudtarkar >>>>>Cc: maker-devel at yandell-lab.org >>>>>Subject: Re: [maker-devel] AED score >>>>>Also, are there any other parameters that are required when filtering >based on AED score? >>>>>> Hello Carson, >>>>>> Just to confirm, Is there a script that would filter gene models at >specific AED score. >>>>>> Alternatively if I were to do this within maker with regards to >>>>>>parameters >>>>>> in maker_opts.ctl file I would have to provide my predicted genes >>>>>>gff3 >>>>>> file to model_gff and set AED_threshold at desired threshold? >Thanks and regards, >>>>>> Parul Kudtarkar >>>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >worst >>>>>>> as >>>>>>> it is a distance metric. You can use the AED_threshold parameter >to >>>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>>You >>>>>>> can >>>>>>> also try to increase protein homology evidence as some of your >calls >>>>>>>may >>>>>>> be split genes due to lack of evidence linking them. >>>>>>> --Carson >>>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>>Dear Maker community, >>>>>>>>For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect >20-30K >>>>>>>>genes however I am getting 8 times the expected gene count >>>>>>>> indicating >>>>>>>> too >>>>>>>>many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if >yes >>>>>>>>how >>>>>>>>to go about this? >>>>>>>>Thanks and regards, >>>>>>>>Parul Kudtarkar >>>>>>>>-- >>>>>>>>Scientific Programmer >>>>>>>>Center for Computational Regulatory Genomics >>>>>>>>Beckman Institute, >>>>>>>>California Institute of Technology >>>>>>>>http://www.spbase.org >>>>>>>>_______________________________________________ >>>>>>>>maker-devel mailing list >>>>>>>>maker-devel at box290.bluehost.com >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab >>>>>>>>.o >rg >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > > > From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 02:20:19 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 01:20:19 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. Message-ID: Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 03:01:46 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 02:01:46 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: References: Message-ID: Hi Carson, when I tried running genemark as below, I see the *.lst files (protein & nuc fasta) produced. But no gtf2 at all... And no gms.log files at all. Any ideas? /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p 0 -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -a Enmo_susu.11.fsa Thanks, Gowthaman ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org] Sent: Sunday, November 04, 2012 1:20 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Chunk failed at level 6 error.. Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 07:18:24 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:18:24 -0500 Subject: [maker-devel] Conensus gene model In-Reply-To: <1640.131.215.15.234.1351728273.squirrel@webmail.caltech.edu> Message-ID: The way models are generated, it really doesn't so much matter where the protein alignments came from. Basically the protein alignment is just creating a region of potential CDS. MAKER than gives that region as a hint to the gene predictors, but the gene predictors really make the call on how to finally structure the gene based on their training sets. You can short circuit this by using the protein2genome option as a separate run with only your primary proteins. MAKER will then try and turn those protein alignments directly into genes. Results from that run can sometimes be useful for generating training sets as well, or can be passed back into MAKER as pred_gff so MAKEr has the option to turn those into models as an alternative to the models produced by the ab initio predictors. --Carson On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: >Hi Jason, thanks for directions on generating training-set for augustus. >Also as alignment evidence if we are providing protein sequences from the >primary organism as well as other closely related species is there an >option to give the primary protein file precedence over others? >At the moment I have all the proteins(from primary organism as well as >related species) into a single file as protein option in maker_opts.ctl > >Thanks and regards, >Parul Kudtarkar > >> Paul - >> >> I think I've posted on this before here if you are asking how to go from >> SNAP training to Augustus training. >> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >> >> I do this type of training a lot - here some pointers. >> >> I often train by generating models using cegma on the genome and get >>these >> 400 or so good models as my training set. when I have EST or RNA-Seq I >> use PASA to generate the best set of annotations. >> >> For CEGMA - then I run this script that comes with MAKER: >> cegma2zff output.cegma.gff genome.fa >> >> Then I follow the SNAP directions >> >> fathom genome.ann genome.dna -categorize 1000 >> fathom uni.ann uni.dna -export 1000 -plus >> mkdir MYGENOME >> cd MYGENOME >> forge ../export.ann ../export.dna --OPTIONS >> cd ../MYGENOME >> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >> >> I then also make the augustus training data like this running in the >> directory that has the export.ann and export.dna files: >> perl gene_prediction/zff2augustus_gbk.pl > train.gb >> >> using this script: >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>ff2augustus_gbk.pl >> >> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>and >> best models from PASA and incorporate all these data in to my SNAP >> training set, and then export again back to gbk for the augustus >>training. >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>asatraining2zff.pl >> >> Then you just need to run the Augustus training (autoAugTrain.pl) on the >> train.gb file. >> >> Jason >> >> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar wrote: >> >>> Hello Carson and maker community, >>> >>> Thank you very much for your guidelines on using the maker-pipeline. >>> Yes, >>> green sea urchin genome that we are trying to annotate. >>> We are running the on scaffolds and most of these scaffolds are small >>>in >>> size(very first genome assembly). We would typically expect 20,000 >>>genes >>> in this genome. So we are running maker using EST and proteins from the >>> genome and out-groups to generate training dataset for SNAP and >>> Augustus. >>> Depending on the resulting predictions we may bootstrap the predicted >>> genes once again using EST and proteins. >>> >>> Do you have any further suggestions? Also could you point how to >>>convert >>> training set generated for SNAP to be used as training set for Augustus >>> as >>> well? Would maker give equal weightage to SNAP and Augustus predictions >>> for generating gene model? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> One thing you seem to be missing is protein evidence. >>>> >>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>> recommend adding all proteins from the Strongylocentrotus purpuratus >>> genome, then throw in another Deuterstome of your choice. Perhaps you >>> should also add a couple of outgroup organisms like Nematostella >>> vectensis >>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>> adding >>> to many protostome outgroups (i.e. C. elegans and Drosophila) because a >>> big part of their evolution is gene loss (so distant cnidaria often >>> match >>>> deuterstomes better than most protostomes do). >>>> >>>> You could take the maker results when protein data is included and use >>> it >>>> to retrain SNAP again. >>>> >>>> Even a 22 kb contig is still really short. Is this genome primarily >>> constituted by short contigs like this? I would recommend running >>>CEGMA >>> once on this genome to get an appropriate estimate of how recoverable >>> the >>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>> Cegma >>>> will give you an estimate for genome completeness as well as estimates >>> of >>>> what percentage of genes will be found in their entirety and what >>> percent >>>> will be partial genes. This is important to do if your genome is >>> fragmented as it will give you a reasonable expectation of what you can >>> expected to recover (as short contigs don't annotate very well - you >>> tend >>>> to loose a lot). >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>> >>>>> Hi Carson, >>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>as >>>>> 3 >>> exons EST alignments. Could you please recommend additional training. >>>We >>> are currently running maker on the entire contig set and eventually >>> merge >>>>> all the gff3 contig predictions. The using suggested >>>>>parameter/methods >>> we >>>>> would like to get a consensus gene-set with minimal false >>>>> positives/negatives. >>>>> Thanks, >>>>> Parul >>>>>> The contig in question is really too small to get much out of it >>>>>> (only 5 >>>>> kb). There was only one single exon EST alignments and a couple of >>> predictions with no evidence support. Anything smaller than 10 kb is >>> mostly useless for annotation purposes. You would really need a few >>> 100kb >>>>>> length or longer contigs to glean enough information for optimizing >>>>>> your >>>>> parameters. >>>>>> The general suggestions for any maker run are to use proteins from a >>>>> closely related organism or a couple of closely related organisms for >>>>> the >>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>> for >>>>> certain eukaryotes that have a bias for single exon transcripts (i.e. >>>>> some >>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>> initio >>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>> positives). >>>>>> Additional training would really depend on what your other contigs >>> look >>>>> like. Do you have any large contigs? I could look at one of those >>>>> and >>> give suggestions but the provided contig is just too short to glean >>> much. >>>>>> Thanks, >>>>>> Carson >>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>> Hello, >>>>>>> Please advice on the aforementioned query? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> ---------------------------- Original Message >>>>>>> ---------------------------- >>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>> From: "Parul Kudtarkar" >>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>> To: maker-devel at yandell-lab.org >>>>>>> >>>>>>>-------------------------------------------------------------------- >>>>>>>---- >>> -- >>>>> Hi, >>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>est,protein >>>>>>> and >>>>> contig file), agustus,genemarkE(we ran it outside maker and have gff3 >>>>>>> file >>>>>>> as input). The output that we get is combination of various >>>>>>> gene-predictors and evidences. I have attached sample result file. >>> What >>>>> would you recommend to get consensus result set? Bootstrapping the >>> resulting gff3 file (rerunning maker)? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 07:36:08 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:36:08 -0500 Subject: [maker-devel] Strange error at blastn step In-Reply-To: Message-ID: Sorry for the slow reply. I've been way for most of the last week. Could you do two more things before running another test. Update again to the latest development version, also set TMP to a non-NFS location like /tmp. Thanks, Carson From: Daniel Standage Date: Monday, 29 October, 2012 8:43 AM To: Carson Holt Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Strange error at blastn step I just ran svn update and tried again with the development version of Maker. Same long list of errors as in the last message. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Oct 29, 2012 at 9:39 AM, Daniel Standage wrote: > Carson, > > I was able to run the first svn update before the test job ran, but I didn't > get the message about this second update until after it has already executed > and failed. I got about 372 lines of such. > >> STATUS: Parsing control files... >> STATUS: Processing and indexing input FASTA files... >> STATUS: Setting up database for any GFF3 input... >> A data structure will be created for you at: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_datastore >> >> To access files for individual sequences use the datastore index: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_master_datastore_index.log >> >> STATUS: Now running MAKER... >> WARNING: Cannot find >scaffold_0, trying to re-index the fasta. >> stop here: scaffold_0 >> ERROR: Fasta index error >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 239. >> Process::MpiChunk::_prepare('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 73 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c808b0)', 'HASH(0x3c8ec40)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 79 >> Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x3c71f30)') >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 56 >> Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x3c80640)', 0, >> 'Process::MpiChunk') called at >> /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 627 >> --> rank=NA, hostname=c4 >> ERROR: Failed in tier preparation >> WARNING: You must always set a rank before running MpiTiers >> FATAL: argument `seq_id` does not exist in MpiTier object >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 86. >> >> Process::MpiChunk::_initialize_vars('Process::MpiChunk=HASH(0x3cc93d0)', >> 'HASH(0x3cc9400)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 47 >> Process::MpiChunk::new('Process::MpiChunk', 'HASH(0x3c80820)', 0, 0) >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 407 >> Process::MpiChunk::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f498)', 'HASH(0x3cc8f20)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 3811 >> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x3c8b300)', 'load', >> 'HASH(0x3c80820)', 0, 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 310 >> Process::MpiChunk::_loader('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0, 0, 'Process::MpiTiers=HASH(0x3c71f30)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 364 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f9c0)', 'HASH(0x3c8fb28)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 375 > > I'll try the next update and run the test again. I see a lot of references in > there to MPI, and just thought I would make it clear that although I am > running in a cluster environment, I am using the default serial version of > Maker, not the parallel MPI version. > > Also, after this failed, I tried changing the TMP directory so that it was > located on the same NFS mount as the scratch disk to which the output was > written. This did not seem to have any affect, and I saw the same issues with > the EST sequences unable to be found. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Fri, Oct 26, 2012 at 6:59 PM, Carson Holt wrote: >> >> >> From: Carson Holt >> Date: Friday, 26 October, 2012 6:10 PM >> To: Daniel Standage >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> I've been going over the indexing code using different scenarios and I may >> have isolated a candidate for what is causing this. Could you do one more >> 'svn update' inside the maker devel directory before running a test job? >> >> Thanks, >> Carson >> >> From: Daniel Standage >> Date: Friday, 26 October, 2012 2:29 PM >> To: Carson Holt >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> Got this from the compute node. Looks like native disk space to me. >> >> [dstandag at mason ~] df /tmp >> Filesystem 1K-blocks Used Available Use% Mounted on >> /dev/sda1 478573472 12319684 441943620 3% /tmp >> >> Installing a bundle of Perl prereqs for development version, will try that >> soon. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Fri, Oct 26, 2012 at 2:24 PM, Carson Holt wrote: >>> Ok. Try the developer release and see if it still happens. >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>> Date: Friday, 26 October, 2012 2:19 PM >>> >>> To: Carson Holt >>> Cc: "maker-devel at yandell-lab.org" >>> >>> Subject: Re: [maker-devel] Strange error at blastn step >>> >>> Unfortunately, the job is no longer running and as a result I cannot connect >>> to the compute nodes as I could while it was running. On the interactive >>> node, it looks like it's real disk, although it looks like there are some >>> tmpfs mounts. >>> >>> [dstandag at mason src] df /tmp >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> [dstandag at mason src] df >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> login_x86_64 16497564 3077352 13420212 19% / >>> tmpfs 16497564 0 16497564 0% /dev/shm >>> tmpfs 10240 0 10240 0% /var/tmp >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> AFS 9000000 0 9000000 0% /afs >>> bl-nas1:/vol/hd00 3435973856 1775658144 1660315712 52% /N/hd00 >>> bl-nas1:/vol/hd01 3435973856 1684116928 1751856928 50% /N/hd01 >>> bl-nas2:/vol/hd02 3435973856 1856598656 1579375200 55% /N/hd02 >>> bl-nas2:/vol/hd03 3435973856 2747626240 688347616 80% /N/hd03 >>> bl-nas1:/vol/hdln 81920 3424 78496 5% /N/u >>> bl-nas2:/vol/soft 1258291200 837003424 421287776 67% /N/soft >>> bl-nas1:/vol/logs 419430400 67163328 352267072 17% /N/logs >>> ... >>> ... >>> >>> I'll see if I can launch another short job and verify this on the compute >>> nodes. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Fri, Oct 26, 2012 at 2:14 PM, Carson Holt wrote: >>>> The command 'df /tmp' will tell you whether /tmp is a tmpfs mount >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Friday, 26 October, 2012 2:12 PM >>>> To: Carson Holt >>>> Cc: "maker-devel at yandell-lab.org" >>>> >>>> Subject: Re: [maker-devel] Strange error at blastn step >>>> >>>> It looks like /tmp is indeed being used: the files I played with were under >>>> /tmp/maker_1YQF9o. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Fri, Oct 26, 2012 at 2:09 PM, Carson Holt wrote: >>>>> Check to see where /tmp is located? Some clusters have it set up as a >>>>> tmpfs directory and I have had problems with fasta indexes running from >>>>> tmpfs mounts in the past. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Friday, 26 October, 2012 2:05 PM >>>>> To: Carson Holt >>>>> >>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>> >>>>> The maker working directory is in a cluster environment with shared >>>>> scratch space (I'm guessing NFS-mounted). I didn't change the temp >>>>> directory setting, so it should be the local default (/tmp). >>>>> >>>>> I'll give the dev version a shot. Thanks. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Fri, Oct 26, 2012 at 1:57 PM, Carson Holt wrote: >>>>>> Could you try this development version and tell me if the error still >>>>>> happens? >>>>>> >>>>>> Use this command to download --> >>>>>> <> >>>>>> >>>>>> Username: <> >>>>>> Password: <> >>>>>> >>>>>> Are you running in an NFS mounted directory or are you resetting TMP to a >>>>>> different location? >>>>>> >>>>>> Thanks, >>>>>> Carson >>>>>> >>>>>> >>>>>> From: Daniel Standage >>>>>> Date: Friday, 26 October, 2012 1:52 PM >>>>>> To: Maker Mailing List >>>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>>> >>>>>> I have since installed Maker on a different machine and tried it out. The >>>>>> test run completed successfully, but as I commenced with the full genome >>>>>> annotation, I have noticed the following error popping up frequently. >>>>>> >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.8.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-10 hits >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.9.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-6 hits >>>>>>> WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta. >>>>>>> stop here:comp59088_c1_seq7 >>>>>>> ERROR: Fasta index error >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while polishig ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 14 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_0 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> --Next Contig-- >>>>>>> >>>>>>> #--------------------------------------------------------------------- >>>>>>> Now starting the contig!! >>>>>>> SeqID: scaffold_1 >>>>>>> Length: 5805686 >>>>>>> #--------------------------------------------------------------------- >>>>>> >>>>>> My first thought based on the message is that blastdbcmd could not find >>>>>> the sequence in the database. I verified this was the case--I could not >>>>>> extract sequence comp59088_c1_seq7 from the database Maker had created >>>>>> under /tmp. However, after removing the index files and re-running >>>>>> makeblastdb with the -parse_seqids option set, blastdbcmd successfully >>>>>> extracted the sequence. >>>>>> >>>>>> I was initially happy with this finding, but upon closer inspection it >>>>>> looks like Maker does not use blastdbcmd to extract sequences, but rather >>>>>> its own internal code. Therefore I'm still not sure where the problem is >>>>>> and how I might fix it. Any insights? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> -- >>>>>> Daniel S. Standage >>>>>> Ph.D. Candidate >>>>>> Bioinformatics and Computational Biology Program >>>>>> Department of Genetics, Development, and Cell Biology >>>>>> Iowa State University >>>>>> >>>>>> >>>>>> >>>>>> On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage >>>>>> wrote: >>>>>>> Greetings! >>>>>>> >>>>>>> I am doing a test run of my Maker setup on a new machine, annotating a >>>>>>> pretty short contig (about 3kb). However, there seems to be a hiccup >>>>>>> during the blastn stage. This is the terminal message. >>>>>>> >>>>>>> #--------- command -------------# >>>>>>> Widget::blastn: >>>>>>> /share/home/01854/standage/local/bin/blastn -db >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Ef >>>>>>> asta.mpi.10.7 -query >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0 >>>>>>> -num_alignments 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend >>>>>>> 3 -word_size 15 -reward 1 -penalty -3 -gapopen 3 -dbsize 1000 -searchsp >>>>>>> 500000000 -num_threads 16 -lcase_masking -dust yes -soft_masking true >>>>>>> -show_gis -out >>>>>>> /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker >>>>>>> .output/maker.bogus_datastore/scaffold_866/theVoid.scaffold_866/scaffold >>>>>>> _866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrini >>>>>>> ty%2ETrimmomatic%2Efasta.mpi.10.7.blastn >>>>>>> #-------------------------------# >>>>>>> deleted:0 hits >>>>>>> ERROR: Could not obtain lock to format database >>>>>>> >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while doing blastn of ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 8 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_866 >>>>>>> >>>>>>> Several blastn steps appeared to have completed successfully to this one >>>>>>> failing. Any ideas what could be causing this? >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> -- >>>>>>> Daniel S. Standage >>>>>>> Ph.D. Candidate >>>>>>> Bioinformatics and Computational Biology Program >>>>>>> Department of Genetics, Development, and Cell Biology >>>>>>> Iowa State University >>>>>>> >>>>>> >>>>>> _______________________________________________ maker-devel mailing list >>>>>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinf >>>>>> o/maker-devel_yandell-lab.org >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 5 07:41:57 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:41:57 -0500 Subject: [maker-devel] gff3_preds2models script In-Reply-To: <3207.131.215.15.234.1350942378.squirrel@webmail.caltech.edu> Message-ID: The gff3_preds2models doesn't support the shared ID method for model assembly. You will need to create a parent match feature and child match_part features (each with a unique ID and Parent= attribute). You can find examples in the GFF3 specification here --> http://www.sequenceontology.org/gff3.shtml Thanks, Carson On 12-10-22 5:46 PM, "Parul Kudtarkar" wrote: >Hello, > >I want to add gene structure(gene/mRNA/exon) to gff3 file. I am using >gff3_preds2models for this purpose. However I get following error >**WARNING: No top level feature found for ID WHL22.100252 >I have attached the sample input gff3 file and the list of ids > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 08:08:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 10:08:36 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt , Maker Mailing List Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 08:14:18 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:14:18 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List < > maker-devel at yandell-lab.org> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PdomMaker9.e44232.bz2 Type: application/x-bzip2 Size: 5881 bytes Desc: not available URL: From parulk at caltech.edu Mon Nov 5 14:40:46 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 5 Nov 2012 13:40:46 -0800 (PST) Subject: [maker-devel] Conensus gene model In-Reply-To: References: Message-ID: <4116.131.215.15.234.1352151646.squirrel@webmail.caltech.edu> Dear Carson, Thanks you very much, this is helpful. > The way models are generated, it really doesn't so much matter where the > protein alignments came from. Basically the protein alignment is just > creating a region of potential CDS. MAKER than gives that region as a > hint to the gene predictors, but the gene predictors really make the call > on how to finally structure the gene based on their training sets. You > can short circuit this by using the protein2genome option as a separate > run with only your primary proteins. MAKER will then try and turn those > protein alignments directly into genes. Results from that run can > sometimes be useful for generating training sets as well, or can be passed > back into MAKER as pred_gff so MAKEr has the option to turn those into > models as an alternative to the models produced by the ab initio > predictors. > > --Carson > > > On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: > >>Hi Jason, thanks for directions on generating training-set for augustus. >>Also as alignment evidence if we are providing protein sequences from the >>primary organism as well as other closely related species is there an >>option to give the primary protein file precedence over others? >>At the moment I have all the proteins(from primary organism as well as >>related species) into a single file as protein option in maker_opts.ctl >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Paul - >>> >>> I think I've posted on this before here if you are asking how to go >>> from >>> SNAP training to Augustus training. >>> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >>> >>> I do this type of training a lot - here some pointers. >>> >>> I often train by generating models using cegma on the genome and get >>>these >>> 400 or so good models as my training set. when I have EST or RNA-Seq I >>> use PASA to generate the best set of annotations. >>> >>> For CEGMA - then I run this script that comes with MAKER: >>> cegma2zff output.cegma.gff genome.fa >>> >>> Then I follow the SNAP directions >>> >>> fathom genome.ann genome.dna -categorize 1000 >>> fathom uni.ann uni.dna -export 1000 -plus >>> mkdir MYGENOME >>> cd MYGENOME >>> forge ../export.ann ../export.dna --OPTIONS >>> cd ../MYGENOME >>> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >>> >>> I then also make the augustus training data like this running in the >>> directory that has the export.ann and export.dna files: >>> perl gene_prediction/zff2augustus_gbk.pl > train.gb >>> >>> using this script: >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>>ff2augustus_gbk.pl >>> >>> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>>and >>> best models from PASA and incorporate all these data in to my SNAP >>> training set, and then export again back to gbk for the augustus >>>training. >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>>asatraining2zff.pl >>> >>> Then you just need to run the Augustus training (autoAugTrain.pl) on >>> the >>> train.gb file. >>> >>> Jason >>> >>> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar >>> wrote: >>> >>>> Hello Carson and maker community, >>>> >>>> Thank you very much for your guidelines on using the maker-pipeline. >>>> Yes, >>>> green sea urchin genome that we are trying to annotate. >>>> We are running the on scaffolds and most of these scaffolds are small >>>>in >>>> size(very first genome assembly). We would typically expect 20,000 >>>>genes >>>> in this genome. So we are running maker using EST and proteins from >>>> the >>>> genome and out-groups to generate training dataset for SNAP and >>>> Augustus. >>>> Depending on the resulting predictions we may bootstrap the predicted >>>> genes once again using EST and proteins. >>>> >>>> Do you have any further suggestions? Also could you point how to >>>>convert >>>> training set generated for SNAP to be used as training set for >>>> Augustus >>>> as >>>> well? Would maker give equal weightage to SNAP and Augustus >>>> predictions >>>> for generating gene model? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> One thing you seem to be missing is protein evidence. >>>>> >>>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>>> recommend adding all proteins from the Strongylocentrotus purpuratus >>>> genome, then throw in another Deuterstome of your choice. Perhaps you >>>> should also add a couple of outgroup organisms like Nematostella >>>> vectensis >>>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>>> adding >>>> to many protostome outgroups (i.e. C. elegans and Drosophila) because >>>> a >>>> big part of their evolution is gene loss (so distant cnidaria often >>>> match >>>>> deuterstomes better than most protostomes do). >>>>> >>>>> You could take the maker results when protein data is included and >>>>> use >>>> it >>>>> to retrain SNAP again. >>>>> >>>>> Even a 22 kb contig is still really short. Is this genome primarily >>>> constituted by short contigs like this? I would recommend running >>>>CEGMA >>>> once on this genome to get an appropriate estimate of how recoverable >>>> the >>>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>>> Cegma >>>>> will give you an estimate for genome completeness as well as >>>>> estimates >>>> of >>>>> what percentage of genes will be found in their entirety and what >>>> percent >>>>> will be partial genes. This is important to do if your genome is >>>> fragmented as it will give you a reasonable expectation of what you >>>> can >>>> expected to recover (as short contigs don't annotate very well - you >>>> tend >>>>> to loose a lot). >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>> Hi Carson, >>>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>>as >>>>>> 3 >>>> exons EST alignments. Could you please recommend additional training. >>>>We >>>> are currently running maker on the entire contig set and eventually >>>> merge >>>>>> all the gff3 contig predictions. The using suggested >>>>>>parameter/methods >>>> we >>>>>> would like to get a consensus gene-set with minimal false >>>>>> positives/negatives. >>>>>> Thanks, >>>>>> Parul >>>>>>> The contig in question is really too small to get much out of it >>>>>>> (only 5 >>>>>> kb). There was only one single exon EST alignments and a couple of >>>> predictions with no evidence support. Anything smaller than 10 kb is >>>> mostly useless for annotation purposes. You would really need a few >>>> 100kb >>>>>>> length or longer contigs to glean enough information for optimizing >>>>>>> your >>>>>> parameters. >>>>>>> The general suggestions for any maker run are to use proteins from >>>>>>> a >>>>>> closely related organism or a couple of closely related organisms >>>>>> for >>>>>> the >>>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>>> for >>>>>> certain eukaryotes that have a bias for single exon transcripts >>>>>> (i.e. >>>>>> some >>>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>>> initio >>>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>>> positives). >>>>>>> Additional training would really depend on what your other contigs >>>> look >>>>>> like. Do you have any large contigs? I could look at one of those >>>>>> and >>>> give suggestions but the provided contig is just too short to glean >>>> much. >>>>>>> Thanks, >>>>>>> Carson >>>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>>> Hello, >>>>>>>> Please advice on the aforementioned query? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>>> From: "Parul Kudtarkar" >>>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>>> To: maker-devel at yandell-lab.org >>>>>>>> >>>>>>>>-------------------------------------------------------------------- >>>>>>>>---- >>>> -- >>>>>> Hi, >>>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>>est,protein >>>>>>>> and >>>>>> contig file), agustus,genemarkE(we ran it outside maker and have >>>>>> gff3 >>>>>>>> file >>>>>>>> as input). The output that we get is combination of various >>>>>>>> gene-predictors and evidences. I have attached sample result file. >>>> What >>>>>> would you recommend to get consensus result set? Bootstrapping the >>>> resulting gff3 file (rerunning maker)? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Wed Nov 7 07:00:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 09:00:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line for a > few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on > native disk space, and relaunched. I have attached the output of the job that > failed in <5 minutes. It looks pretty similar to the errors I got the last > time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 08:05:45 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:05:45 -0500 Subject: [maker-devel] Maker issues Message-ID: Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker.log Type: application/octet-stream Size: 48916 bytes Desc: not available URL: From daniel.standage at gmail.com Wed Nov 7 07:30:11 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 09:30:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > >> Thanks. Could you also run with the --debug flag set on the command line >> for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt , Maker Mailing List < >> maker-devel at yandell-lab.org> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory >> is on native disk space, and relaunched. I have attached the output of the >> job that failed in <5 minutes. It looks pretty similar to the errors I got >> the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 08:29:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 10:29:34 -0500 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: Message-ID: Sorry for the slow reply. I'm not on a long drive, but I am away this week. Could you send me the genemark hmm file and one of the contigs that fails. Thanks, Carson On 12-11-04 3:20 AM, "Gowthaman Ramasamy" wrote: >Hi Carson, >As it happens, I am sorry to bother you again on a weekend. Here is my >hoping that you are not on a long drive this time. > >I am running genemark prokaryote via maker on a genome with 36 >chromosomes. All but two finishes well. > >On those two, i am not able to find anything unusual. Following is the >error message i see. Could you please point to me what could be the >possible source of these errors. Thanks verymuch in advance... > >Widget::genemark: >/depot/perl-5.12.1/bin/perl >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gm >hmm_wrap -m >./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokar >yotic%2Emod_hmm%2Emod.genemark >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/query.fasta >#-------------------------------# >substr outside of string at >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMac >hine.pm line 223. > >FATAL ERROR >ERROR: Failed while preparing masked sequence and ab-inits!! > >ERROR: Chunk failed at level 6 >!! >FAILED CONTIG:Enmo_susu.05 > > >Thanks once again, >Gowthaman From daniel.standage at gmail.com Wed Nov 7 09:43:17 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 11:43:17 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed *loalize* to *localize* and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >> fasta indexer is broken. I have an open bug I am trying to resolve with >> the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >> >>> Thanks. Could you also run with the --debug flag set on the command line >>> for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List < >>> maker-devel at yandell-lab.org> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory >>> is on native disk space, and relaunched. I have attached the output of the >>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>> the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 09:46:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 11:46:31 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Looked good for a while, but came across this error. > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > > > > --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is > repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live >> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >> indexer is broken. I have an open bug I am trying to resolve with the >> Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> Thanks. Could you also run with the --debug flag set on the command line for >>> a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List >>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory is >>> on native disk space, and relaunched. I have attached the output of the job >>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>> last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Thu Nov 8 07:32:59 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 09:32:59 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > > It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to > *localize* and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >> and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>> fasta indexer is broken. I have an open bug I am trying to resolve with >>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List < >>>> maker-devel at yandell-lab.org> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>> errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Thu Nov 8 07:47:20 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Thu, 8 Nov 2012 14:47:20 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Hi Daniel, is it possible you have some proteins in your EST files? '------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw' Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [daniel.standage at gmail.com] Sent: Thursday, November 08, 2012 7:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From daniel.standage at gmail.com Thu Nov 8 08:48:52 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 10:48:52 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> References: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Message-ID: Based on Mark's suggestion, I took a look at the EST files. Luckily there is no protein sequence contamination. [dstandag at mason Transcriptome] grep -v '^>' Pdom.Trinity.Trimmomatic.fasta | grep -o . | sort | uniq -c 79400764 A 39834991 C 40702954 G 77980105 T [dstandag at mason Transcriptome] grep -v '^>' Pmet.Trinity.R.fasta | grep -o . | sort | uniq -c 18294708 A 9108213 C 9449127 G 17756470 T -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Thu, Nov 8, 2012 at 9:47 AM, Mark Yandell wrote: > Hi Daniel, > > is it possible you have some proteins in your EST files? > > '------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw' > > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [ > daniel.standage at gmail.com] > Sent: Thursday, November 08, 2012 7:32 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 08:02:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:02:21 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.make r.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold _7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffo ld_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58 983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 > --maxintron 10000 --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq37.for.716125-723330.0.fasta at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. ...as well as one occurrence of this error. > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869 > 077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sca > ffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar > --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7 > /theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm > :86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is >> repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl live >>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >>> indexer is broken. I have an open bug I am trying to resolve with the >>> Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> Thanks. Could you also run with the --debug flag set on the command line >>>> for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List >>>> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP directory is >>>> on native disk space, and relaunched. I have attached the output of the job >>>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>>> last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 08:13:38 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:13:38 -0500 Subject: [maker-devel] Query on genemark results In-Reply-To: Message-ID: The previous bug was a complete lack of GeneMark results in the GFF3, not just a lack of consensus models from GeneMark. It is possible to get no consensus models from GeneMark if they score poorly. Send me the GFF3 results of your larger contigs and I can review it and tell you if any models are being improperly categorized. Thanks, Carson On 12-10-28 1:50 PM, "kokwei" wrote: >Hi, > >I have the same problems as posted by Andr? Gomes on 10/4/10. I still >have the same problems even though using the current available version >of maker (maker 2.1 and maker 2.26 beta version). > >I have tried to do the gene prediction on eukaryotic genome using 3 >ab-initio gene predictors (SNAP, Augustus and GeneMark-ES) using Maker. >From the fasta_merge output, I have 3 separate files of gene models >($prefix.all.maker.augustus_masked.proteins.fasta, >$prefix.all.maker.snap_masked.proteins.fasta and >$prefix.all.maker.genemark.proteins.fasta) and one >$prefix.all.maker.proteins.fasta (I presume this should be the consensus >gene models from 3 predictors' results, right?). > > From the consensus gene models file, I don't see even one result from >genemark but all from snap/augustus only. Is that normal? >Also from the file naming and gene model label in final gff file, it's >showing that genemark is not masked like those of augustus and snap? Is >that true? Why only augustus and snap masked but not genemark? Please >assist and thanks for your helps. > >Kok Wei > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From mikael.durling at slu.se Tue Nov 13 06:57:36 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 13 Nov 2012 13:57:36 +0000 Subject: [maker-devel] NULs in master_datastore_index.log Message-ID: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Hello, In order to work around locking problems with SQLite, I tried running (latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason it seems maker does not detect the automounted volumes as being nfs mounted?). Running over NFSv4 makes SQLite happy, but then another problem popped up. It seems ds_utility.pm happens to write simultaneously to the datastore_index from several MPI ranks, which in my case results in stretches of NULs in the datastore file. This seems to result in maker trying to analyse the same contig simultaneously on two different MPI ranks. (I get rank failure notices on the output twice for the same rank, and maker complaining that the same GFF3 ID appears more than once). Any hints on how this can be handled? It appears as I should have installed and run maker on some other cluster without NFS mounted volumes to save myself a lot of hassles. Thanks in advance, Mikael From carsonhh at gmail.com Tue Nov 13 07:12:58 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 13 Nov 2012 09:12:58 -0500 Subject: [maker-devel] NULs in master_datastore_index.log In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Message-ID: Locks for not running contigs are a separate thing from the datastore index. They are handled by file locks in the directory for each contig. For the datastore index, it can be subject to race conditions if two processes happen to write an output string at the exact same time, but can be rebuilt in less than 2 min at the end of your job using the -dsindex flag. The failure notices you are getting might be because of the configuration of the NFS mount. MAKER will check the locks it creates several times while running a given contig to see if the lock was broken, and if it was then that contig will fail producing an error. This will happen before it does any activity that might conflict with the other active run of that contig by another process, so the process that broke the lock should continue without issue somewhere else, but you will get a trail of messages in the error log and maybe some ugliness in the datastore index. You can try altering the flags set for the NFS mount, or just set the retry count really high. You will have to run maker -dsindex once your MPI job finishes to get the datastore index log back in order on completion, but that only takes a couple of minutes to rebuild. --Carson On 12-11-13 8:57 AM, "Mikael Brandstr?m Durling" wrote: >Hello, > >In order to work around locking problems with SQLite, I tried running >(latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason >it seems maker does not detect the automounted volumes as being nfs >mounted?). Running over NFSv4 makes SQLite happy, but then another >problem popped up. It seems ds_utility.pm happens to write simultaneously >to the datastore_index from several MPI ranks, which in my case results >in stretches of NULs in the datastore file. This seems to result in maker >trying to analyse the same contig simultaneously on two different MPI >ranks. (I get rank failure notices on the output twice for the same rank, >and maker complaining that the same GFF3 ID appears more than once). > >Any hints on how this can be handled? > >It appears as I should have installed and run maker on some other cluster >without NFS mounted volumes to save myself a lot of hassles. > >Thanks in advance, >Mikael > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From es9 at sanger.ac.uk Thu Nov 15 03:20:56 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 10:20:56 +0000 Subject: [maker-devel] Augustus training within Maker Message-ID: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Hi, Could you please confirm something for me: If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. To achieve this, do I need to change anything in maker_opts.ctl or do I leave augustus_species= #Augustus gene prediction species model as is, or should it be edited for the 2nd run? Many thanks Eleanor -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From dsth at ebi.ac.uk Thu Nov 15 04:14:31 2012 From: dsth at ebi.ac.uk (Daniel Hughes) Date: Thu, 15 Nov 2012 11:14:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: heya, Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus > species config folder of gene parameters, then Augustus runs using this > data alone. > I understand that with a second Maker run Augustus retrains using the > BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I > leave > augustus_species= #Augustus gene prediction species model > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. dan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Thu Nov 15 04:34:09 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 11:34:09 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this Ele On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > heya, > > Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. > I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I leave > augustus_species= #Augustus gene prediction species model > > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. > > dan. > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 16 07:19:47 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 16 Nov 2012 09:19:47 -0500 Subject: [maker-devel] segmentation fault (core dumped) for maker running In-Reply-To: Message-ID: The correct file to update in Bioperl is /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm not Bioperl.pm, but technically you only have to fix whichever .pm file loads last. So if it's working then don't worry about it because one of the files fixed by the first command are loading after /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm. Thanks, Carson From: Hung Chih-Ming Date: Thursday, 15 November, 2012 2:02 AM To: Carson Holt Cc: Subject: segmentation fault (core dumped) for maker running Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ymwur1 at gmail.com Thu Nov 15 00:02:55 2012 From: ymwur1 at gmail.com (Hung Chih-Ming) Date: Thu, 15 Nov 2012 15:02:55 +0800 Subject: [maker-devel] segmentation fault (core dumped) for maker running Message-ID: Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Fri Nov 16 17:37:53 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri, 16 Nov 2012 17:37:53 -0700 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Message-ID: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Dan is correct about the workings of the hint based communication between MAKER and the gene predictors - and just to clarify further. MAKER never 're-trains' Augustus or any of the other gene predictors. Many people will retrain the gene predictors between iterative MAKER runs, but this is a manual (and for Augustus non-trivial) step. B On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this > > Ele > > > On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > >> heya, >> >> Could you please confirm something for me: >> >> If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. >> I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. >> >> To achieve this, do I need to change anything in maker_opts.ctl or do I leave >> augustus_species= #Augustus gene prediction species model >> >> >> AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. >> >> dan. >> >> >> > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Sat Nov 17 03:42:31 2012 From: es9 at sanger.ac.uk (es9) Date: Sat, 17 Nov 2012 10:42:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Message-ID: Thank you to you both for clarifying this ... I was get a smidge confused and reading previous posts I can see the answer had already been asked and replied to. Next time I will cruise the archives before posting! Regards, Eleanor > Dan is correct about the workings of the hint based communication > between MAKER and the gene predictors - and just to clarify further. > MAKER never 're-trains' Augustus or any of the other gene predictors. > Many people will retrain the gene predictors between iterative MAKER > runs, but this is a manual (and for Augustus non-trivial) step. > > B > > On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > >> Aha - that makes sense, so with every run Augustus is run with the >> BLAST hints available, thanks for clarifying this >> >> Ele >> >> On 15 Nov 2012, at 11:14, Daniel Hughes wrote: >> >>> heya, >>> >>>> Could you please confirm something for me: >>>> >>>> If with the first Maker run you provide the location of the >>>> Augustus species config folder of gene parameters, then Augustus >>>> runs using this data alone. >>>> I understand that with a second Maker run Augustus retrains >>>> using the BLAST evidence from the 1st run. >>>> >>>> To achieve this, do I need to change anything in maker_opts.ctl >>>> or do I leave >>>> augustus_species= #Augustus gene prediction species model >>> >>> AFAIK maker runs augustus, blast etc., as sort of raw compute >>> stages in the earlier tier_types, the results of these stages e.g. >>> protein alignments etc., are then 'synthesised' into 'hints' >>> (early tier_type 3) that are provided to ab initio predicters >>> capable of taking external 'hints' - such as augustus - that are >>> used to generate the final models (after further adjustmnets wrt., >>> utrs etc.). that is to say i think what you mean by first and >>> second maker runs are actually internal usage of ab initios that >>> occur at different stages of any single maker run and you should >>> be shielded from this. >>> >>> dan. >> >> -- The Wellcome Trust Sanger Institute is operated by Genome >> Research Limited, a charity registered in England with number >> 1021457 and a company registered in England with number 2742969, >> whose registered office is 215 Euston Road, London, NW1 2BE. >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com [1] >> > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > Links: > ------ > [1] mailto:maker-devel at box290.bluehost.com -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From parulk at caltech.edu Tue Nov 20 16:35:34 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:35:34 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction Message-ID: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Hello, I am running SNAP, Augustus and genemark(genemarkE results were calculated externally and gff3 file was provided to option pred_gff). However the resulting gff3 source field does not mention if the prediction were derived from SNAP, Augustus or genemark. I have attached the configuration file. Also is there any option where were could have priority for SNAP predictions? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4630 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 20 16:39:42 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:39:42 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> References: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Message-ID: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Hello, Just found that for Scaffold of larger size it does explicitly specify the prediction source. Thanks, Parul > Hello, > > I am running SNAP, Augustus and genemark(genemarkE results were calculated > externally and gff3 file was provided to option pred_gff). However the > resulting gff3 source field does not mention if the prediction were > derived from SNAP, Augustus or genemark. I have attached the > configuration file. Also is there any option where were could have > priority for SNAP predictions? > > Thanks and regards, > Parul Kudtarkar > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From barry.utah at gmail.com Tue Nov 20 20:21:47 2012 From: barry.utah at gmail.com (Barry Moore) Date: Tue, 20 Nov 2012 20:21:47 -0700 Subject: [maker-devel] email about Maker In-Reply-To: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> References: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> Message-ID: Hi Jorge, These would be two different proteins identified on the same scaffold. The numbers don't have any meaning other than that the genes are numbered sequentially and so these two genes would be adjacent to each other. If you have access to the GFF3 file produced by Maker for this genome you should see those two IDs with adjacent but different coordinates as well. B On Nov 19, 2012, at 10:48 AM, Jorge Ibarra wrote: > Dear Dr Moore > > I have a quick question about Maker and I'd appreciate if you could answer that to me. I downloaded two protein sequences predicted by Maker with the following indentifiers: > > >maker_scaffold_7-snap-gene-1.23-mRNA-1 Glucosylceramidase > >maker_scaffold_7-snap-gene-1.24-mRNA-1 Glucosylceramidase > > The only thing that varies in the two sequences identifiers are the number 1.23 and 1.24, and I was wondering what this numbers mean. Their sequence are also really similar (96%). > > I wonder if these sequences represent two genes in the same scaffold (scaffold_7) or if they are two slightly different predictions of the same gene. > > So my question is what do those numbers (1.23 and 1.24) represent in Maker? > > Thank you. > > Jorge Ibarra > PhD student Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 07:25:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 09:25:36 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Message-ID: Is it possible that you just picked a contig that didn't have any pred_gff entries for snap and augustus the first time? The predictions you pass through should be of type match/match_part and will have the source as pred_gff:snap or pred_gff:augustus. Could you check and let me know or send me an example of entries from a contig you passed through and the results you are seeing? No. there is no priority given to one prediction over the other. They are choses based on evidence overlap similarity. Thanks, Carson On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >Hello, > >Just found that for Scaffold of larger size it does explicitly specify the >prediction source. > >Thanks, >Parul > >> Hello, >> >> I am running SNAP, Augustus and genemark(genemarkE results were >>calculated >> externally and gff3 file was provided to option pred_gff). However the >> resulting gff3 source field does not mention if the prediction were >> derived from SNAP, Augustus or genemark. I have attached the >> configuration file. Also is there any option where were could have >> priority for SNAP predictions? >> >> Thanks and regards, >> Parul Kudtarkar >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From benayoun at stanford.edu Wed Nov 21 11:45:55 2012 From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=) Date: Wed, 21 Nov 2012 10:45:55 -0800 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Message-ID: Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department *BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 13:58:05 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 15:58:05 -0500 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? In-Reply-To: Message-ID: There are many ways of doing this. You can run everything separately and then copy all GFF3 files into a common folder and use the gff3_merge script that comes with maker to combine them. Alternatively you can run maker with the -g and -base options. This allows you to specify a new genome on the command line and the base name of the directory to write to. Using those flags you can swap in a different contig file while maintaining the same output directory for your job as a whole. Just run maker at the end of the run using the original fasta and the -dsindex flag, to sync the datastore index file so it is complete if you do this option. To split out contigs of interest you can also use the fasta_tool that comes with maker and use the -grep_header or ?select flags to indicate which contigs to retrieve. --Carson From: B?r?nice Benayoun Date: Wednesday, 21 November, 2012 1:45 PM To: Cc: Dario Riccardo Valenzano Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 21 14:15:00 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 21 Nov 2012 13:15:00 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Dear Carson, That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb which is very small). I have attached a Scaffold of 1.5kb with no predictions and another Scaffold of 28kb. It is of course expected that we would not get any gene-prediction for small size Scaffolds. For next maker run would you recommend bootstrap to reduce false positives? Thanks and regards, Parul Kudtarkar > Is it possible that you just picked a contig that didn't have any pred_gff > entries for snap and augustus the first time? The predictions you pass > through should be of type match/match_part and will have the source as > pred_gff:snap or pred_gff:augustus. Could you check and let me know or > send me an example of entries from a contig you passed through and the > results you are seeing? > > No. there is no priority given to one prediction over the other. They are > choses based on evidence overlap similarity. > > Thanks, > Carson > > > > > On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: > >>Hello, >> >>Just found that for Scaffold of larger size it does explicitly specify >> the >>prediction source. >> >>Thanks, >>Parul >> >>> Hello, >>> >>> I am running SNAP, Augustus and genemark(genemarkE results were >>>calculated >>> externally and gff3 file was provided to option pred_gff). However the >>> resulting gff3 source field does not mention if the prediction were >>> derived from SNAP, Augustus or genemark. I have attached the >>> configuration file. Also is there any option where were could have >>> priority for SNAP predictions? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold118825.gff Type: application/octet-stream Size: 1718 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold20.gff Type: application/octet-stream Size: 377513 bytes Desc: not available URL: From carsonhh at gmail.com Sun Nov 25 15:55:32 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 17:55:32 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Message-ID: I see both augustus and snap derived predictions (match/match_part) with augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that were derived from these predictions. There are no predictions from genemark. Is that what you were expecting? If not could you specify how it varies. With respect to bootstrapping, it really depends how well trained your gene predictors are. In general only one round of bootstrapping may be necessary after newly training a gene predictor. Thanks, Carson On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >Dear Carson, > >That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >which is very small). I have attached a Scaffold of 1.5kb with no >predictions and another Scaffold of 28kb. It is of course expected that we >would not get any gene-prediction for small size Scaffolds. > >For next maker run would you recommend bootstrap to reduce false >positives? > >Thanks and regards, >Parul Kudtarkar > >> Is it possible that you just picked a contig that didn't have any >>pred_gff >> entries for snap and augustus the first time? The predictions you pass >> through should be of type match/match_part and will have the source as >> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >> send me an example of entries from a contig you passed through and the >> results you are seeing? >> >> No. there is no priority given to one prediction over the other. They >>are >> choses based on evidence overlap similarity. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >> >>>Hello, >>> >>>Just found that for Scaffold of larger size it does explicitly specify >>> the >>>prediction source. >>> >>>Thanks, >>>Parul >>> >>>> Hello, >>>> >>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>calculated >>>> externally and gff3 file was provided to option pred_gff). However the >>>> resulting gff3 source field does not mention if the prediction were >>>> derived from SNAP, Augustus or genemark. I have attached the >>>> configuration file. Also is there any option where were could have >>>> priority for SNAP predictions? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Sun Nov 25 21:10:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 23:10:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more detail > to the errors in the development version if you do an 'svn update'. Then you > will know the system specific reason why close or opened failed. For the > other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1 > 869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, > there are some intermittent issues. I've seen a couple occurrences of the > following error... > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq101.for.716125-721460.0.fasta -t >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 >> --maxintron 10000 --showcigar --percent 20 > >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq37.for.716125-723330.0.fasta at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > > ...as well as one occurrence of this error. > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker >> .output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.186 >> 9077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >> affold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >> --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_ >> 7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.p >> m:86 >> STACK: Widget::exonerate::est2genome::assemble >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:82 >> STACK: polisher::exonerate::est::polish >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:44 >> STACK: GI::to_polisher >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:166>> 3 >> STACK: Process::MpiChunk::run >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling uri_escape at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling File::Path::mkpath at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> >>> >>> >>> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to >> localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps and >>> is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl live >>>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command line >>>>> for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List >>>>> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP directory >>>>> is on native disk space, and relaunched. I have attached the output of the >>>>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>>>> the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Sun Nov 25 21:56:31 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 26 Nov 2012 04:56:31 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> good detective work there Carson! Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] Sent: Sunday, November 25, 2012 9:10 PM To: Daniel Standage Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage > Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From cjfields at illinois.edu Sun Nov 25 22:33:52 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 05:33:52 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { if ( $str =~ m/U/i ) { $alphabet = 'rna'; } else { $alphabet = 'dna'; } } else { $alphabet = 'protein'; } Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. chris On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > good detective work there Carson! > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] > Sent: Sunday, November 25, 2012 9:10 PM > To: Daniel Standage > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. > That is why you get --> > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > > You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. > > Thanks, > Carson > > > > From: Daniel Standage > > Date: Friday, 23 November, 2012 3:06 PM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Thanks for your reply, and sorry for my delayed response. > > I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 > STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 > STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: > 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: > Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From daniel.standage at gmail.com Mon Nov 26 04:08:56 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 26 Nov 2012 06:08:56 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thanks for the responses from everybody! The genomic sequence I am annotating is coming directly from AllPaths-LG, which I've noticed retains as much ambiguity as possible--thus the seldom seen ambiguity nucleotides which in this case seem to outnumber the resolved nucleotides. On one hand, I would hate to lose all the information these ambiguity characters provide by replacing them with Ns, but on the other hand if most tools treat them as such, then it might not make much of a difference. Another option I guess would be to replace ambiguity nucleotides by the most likely explicit nucleotide based solely on sequence composition. This would retain more information than an N, and would at least partially correct. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 26, 2012 at 12:33 AM, Fields, Christopher J < cjfields at illinois.edu> wrote: > This is coming from BioPerl trying to guess the alphabet if one is not > provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just > committed, in fact). It's probably best to explicitly set this when > possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell > wrote: > > > good detective work there Carson! > > > > > > Mark Yandell > > Professor of Human Genetics > > H.A. & Edna Benning Presidential Endowed Chair > > Eccles Institute of Human Genetics > > University of Utah > > 15 North 2030 East, Room 2100 > > Salt Lake City, UT 84112-5330 > > ph:801-587-7707 > > > > ________________________________________ > > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [ > carsonhh at gmail.com] > > Sent: Sunday, November 25, 2012 9:10 PM > > To: Daniel Standage > > Cc: Maker Mailing List > > Subject: Re: [maker-devel] Maker issues > > > > I think the problem is in the sequence of your scaffold. I pulled this > out of the exonerate alignment --> > > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > > > Notice the letters W, K, R, M, etc. While these are technically legal > nucleotides, many external programs, and in this case BioPerl doesn't > handle them well. > > That is why you get --> > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > > > You might want to replace them in your input fasta with the letter 'N' > so they are treated as masked. You will have to delete the mpi_blastdb > directory to let maker rebuild the fasta indexes and you will probably have > to set clean_try=1 in the control files so that MAKER deletes old result > files that contain those characters on the retry. The other error may be > just a snowball effect from the first error, so you should see of it still > happens after fixing the input fasta file. > > > > Thanks, > > Carson > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Friday, 23 November, 2012 3:06 PM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Thanks for your reply, and sorry for my delayed response. > > > > I have attached the first file you requested, but the other two do not > exist. I have attached a listing of the files in that directory. Let me > know if you need anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > > > thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Thursday, 8 November, 2012 9:32 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_23 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_23 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > ...as well as one occurrence of this error. > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > > > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > > q93.est_exonerate.0 > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > > ----------------------------------------------------------- > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_7 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_7 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > I'll let you know if I see anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Typo now fixed on my end too ;-) > > > > Thanks, > > Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Wednesday, 7 November, 2012 11:43 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Looked good for a while, but came across this error. > > > > total clusters:20 now processing 0 > > flattening EST clusters > > doing tblastx of alt-ESTs > > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > > --> rank=NA, hostname=c4 > > ERROR: Failed while doing tblastx of alt-ESTs > > ERROR: Chunk failed at level:4, tier_type:2 > > FAILED CONTIG:scaffold_58 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_58 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > > > --Next Contig-- > > > > It seems pretty clear that there is a typo in GI.pm. I changed loalize > to localize and relaunched. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < > daniel.standage at gmail.com> wrote: > > Done. > > > > Test job has successfully cleared the preliminary Fasta indexing steps > and is repeat masking. I'll let you know if there are any problems. Thanks! > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > > > Thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:14 AM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Debug output attached (bzip2 compressed). > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > > > --Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:05 AM > > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > > Subject: Maker issues > > > > Carson, > > > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > > > > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Nov 26 09:53:59 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 26 Nov 2012 16:53:59 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thank you for the commit to Bioperl. I'll can also manipulate the alphabet value in the object hash right before calling the revcomp method, it's not the most elegant solution but the seq object creation is insulated from my control so I can't set it there --> Bio::Search::HSP::HSPI.pm line 578 I would still recommend losing the ambiguous bases though as they will very likely still cause problems in some downstream application. Thanks, Carson On 12-11-26 12:33 AM, "Fields, Christopher J" wrote: >This is coming from BioPerl trying to guess the alphabet if one is not >provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > >Easy enough to fix to allow for additional ambiguous nucleotides (just >committed, in fact). It's probably best to explicitly set this when >possible, though; it is a guess, after all. > >chris > >On Nov 25, 2012, at 10:56 PM, Mark Yandell >wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>[carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this >>out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal >>nucleotides, many external programs, and in this case BioPerl doesn't >>handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' >>so they are treated as masked. You will have to delete the mpi_blastdb >>directory to let maker rebuild the fasta indexes and you will probably >>have to set clean_try=1 in the control files so that MAKER deletes old >>result files that contain those characters on the retry. The other >>error may be just a snowball effect from the first error, so you should >>see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage >>> >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not >>exist. I have attached a listing of the files in that directory. Let me >>know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>> wrote: >> The first error is an IO error with your system. I've added some more >>detail to the errors in the development version if you do an 'svn >>update'. Then you will know the system specific reason why close or >>opened failed. For the other error, could you send me this file --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/sc >>affold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta >> >> And this one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. >>However, there are some intermittent issues. I've seen a couple >>occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta -t >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq37.for.716125-723330.0.fasta at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pd >> >>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for >>.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> >>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastor >>e/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>--showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> >>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaff >>old_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_in >>fo.pm:86 >> STACK: Widget::exonerate::est2genome::assemble >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:82 >> STACK: polisher::exonerate::est::polish >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:44 >> STACK: GI::to_polisher >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:1663 >> STACK: Process::MpiChunk::run >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:335 >> STACK: Process::MpiChunk::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:351 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>> wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >>> >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>> wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >>and is repeat masking. I'll let you know if there are any problems. >>Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>> wrote: >> 1.006902 Bio::Root::Version >>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>It's fasta indexer is broken. I have an open bug I am trying to resolve >>with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>> wrote: >> Thanks. Could you also run with the --debug flag set on the command >>line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker >>Mailing List >>> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP >>directory is on native disk space, and relaunched. I have attached the >>output of the job that failed in <5 minutes. It looks pretty similar to >>the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From parulk at caltech.edu Mon Nov 26 12:21:23 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 11:21:23 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Hello Carson, Thanks for the feedback.Genemark was run outside maker and the resulting gff3 file was provided as option to pred_gff. What would the source in the gff3 of maker result state of the predictions where made from pred_gff? Thanks and regards, Parul Kudtarkar > I see both augustus and snap derived predictions (match/match_part) with > augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that > were derived from these predictions. There are no predictions from > genemark. Is that what you were expecting? If not could you specify how > it varies. > > With respect to bootstrapping, it really depends how well trained your > gene predictors are. In general only one round of bootstrapping may be > necessary after newly training a gene predictor. > > Thanks, > Carson > > > > On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: > >>Dear Carson, >> >>That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >>which is very small). I have attached a Scaffold of 1.5kb with no >>predictions and another Scaffold of 28kb. It is of course expected that >> we >>would not get any gene-prediction for small size Scaffolds. >> >>For next maker run would you recommend bootstrap to reduce false >>positives? >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Is it possible that you just picked a contig that didn't have any >>>pred_gff >>> entries for snap and augustus the first time? The predictions you pass >>> through should be of type match/match_part and will have the source as >>> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >>> send me an example of entries from a contig you passed through and the >>> results you are seeing? >>> >>> No. there is no priority given to one prediction over the other. They >>>are >>> choses based on evidence overlap similarity. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>> >>>>Hello, >>>> >>>>Just found that for Scaffold of larger size it does explicitly specify >>>> the >>>>prediction source. >>>> >>>>Thanks, >>>>Parul >>>> >>>>> Hello, >>>>> >>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>calculated >>>>> externally and gff3 file was provided to option pred_gff). However >>>>> the >>>>> resulting gff3 source field does not mention if the prediction were >>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>> configuration file. Also is there any option where were could have >>>>> priority for SNAP predictions? >>>>> >>>>> Thanks and regards, >>>>> Parul Kudtarkar >>>>> >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From jason.stajich at gmail.com Mon Nov 26 14:32:42 2012 From: jason.stajich at gmail.com (Jason Stajich) Date: Mon, 26 Nov 2012 13:32:42 -0800 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: right - you can explicitly set the alphabet to 'dna' when building a sequence object but I don't know if this down in MAKER code that is tripping up? Jason On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" wrote: > This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage > >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: >> The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta >> >> And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 >> STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 >> STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 >> STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 >> STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage > >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: >> 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: >> Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker Mailing List > >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Jason Stajich jason.stajich at gmail.com jason at bioperl.org From parulk at caltech.edu Mon Nov 26 14:35:48 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 13:35:48 -0800 (PST) Subject: [maker-devel] AED score Message-ID: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Dear Maker community, For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K genes however I am getting 8 times the expected gene count indicating too many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes how to go about this? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Mon Nov 26 14:37:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:37:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The sequence object is being created well down into BioPerl (outside of my control), but I think I can explicitly set the alphabet to 'dna' by modifying the existing object just before calling the revcomp method to get around that. Thanks, Carson On 12-11-26 4:32 PM, "Jason Stajich" wrote: >right - you can explicitly set the alphabet to 'dna' when building a >sequence object but I don't know if this down in MAKER code that is >tripping up? > >Jason >On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" > wrote: > >> This is coming from BioPerl trying to guess the alphabet if one is not >>provided. The specific spot: >> >> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >> if ( $str =~ m/U/i ) { >> $alphabet = 'rna'; >> } else { >> $alphabet = 'dna'; >> } >> } else { >> $alphabet = 'protein'; >> } >> >> Easy enough to fix to allow for additional ambiguous nucleotides (just >>committed, in fact). It's probably best to explicitly set this when >>possible, though; it is a guess, after all. >> >> chris >> >> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>wrote: >> >>> good detective work there Carson! >>> >>> >>> Mark Yandell >>> Professor of Human Genetics >>> H.A. & Edna Benning Presidential Endowed Chair >>> Eccles Institute of Human Genetics >>> University of Utah >>> 15 North 2030 East, Room 2100 >>> Salt Lake City, UT 84112-5330 >>> ph:801-587-7707 >>> >>> ________________________________________ >>> From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>[carsonhh at gmail.com] >>> Sent: Sunday, November 25, 2012 9:10 PM >>> To: Daniel Standage >>> Cc: Maker Mailing List >>> Subject: Re: [maker-devel] Maker issues >>> >>> I think the problem is in the sequence of your scaffold. I pulled >>>this out of the exonerate alignment --> >>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>> >>> Notice the letters W, K, R, M, etc. While these are technically legal >>>nucleotides, many external programs, and in this case BioPerl doesn't >>>handle them well. >>> That is why you get --> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> >>> You might want to replace them in your input fasta with the letter 'N' >>>so they are treated as masked. You will have to delete the mpi_blastdb >>>directory to let maker rebuild the fasta indexes and you will probably >>>have to set clean_try=1 in the control files so that MAKER deletes old >>>result files that contain those characters on the retry. The other >>>error may be just a snowball effect from the first error, so you should >>>see of it still happens after fixing the input fasta file. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Friday, 23 November, 2012 3:06 PM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Thanks for your reply, and sorry for my delayed response. >>> >>> I have attached the first file you requested, but the other two do not >>>exist. I have attached a listing of the files in that directory. Let me >>>know if you need anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> wrote: >>> The first error is an IO error with your system. I've added some more >>>detail to the errors in the development version if you do an 'svn >>>update'. Then you will know the system specific reason why close or >>>opened failed. For the other error, could you send me this file --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>> >>> This one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta >>> >>> And this one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta >>> >>> thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Thursday, 8 November, 2012 9:32 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Scaling up to whole-genome annotation, things seem to be going well. >>>However, there are some intermittent issues. I've seen a couple >>>occurrences of the following error... >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> couldn't close >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>60. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_23 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_23 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> ...as well as one occurrence of this error. >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pd >>> >>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>> >>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>--showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>> >>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>> q93.est_exonerate.0 >>> #-------------------------------# >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>> STACK: Bio::PrimarySeqI::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>> STACK: Bio::LocatableSeq::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>nfo.pm:86 >>> STACK: Widget::exonerate::est2genome::assemble >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:686 >>> STACK: Widget::exonerate::est2genome::parse >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:961 >>> STACK: polisher::exonerate::est::e_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:82 >>> STACK: polisher::exonerate::est::polish >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:44 >>> STACK: GI::to_polisher >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>> STACK: GI::polish_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>> STACK: Process::MpiChunk::_go >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:1663 >>> STACK: Process::MpiChunk::run >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:335 >>> STACK: Process::MpiChunk::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:351 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_7 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_7 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> I'll let you know if I see anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> wrote: >>> Thanks. Typo now fixed on my end too ;-) >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Wednesday, 7 November, 2012 11:43 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Looked good for a while, but came across this error. >>> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> >>> --Next Contig-- >>> >>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>to localize and relaunched. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>>and is repeat masking. I'll let you know if there are any problems. >>>Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> wrote: >>> 1.006902 Bio::Root::Version >>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>It's fasta indexer is broken. I have an open bug I am trying to >>>resolve with the Bioperl developers, but for now use the CPAN version >>>of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> wrote: >>> Thanks. Could you also run with the --debug flag set on the command >>>line for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt >, Maker >>>Mailing List >>>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP >>>directory is on native disk space, and relaunched. I have attached the >>>output of the job that failed in <5 minutes. It looks pretty similar to >>>the errors I got the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >Jason Stajich >jason.stajich at gmail.com >jason at bioperl.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 14:46:48 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:46:48 -0500 Subject: [maker-devel] AED score In-Reply-To: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Message-ID: AED score with 1 are the ones you don't want. 0 is best and 1 is worst as it is a distance metric. You can use the AED_threshold parameter to require better matching to the evidence by setting it closer to 0. You can also try to increase protein homology evidence as some of your calls may be split genes due to lack of evidence linking them. --Carson On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >Dear Maker community, > >For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect 20-30K >genes however I am getting 8 times the expected gene count indicating too >many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if yes how >to go about this? > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 14:48:18 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:48:18 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Message-ID: They should show up as genemark or pred_gff:genemark. Could you verify that the input file from genemark indeed contained predictions that should have been on this contig as not all contigs may have calls from genemark? --Carson On 12-11-26 2:21 PM, "Parul Kudtarkar" wrote: >Hello Carson, > >Thanks for the feedback.Genemark was run outside maker and the resulting >gff3 file was provided as option to pred_gff. What would the source in the >gff3 of maker result state of the predictions where made from pred_gff? > >Thanks and regards, >Parul Kudtarkar > >> I see both augustus and snap derived predictions (match/match_part) with >> augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that >> were derived from these predictions. There are no predictions from >> genemark. Is that what you were expecting? If not could you specify how >> it varies. >> >> With respect to bootstrapping, it really depends how well trained your >> gene predictors are. In general only one round of bootstrapping may be >> necessary after newly training a gene predictor. >> >> Thanks, >> Carson >> >> >> >> On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson, >>> >>>That is correct. There were no pred_gff for smaller size >>>Scaffolds(~1.5kb >>>which is very small). I have attached a Scaffold of 1.5kb with no >>>predictions and another Scaffold of 28kb. It is of course expected that >>> we >>>would not get any gene-prediction for small size Scaffolds. >>> >>>For next maker run would you recommend bootstrap to reduce false >>>positives? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>> Is it possible that you just picked a contig that didn't have any >>>>pred_gff >>>> entries for snap and augustus the first time? The predictions you >>>>pass >>>> through should be of type match/match_part and will have the source as >>>> pred_gff:snap or pred_gff:augustus. Could you check and let me know >>>>or >>>> send me an example of entries from a contig you passed through and the >>>> results you are seeing? >>>> >>>> No. there is no priority given to one prediction over the other. They >>>>are >>>> choses based on evidence overlap similarity. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Hello, >>>>> >>>>>Just found that for Scaffold of larger size it does explicitly specify >>>>> the >>>>>prediction source. >>>>> >>>>>Thanks, >>>>>Parul >>>>> >>>>>> Hello, >>>>>> >>>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>>calculated >>>>>> externally and gff3 file was provided to option pred_gff). However >>>>>> the >>>>>> resulting gff3 source field does not mention if the prediction were >>>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>>> configuration file. Also is there any option where were could have >>>>>> priority for SNAP predictions? >>>>>> >>>>>> Thanks and regards, >>>>>> Parul Kudtarkar >>>>>> >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > From cjfields at illinois.edu Mon Nov 26 14:55:04 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 21:55:04 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> That makes sense. The change I made should also allow these sequences to 'just work', but this would of course require a BioPerl update. We could also make that change within BioPerl if needed if we know where it might be; it seems in this case a returned sequence should be 'dna' if the application is exonerate. chris On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > The sequence object is being created well down into BioPerl (outside of my > control), but I think I can explicitly set the alphabet to 'dna' by > modifying the existing object just before calling the revcomp method to > get around that. > > Thanks, > Carson > > > On 12-11-26 4:32 PM, "Jason Stajich" wrote: > >> right - you can explicitly set the alphabet to 'dna' when building a >> sequence object but I don't know if this down in MAKER code that is >> tripping up? >> >> Jason >> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >> wrote: >> >>> This is coming from BioPerl trying to guess the alphabet if one is not >>> provided. The specific spot: >>> >>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>> if ( $str =~ m/U/i ) { >>> $alphabet = 'rna'; >>> } else { >>> $alphabet = 'dna'; >>> } >>> } else { >>> $alphabet = 'protein'; >>> } >>> >>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>> committed, in fact). It's probably best to explicitly set this when >>> possible, though; it is a guess, after all. >>> >>> chris >>> >>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>> wrote: >>> >>>> good detective work there Carson! >>>> >>>> >>>> Mark Yandell >>>> Professor of Human Genetics >>>> H.A. & Edna Benning Presidential Endowed Chair >>>> Eccles Institute of Human Genetics >>>> University of Utah >>>> 15 North 2030 East, Room 2100 >>>> Salt Lake City, UT 84112-5330 >>>> ph:801-587-7707 >>>> >>>> ________________________________________ >>>> From: maker-devel-bounces at yandell-lab.org >>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>> [carsonhh at gmail.com] >>>> Sent: Sunday, November 25, 2012 9:10 PM >>>> To: Daniel Standage >>>> Cc: Maker Mailing List >>>> Subject: Re: [maker-devel] Maker issues >>>> >>>> I think the problem is in the sequence of your scaffold. I pulled >>>> this out of the exonerate alignment --> >>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>> >>>> Notice the letters W, K, R, M, etc. While these are technically legal >>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>> handle them well. >>>> That is why you get --> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> >>>> You might want to replace them in your input fasta with the letter 'N' >>>> so they are treated as masked. You will have to delete the mpi_blastdb >>>> directory to let maker rebuild the fasta indexes and you will probably >>>> have to set clean_try=1 in the control files so that MAKER deletes old >>>> result files that contain those characters on the retry. The other >>>> error may be just a snowball effect from the first error, so you should >>>> see of it still happens after fixing the input fasta file. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Friday, 23 November, 2012 3:06 PM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Thanks for your reply, and sorry for my delayed response. >>>> >>>> I have attached the first file you requested, but the other two do not >>>> exist. I have attached a listing of the files in that directory. Let me >>>> know if you need anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> > wrote: >>>> The first error is an IO error with your system. I've added some more >>>> detail to the errors in the development version if you do an 'svn >>>> update'. Then you will know the system specific reason why close or >>>> opened failed. For the other error, could you send me this file --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>> >>>> This one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta >>>> >>>> And this one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>> >>>> thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Thursday, 8 November, 2012 9:32 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Scaling up to whole-genome annotation, things seem to be going well. >>>> However, there are some intermittent issues. I've seen a couple >>>> occurrences of the following error... >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> couldn't close >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>> 60. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> ...as well as one occurrence of this error. >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pd >>>> >>>> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>> >>>> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>> --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>> >>>> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>> q93.est_exonerate.0 >>>> #-------------------------------# >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>> STACK: Bio::PrimarySeqI::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>>> STACK: Bio::LocatableSeq::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>> nfo.pm:86 >>>> STACK: Widget::exonerate::est2genome::assemble >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:686 >>>> STACK: Widget::exonerate::est2genome::parse >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:961 >>>> STACK: polisher::exonerate::est::e_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:82 >>>> STACK: polisher::exonerate::est::polish >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:44 >>>> STACK: GI::to_polisher >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>> STACK: GI::polish_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>> STACK: Process::MpiChunk::_go >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:1663 >>>> STACK: Process::MpiChunk::run >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:335 >>>> STACK: Process::MpiChunk::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:351 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> I'll let you know if I see anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> > wrote: >>>> Thanks. Typo now fixed on my end too ;-) >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Looked good for a while, but came across this error. >>>> >>>> total clusters:20 now processing 0 >>>> flattening EST clusters >>>> doing tblastx of alt-ESTs >>>> Undefined subroutine &GI::loalize_file called at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while doing tblastx of alt-ESTs >>>> ERROR: Chunk failed at level:4, tier_type:2 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> >>>> --Next Contig-- >>>> >>>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>> to localize and relaunched. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> > wrote: >>>> Done. >>>> >>>> Test job has successfully cleared the preliminary Fasta indexing steps >>>> and is repeat masking. I'll let you know if there are any problems. >>>> Thanks! >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> > wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>> It's fasta indexer is broken. I have an open bug I am trying to >>>> resolve with the Bioperl developers, but for now use the CPAN version >>>> of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> > wrote: >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt >, Maker >>>> Mailing List >>>> > >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to >>>> the errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > From carsonhh at gmail.com Mon Nov 26 15:07:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 17:07:46 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> Message-ID: The seq object is being create in Bio::Search::HSP::HSPI.pm line 578 which itself is several layers deep into BioPerl after creation of a Bio::Search::Hit object. I think explicitly setting the alphabet would require modifications to a number of modules that create hits from Bio::SearchIO so that the alphabet gets stored early on, but that seems like a lot of work and could break any number of things along the way. The current change should allow BioPerl to guess right. After all the upstream code did explicitly call revcomp, so it obviously thinks that the sequence can be reverse complimented, so BioPerl is now just verifying that the alphabet matches legal characters, even if it is an unlikely match. --Carson On 12-11-26 4:55 PM, "Fields, Christopher J" wrote: >That makes sense. The change I made should also allow these sequences to >'just work', but this would of course require a BioPerl update. > >We could also make that change within BioPerl if needed if we know where >it might be; it seems in this case a returned sequence should be 'dna' if >the application is exonerate. > >chris > >On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > >> The sequence object is being created well down into BioPerl (outside of >>my >> control), but I think I can explicitly set the alphabet to 'dna' by >> modifying the existing object just before calling the revcomp method to >> get around that. >> >> Thanks, >> Carson >> >> >> On 12-11-26 4:32 PM, "Jason Stajich" wrote: >> >>> right - you can explicitly set the alphabet to 'dna' when building a >>> sequence object but I don't know if this down in MAKER code that is >>> tripping up? >>> >>> Jason >>> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >>> wrote: >>> >>>> This is coming from BioPerl trying to guess the alphabet if one is not >>>> provided. The specific spot: >>>> >>>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>>> if ( $str =~ m/U/i ) { >>>> $alphabet = 'rna'; >>>> } else { >>>> $alphabet = 'dna'; >>>> } >>>> } else { >>>> $alphabet = 'protein'; >>>> } >>>> >>>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>>> committed, in fact). It's probably best to explicitly set this when >>>> possible, though; it is a guess, after all. >>>> >>>> chris >>>> >>>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>>> >>>> wrote: >>>> >>>>> good detective work there Carson! >>>>> >>>>> >>>>> Mark Yandell >>>>> Professor of Human Genetics >>>>> H.A. & Edna Benning Presidential Endowed Chair >>>>> Eccles Institute of Human Genetics >>>>> University of Utah >>>>> 15 North 2030 East, Room 2100 >>>>> Salt Lake City, UT 84112-5330 >>>>> ph:801-587-7707 >>>>> >>>>> ________________________________________ >>>>> From: maker-devel-bounces at yandell-lab.org >>>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>>> [carsonhh at gmail.com] >>>>> Sent: Sunday, November 25, 2012 9:10 PM >>>>> To: Daniel Standage >>>>> Cc: Maker Mailing List >>>>> Subject: Re: [maker-devel] Maker issues >>>>> >>>>> I think the problem is in the sequence of your scaffold. I pulled >>>>> this out of the exonerate alignment --> >>>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>>> >>>>> Notice the letters W, K, R, M, etc. While these are technically >>>>>legal >>>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>>> handle them well. >>>>> That is why you get --> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> >>>>> You might want to replace them in your input fasta with the letter >>>>>'N' >>>>> so they are treated as masked. You will have to delete the >>>>>mpi_blastdb >>>>> directory to let maker rebuild the fasta indexes and you will >>>>>probably >>>>> have to set clean_try=1 in the control files so that MAKER deletes >>>>>old >>>>> result files that contain those characters on the retry. The other >>>>> error may be just a snowball effect from the first error, so you >>>>>should >>>>> see of it still happens after fixing the input fasta file. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Friday, 23 November, 2012 3:06 PM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Thanks for your reply, and sorry for my delayed response. >>>>> >>>>> I have attached the first file you requested, but the other two do >>>>>not >>>>> exist. I have attached a listing of the files in that directory. Let >>>>>me >>>>> know if you need anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>>> > wrote: >>>>> The first error is an IO error with your system. I've added some >>>>>more >>>>> detail to the errors in the development version if you do an 'svn >>>>> update'. Then you will know the system specific reason why close or >>>>> opened failed. For the other error, could you send me this file --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_ >>>>>7/ >>>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>>> >>>>> This one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta >>>>> >>>>> And this one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>>> >>>>> thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Thursday, 8 November, 2012 9:32 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Scaling up to whole-genome annotation, things seem to be going well. >>>>> However, there are some intermittent issues. I've seen a couple >>>>> occurrences of the following error... >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> couldn't close >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm >>>>>line >>>>> 60. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> ...as well as one occurrence of this error. >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> maker.output/maker.pd >>>>> >>>>> >>>>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93. >>>>>fo >>>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>>> >>>>> >>>>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datas >>>>>to >>>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>>> --showcigar --percent 20 > >>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>>> >>>>> >>>>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >>>>>af >>>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>>> q93.est_exonerate.0 >>>>> #-------------------------------# >>>>> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> STACK: Error::throw >>>>> STACK: Bio::Root::Root::throw >>>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>>> STACK: Bio::PrimarySeqI::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:38 >>>>>1 >>>>> STACK: Bio::LocatableSeq::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:5 >>>>>77 >>>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice >>>>>_i >>>>> nfo.pm:86 >>>>> STACK: Widget::exonerate::est2genome::assemble >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:686 >>>>> STACK: Widget::exonerate::est2genome::parse >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:961 >>>>> STACK: polisher::exonerate::est::e_exonerate >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:82 >>>>> STACK: polisher::exonerate::est::polish >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:44 >>>>> STACK: GI::to_polisher >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>>> STACK: GI::polish_exonerate >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>>> STACK: Process::MpiChunk::_go >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:1663 >>>>> STACK: Process::MpiChunk::run >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:335 >>>>> STACK: Process::MpiChunk::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:351 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>>> ----------------------------------------------------------- >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> I'll let you know if I see anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Typo now fixed on my end too ;-) >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Looked good for a while, but came across this error. >>>>> >>>>> total clusters:20 now processing 0 >>>>> flattening EST clusters >>>>> doing tblastx of alt-ESTs >>>>> Undefined subroutine &GI::loalize_file called at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>2648. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while doing tblastx of alt-ESTs >>>>> ERROR: Chunk failed at level:4, tier_type:2 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> >>>>> --Next Contig-- >>>>> >>>>> It seems pretty clear that there is a typo in GI.pm. I changed >>>>>loalize >>>>> to localize and relaunched. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>>> > wrote: >>>>> Done. >>>>> >>>>> Test job has successfully cleared the preliminary Fasta indexing >>>>>steps >>>>> and is repeat masking. I'll let you know if there are any problems. >>>>> Thanks! >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>>> > wrote: >>>>> 1.006902 Bio::Root::Version >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.p >>>>>m >>>>> >>>>> One thing I noticed, in the debug output is that you are using >>>>>Bioperl >>>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>>> It's fasta indexer is broken. I have an open bug I am trying to >>>>> resolve with the Bioperl developers, but for now use the CPAN version >>>>> of Bioperl. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:14 AM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Debug output attached (bzip2 compressed). >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt >, >>>>>Maker >>>>> Mailing List >>>>> > >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached >>>>>the >>>>> output of the job that failed in <5 minutes. It looks pretty similar >>>>>to >>>>> the errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> maker-devel mailing list >>>>> maker-devel at box290.bluehost.com >>>>> >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > From parulk at caltech.edu Mon Nov 26 15:15:58 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 14:15:58 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <2223.131.215.15.234.1353968158.squirrel@webmail.caltech.edu> Dear Carson, Thanks, I retrain/rerun using better AED score to filter false negatives. > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From daniel.standage at gmail.com Fri Nov 23 13:06:34 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Fri, 23 Nov 2012 15:06:34 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> >> It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to >> *localize* and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < >> daniel.standage at gmail.com> wrote: >> >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>> and is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List < >>>>> maker-devel at yandell-lab.org> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached the >>>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>>> errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... 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-rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303233.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303234.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303235.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038212.gnl%7CAmel_4%2E5%7CGB40495-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB40142-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB53378-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038224.gnl%7CAmel_4%2E5%7CGB43258-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:19 scaffold_23.1037324-1038248.gnl%7CAmel_4%2E5%7CGB48486-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 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Nov 8 06:55 scaffold_23.11767-15264.gnl%7CDmel_r5%2E47%7CFBpp0079114.p_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:20 scaffold_23.1177210-1187515.comp55832_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 06:57 scaffold_23.118600-121630.comp56223_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:05 scaffold_23.119493-121535.gnl%7CAmel_4%2E5%7CGB42515-PA.p_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0080719.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0085457.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:24 scaffold_23.11.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 33K Nov 8 06:28 scaffold_23.11.drosophila.rb.out -rw-r--r-- 1 dstandag biol 469K Nov 8 12:05 scaffold_23.11.final.section -rw-r--r-- 1 dstandag biol 198K Nov 8 11:19 scaffold_23.11.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 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-rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:25 scaffold_23.1239438-1240065.comp58697_c2_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:25 scaffold_23.1240020-1240577.comp51041_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:58 scaffold_23.125651-126606.comp51692_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:57 scaffold_23.126190-129712.comp51692_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:58 scaffold_23.126190-129712.comp51692_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:05 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dstandag biol 5.4K Nov 8 07:05 scaffold_23.129450-131047.gnl%7CAmel_4%2E5%7CGB47192-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 11:35 scaffold_23.1296927-1297434.gnl%7CAmel_4%2E5%7CGB43383-PA.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:29 scaffold_23.12.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 24K Nov 8 06:29 scaffold_23.12.drosophila.rb.out -rw-r--r-- 1 dstandag biol 343K Nov 8 12:05 scaffold_23.12.final.section -rw-r--r-- 1 dstandag biol 119K Nov 8 11:24 scaffold_23.12.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 104K Nov 8 11:28 scaffold_23.12.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 41K Nov 8 07:09 scaffold_23.1-2.raw.section -rw-r--r-- 1 dstandag biol 344K Nov 8 11:29 scaffold_23.12.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:29 scaffold_23.12.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1307615-1308418.comp1419599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 26K Nov 8 11:35 scaffold_23.1308043-1330696.gnl%7CAmel_4%2E5%7CGB48919-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1308162-1309528.comp44341_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302629.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302630.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302631.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1330258.gnl%7CDmel_r5%2E47%7CFBpp0302633.p_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:30 scaffold_23.1309128-1310251.comp26811_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 11:30 scaffold_23.1309844-1319042.comp55832_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:58 scaffold_23.131077-131586.comp59045_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 132K Nov 8 11:40 scaffold_23.13-14.raw.section -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1316714-1317272.comp1218705_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:59 scaffold_23.131685-132925.comp58909_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:59 scaffold_23.131685-134704.comp58909_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 8.3K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 11:30 scaffold_23.1318842-1326844.comp55832_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 11:30 scaffold_23.1318842-1329152.comp55832_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 11:30 scaffold_23.1318842-1331426.comp55832_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 06:58 scaffold_23.132429-133368.comp59433_c2_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1325517-1326265.comp1845494_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:59 scaffold_23.132575-133077.comp59433_c2_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 06:59 scaffold_23.132639-133189.comp59433_c2_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:58 scaffold_23.132947-134704.comp58909_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:59 scaffold_23.132947-134801.comp58909_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 11:30 scaffold_23.1331331-1332259.comp40535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:59 scaffold_23.133194-134178.comp58909_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 11:30 scaffold_23.1331948-1333303.comp32761_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1333133-1334007.comp56864_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1333600-1334315.comp56864_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 11:30 scaffold_23.1333918-1335419.comp56864_c3_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1335705.comp56864_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1337728.comp56864_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:35 scaffold_23.1334768-1337724.gnl%7CAmel_4%2E5%7CGB48917-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:05 scaffold_23.133512-135390.gnl%7CAmel_4%2E5%7CGB45366-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1335366-1335970.comp1729875_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:30 scaffold_23.1336887-1337499.comp1746631_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:00 scaffold_23.133757-134452.comp58909_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1340213-1340817.comp3166415_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1341145-1341745.comp2137934_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1341790-1342546.comp2308491_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:58 scaffold_23.134716-136043.comp58909_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:30 scaffold_23.1351224-1351773.comp56864_c3_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1351855-1352444.comp49157_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:30 scaffold_23.1352403-1353237.comp50400_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 11:30 scaffold_23.1352824-1354274.comp50400_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1353863-1354457.comp32051_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:30 scaffold_23.1354103-1354916.comp32051_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 11:30 scaffold_23.1354495-1355883.comp28788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:30 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scaffold_23.1361370-1362023.comp63024_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1361962-1362628.comp56945_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 11:30 scaffold_23.1362208-1364017.comp56945_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1363621-1364241.comp56945_c15_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1363824-1364656.comp56945_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:30 scaffold_23.1364241-1365534.comp56945_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 11:30 scaffold_23.1365475-1366354.comp58627_c6_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1365475-1367018.comp58627_c6_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 11:30 scaffold_23.1366668-1368555.comp58344_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1369001-1370345.comp57731_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1369932-1370651.comp57731_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.137055-137860.comp53917_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1370982-1372429.comp58968_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 scaffold_23.1372006-1372825.comp56955_c2_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 11:30 scaffold_23.1373883-1375967.comp53188_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:00 scaffold_23.137439-138464.comp53917_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1376023-1376568.comp58089_c12_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:35 scaffold_23.1389507.1410090.0.comp58089_c6_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 scaffold_23.1389801-1390543.comp47217_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 07:00 scaffold_23.138981-140060.comp58679_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1389854-1390711.comp47217_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 11:36 scaffold_23.1390291-1390966.comp47217_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 11:36 scaffold_23.1390743-1392000.comp58289_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1391945-1392597.comp58289_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 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-rw-r--r-- 1 dstandag biol 5.4K Nov 8 11:36 scaffold_23.1397553-1399112.comp58089_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.139809-140616.comp39902_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1398718-1399314.comp58089_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1398899-1399721.comp58089_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:36 scaffold_23.1399307-1400290.comp58089_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 11:36 scaffold_23.1399900-1400941.comp58089_c17_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 58K Nov 8 11:35 scaffold_23.13.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 34K Nov 8 06:30 scaffold_23.13.drosophila.rb.out -rw-r--r-- 1 dstandag biol 1.5M Nov 8 12:05 scaffold_23.13.final.section -rw-r--r-- 1 dstandag biol 364K Nov 8 11:29 scaffold_23.13.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 430K Nov 8 11:33 scaffold_23.13.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 1.4M Nov 8 11:35 scaffold_23.13.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:30 scaffold_23.13.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1400609-1401459.comp55139_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1401269-1402022.comp55139_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1401609-1402216.comp55139_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:36 scaffold_23.1402425-1403729.comp53666_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:00 scaffold_23.140332-144653.comp32064_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1403482-1404578.comp48783_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1404302-1405136.comp56313_c10_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1404714-1405577.comp56313_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1404752-1405577.comp56313_c9_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1405378-1406432.comp58905_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406035-1406617.comp58905_c6_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406210-1406799.comp57287_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 11:36 scaffold_23.1406210-1408214.comp57287_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409289.comp57287_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409306.comp57287_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1408987-1409890.comp55527_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:36 scaffold_23.1409724-1410684.comp53099_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410284-1410885.comp53099_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1410463-1411098.comp53099_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410682-1411329.comp53099_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411082-1411787.comp53099_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:40 scaffold_23.1411196-1420373.gnl%7CAmel_4%2E5%7CGB48913-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1411769-1412299.comp53730_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411806-1412343.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 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2.1K Nov 8 11:46 scaffold_23.1628188-1628869.comp53690_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1628995-1629629.comp1757695_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:46 scaffold_23.1629447-1630245.comp2225268_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:51 scaffold_23.1630078-1640599.gnl%7CAmel_4%2E5%7CGB48912-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1633935-1634941.comp469996_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1634612-1635227.comp1032535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:46 scaffold_23.1634842-1635615.comp9891_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:46 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06:46 scaffold_23.47976-52664.comp57565_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481059-481744.comp5788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:15 scaffold_23.481631-482286.comp31314_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481869-482552.comp1406842_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K 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-rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:22 scaffold_23.4.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503515-504045.comp57130_c2_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503604-504201.comp59180_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:20 scaffold_23.503604-504204.comp59180_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.503604-504276.comp59180_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:20 scaffold_23.503604-504336.comp59180_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:20 scaffold_23.503654-504201.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:20 scaffold_23.503654-504350.comp59180_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503699-504221.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 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2.2K Nov 8 07:20 scaffold_23.570506-571138.comp58475_c5_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:47 scaffold_23.57128-61415.comp57935_c3_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 07:20 scaffold_23.577559-578709.comp58715_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 07:20 scaffold_23.577559-578885.comp58715_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.578520-579331.comp17262_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:20 scaffold_23.579634-580662.comp19872_c0_seq1.est_exonerate -rw-r--r-- 1 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dstandag biol 4.5K Nov 8 07:20 scaffold_23.588308-588965.comp58681_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:20 scaffold_23.588513-589494.comp58681_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:21 scaffold_23.588513-589516.comp58681_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:26 scaffold_23.589528-590438.comp56568_c1_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 07:26 scaffold_23.590043-590860.comp56568_c1_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:26 scaffold_23.590182-590860.comp56568_c1_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CAmel_4%2E5%7CGB42672-PA.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0291239.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0293789.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 08:01 scaffold_23.590687-592189.gnl%7CDmel_r5%2E47%7CFBpp0071071.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0081035.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303794.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303795.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303796.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590885-592138.gnl%7CAmel_4%2E5%7CGB44981-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590894-591937.gnl%7CAmel_4%2E5%7CGB44980-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590909-591693.gnl%7CDmel_r5%2E47%7CFBpp0083755.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:26 scaffold_23.591776-592368.comp42067_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.592659-593271.comp59308_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.592659-593380.comp59308_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:26 scaffold_23.592965-593648.comp48548_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.593120-593648.comp48548_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:26 scaffold_23.593237-593841.comp59308_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.594070-594730.comp1421803_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:26 scaffold_23.599941-600713.comp58738_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 47K Nov 8 07:25 scaffold_23.5.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 49K Nov 8 06:22 scaffold_23.5.drosophila.rb.out -rw-r--r-- 1 dstandag biol 917K Nov 8 12:05 scaffold_23.5.final.section -rw-r--r-- 1 dstandag biol 730K Nov 8 07:19 scaffold_23.5.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 416K Nov 8 07:23 scaffold_23.5.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 976K Nov 8 07:25 scaffold_23.5.raw.section -rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:23 scaffold_23.5.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.600393-600917.comp59155_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:26 scaffold_23.600937-601763.comp1225959_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 08:01 scaffold_23.604967-608877.gnl%7CAmel_4%2E5%7CGB43104-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.606823-608989.comp51953_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:26 scaffold_23.608733-612437.comp56721_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:27 scaffold_23.608733-612437.comp56721_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609085-612369.gnl%7CAmel_4%2E5%7CGB54556-PA.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0070184.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303734.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303735.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0071164.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0304872.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.61000-61642.comp57935_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:01 scaffold_23.612645-614365.gnl%7CAmel_4%2E5%7CGB43132-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.612828-614317.gnl%7CDmel_r5%2E47%7CFBpp0074633.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.613400-614111.gnl%7CDmel_r5%2E47%7CFBpp0075906.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:26 scaffold_23.614151-614876.comp1433111_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:27 scaffold_23.614490-616677.comp62542_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615220-616300.gnl%7CDmel_r5%2E47%7CFBpp0080690.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615229-616300.gnl%7CAmel_4%2E5%7CGB48404-PA.p_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 07:30 scaffold_23.616573-622123.comp53298_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 06:55 scaffold_23.61662-63231.gnl%7CAmel_4%2E5%7CGB47823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:01 scaffold_23.617032-621897.gnl%7CAmel_4%2E5%7CGB43186-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.617361-621707.gnl%7CDmel_r5%2E47%7CFBpp0078372.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 06:49 scaffold_23.62025-63600.comp57576_c4_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 scaffold_23.62037-63192.gnl%7CDmel_r5%2E47%7CFBpp0070204.p_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 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-rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:27 scaffold_23.622010-624802.comp57205_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 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dstandag biol 9.8K Nov 8 07:27 scaffold_23.622010-625026.comp57205_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:30 scaffold_23.622010-625026.comp57205_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:28 scaffold_23.622010-625026.comp57205_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:30 scaffold_23.622010-625178.comp57205_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:27 scaffold_23.622010-625178.comp57205_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 scaffold_23.622010-625178.comp57205_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 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-rw-r--r-- 1 dstandag biol 6.9K Nov 8 08:01 scaffold_23.635723-637373.gnl%7CDmel_r5%2E47%7CFBpp0082101.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:30 scaffold_23.637770-638562.comp42460_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:30 scaffold_23.638373-640543.comp40473_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649502.gnl%7CAmel_4%2E5%7CGB43214-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649511.gnl%7CDmel_r5%2E47%7CFBpp0292225.p_exonerate -rw-r--r-- 1 dstandag biol 27K Nov 8 08:01 scaffold_23.638434-649538.gnl%7CAmel_4%2E5%7CGB45049-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.638434-649601.gnl%7CDmel_r5%2E47%7CFBpp0288420.p_exonerate -rw-r--r-- 1 dstandag biol 55K Nov 8 08:01 scaffold_23.638434-650174.gnl%7CAmel_4%2E5%7CGB49952-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638437-649103.gnl%7CAmel_4%2E5%7CGB42359-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638440-647567.gnl%7CAmel_4%2E5%7CGB55144-PA.p_exonerate -rw-r--r-- 1 dstandag biol 28K Nov 8 08:01 scaffold_23.638440-649430.gnl%7CDmel_r5%2E47%7CFBpp0293284.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638443-649532.gnl%7CAmel_4%2E5%7CGB42373-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.63987-64717.comp59376_c14_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 07:30 scaffold_23.640205-641458.comp934535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.641067-641742.comp17454_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 08:01 scaffold_23.641259-642288.gnl%7CAmel_4%2E5%7CGB41007-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K Nov 8 07:30 scaffold_23.641345-642764.comp17454_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:30 scaffold_23.642369-643170.comp1226599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.642760-643453.comp3200316_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.64294-84968.comp42086_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:01 scaffold_23.645509-646340.gnl%7CAmel_4%2E5%7CGB49823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.647483-648154.comp3284778_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:55 scaffold_23.649-1243.gnl%7CDmel_r5%2E47%7CFBpp0290776.p_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:01 scaffold_23.649971-651261.gnl%7CAmel_4%2E5%7CGB49951-PA.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:30 scaffold_23.651850-655866.comp56215_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 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Nov 8 08:02 scaffold_23.659787-662130.gnl%7CDmel_r5%2E47%7CFBpp0293463.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075012.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075013.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0073292.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:02 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0290751.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0304481.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659802-662082.gnl%7CDmel_r5%2E47%7CFBpp0075772.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659802-662088.gnl%7CDmel_r5%2E47%7CFBpp0293948.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662097.gnl%7CAmel_4%2E5%7CGB47477-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662121.gnl%7CAmel_4%2E5%7CGB41363-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662139.gnl%7CAmel_4%2E5%7CGB43707-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662290.gnl%7CAmel_4%2E5%7CGB51586-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662299.gnl%7CAmel_4%2E5%7CGB49425-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0089153.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0290826.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304233.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304234.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0305596.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659808-662094.gnl%7CAmel_4%2E5%7CGB52193-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CAmel_4%2E5%7CGB47284-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0076890.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0085042.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB44431-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB49047-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083843.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083906.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659817-662079.gnl%7CAmel_4%2E5%7CGB46102-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0073585.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0082346.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0305521.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:31 scaffold_23.664598-665339.comp57441_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.664951-665488.comp59321_c5_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 06:55 scaffold_23.66506-67079.gnl%7CAmel_4%2E5%7CGB47837-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088318.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088319.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088320.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089257.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089258.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0288398.p_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:31 scaffold_23.665135-665802.comp285497_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 07:31 scaffold_23.665399-666883.comp53689_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.666469-667197.comp53689_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.667162-667951.comp52180_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:31 scaffold_23.667162-671428.comp52180_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 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dstandag biol 3.3K Nov 8 07:31 scaffold_23.667978-669042.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 07:31 scaffold_23.668017-669001.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 07:31 scaffold_23.668059-668959.comp59180_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.668936-669683.comp382769_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.66912-67979.comp5946_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:31 scaffold_23.669726-671764.comp52180_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 06:49 scaffold_23.67030-67979.comp5946_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:31 scaffold_23.671029-677447.comp52180_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.671054-671764.comp52180_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.671886-672575.comp57527_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671901-672561.comp57527_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672538.comp57527_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672575.comp57527_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41577-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41578-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB46989-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB50263-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.672098-672598.comp59502_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:31 scaffold_23.672970-673610.comp59089_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 07:31 scaffold_23.673324-674422.comp53293_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:31 scaffold_23.673999-677447.comp52180_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076415.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076416.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302862.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302863.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302864.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0081016.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0304068.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.675963-676551.comp408860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:31 scaffold_23.677207-677898.comp772804_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 06:49 scaffold_23.67721-68472.comp350940_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.677525-678233.comp53322_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 scaffold_23.677908-678920.comp53322_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:31 scaffold_23.677908-679249.comp53322_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.9K Nov 8 07:31 scaffold_23.678839-682919.comp32442_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:31 scaffold_23.679979-680866.comp36035_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 07:31 scaffold_23.679979-681267.comp36035_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.1M Nov 8 11:03 scaffold_23.6-7.raw.section -rw-r--r-- 1 dstandag biol 1.8K Nov 8 07:31 scaffold_23.680259-680866.comp36035_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.680259-681267.comp36035_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 08:02 scaffold_23.680843-682232.gnl%7CAmel_4%2E5%7CGB50275-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 08:02 scaffold_23.680846-682172.gnl%7CDmel_r5%2E47%7CFBpp0070979.p_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:50 scaffold_23.682524-683916.comp33074_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:44 scaffold_23.683503-684184.comp59066_c0_seq140.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:46 scaffold_23.683503-688813.comp59066_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:35 scaffold_23.683503-688813.comp59066_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:53 scaffold_23.683503-688813.comp59066_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:50 scaffold_23.683503-688813.comp59066_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:33 scaffold_23.683503-688813.comp59066_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:55 scaffold_23.683503-688813.comp59066_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:37 scaffold_23.683503-688813.comp59066_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:36 scaffold_23.683503-688813.comp59066_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:44 scaffold_23.683503-688813.comp59066_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683763-688813.comp59066_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683882-688813.comp59066_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:36 scaffold_23.683882-688813.comp59066_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:48 scaffold_23.683882-688813.comp59066_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:51 scaffold_23.683882-688813.comp59066_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:56 scaffold_23.683882-688813.comp59066_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:47 scaffold_23.683882-688813.comp59066_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:32 scaffold_23.683882-688813.comp59066_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:42 scaffold_23.683882-688813.comp59066_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:49 scaffold_23.683882-688813.comp59066_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:50 scaffold_23.683882-688813.comp59066_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:35 scaffold_23.683988-688813.comp59066_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:32 scaffold_23.684333-688813.comp59066_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:49 scaffold_23.684333-688813.comp59066_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:51 scaffold_23.684333-688813.comp59066_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:52 scaffold_23.684333-688813.comp59066_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:54 scaffold_23.684333-688813.comp59066_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:33 scaffold_23.684333-688813.comp59066_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:44 scaffold_23.684333-688813.comp59066_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:39 scaffold_23.684333-688813.comp59066_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:43 scaffold_23.684333-688975.comp59066_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:53 scaffold_23.684333-688975.comp59066_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:45 scaffold_23.684333-688975.comp59066_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:55 scaffold_23.684333-688975.comp59066_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721817.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721839.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 12K Nov 8 07:56 scaffold_23.684971-688813.comp59066_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.684971-688813.comp59066_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.684971-688813.comp59066_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:42 scaffold_23.684971-688813.comp59066_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:37 scaffold_23.684971-688975.comp59066_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:41 scaffold_23.684971-688975.comp59066_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.684975-688813.comp59066_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:39 scaffold_23.684975-688813.comp59066_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.684975-688813.comp59066_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.684975-688813.comp59066_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:45 scaffold_23.684975-688975.comp59066_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:53 scaffold_23.684975-688975.comp59066_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq2%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 12K Nov 8 07:38 scaffold_23.685264-688813.comp59066_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.685264-688813.comp59066_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.685264-688813.comp59066_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685264-688813.comp59066_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685264-688813.comp59066_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:52 scaffold_23.685264-688813.comp59066_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:32 scaffold_23.685264-688813.comp59066_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685264-688813.comp59066_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:37 scaffold_23.685264-688975.comp59066_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.685264-688975.comp59066_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685264-688975.comp59066_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685334-688813.comp59066_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685334-688813.comp59066_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685334-688813.comp59066_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:48 scaffold_23.685334-688813.comp59066_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685334-688813.comp59066_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:49 scaffold_23.685334-688813.comp59066_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685334-688975.comp59066_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:46 scaffold_23.685334-688975.comp59066_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.685334-688975.comp59066_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.68540-69483.comp433_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 11:02 scaffold_23.685479.720745.0.gnl%7CAmel_4%2E5%7CGB49172-PA%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072421%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072422%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0290562%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304412%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304413%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304414%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 11K Nov 8 07:44 scaffold_23.685588-688813.comp59066_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685588-688813.comp59066_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:33 scaffold_23.685588-688813.comp59066_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:51 scaffold_23.685588-688813.comp59066_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:32 scaffold_23.685588-688813.comp59066_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:49 scaffold_23.685588-688813.comp59066_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:52 scaffold_23.685801-688813.comp59066_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:41 scaffold_23.685801-688813.comp59066_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:44 scaffold_23.685801-688813.comp59066_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:42 scaffold_23.685801-688813.comp59066_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:46 scaffold_23.685801-688813.comp59066_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:54 scaffold_23.685801-688813.comp59066_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:51 scaffold_23.685801-688813.comp59066_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:45 scaffold_23.685801-688975.comp59066_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:42 scaffold_23.685801-688975.comp59066_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:32 scaffold_23.685801-688975.comp59066_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:37 scaffold_23.685801-688975.comp59066_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:38 scaffold_23.686019-688813.comp59066_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:37 scaffold_23.686019-688813.comp59066_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 07:52 scaffold_23.686019-688813.comp59066_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:42 scaffold_23.686019-688813.comp59066_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:45 scaffold_23.686019-688975.comp59066_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:56 scaffold_23.686019-688975.comp59066_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:32 scaffold_23.686019-688975.comp59066_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:55 scaffold_23.686019-688975.comp59066_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:52 scaffold_23.686019-688975.comp59066_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:43 scaffold_23.686506-688813.comp59066_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686506-688813.comp59066_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:48 scaffold_23.686506-688813.comp59066_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:38 scaffold_23.686506-688813.comp59066_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:54 scaffold_23.686506-688813.comp59066_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:34 scaffold_23.686506-688813.comp59066_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:44 scaffold_23.686506-688813.comp59066_c0_seq135.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:35 scaffold_23.686506-688975.comp59066_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:51 scaffold_23.686506-688975.comp59066_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:43 scaffold_23.686506-688975.comp59066_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:38 scaffold_23.686506-688975.comp59066_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:51 scaffold_23.686591-688813.comp59066_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686591-688813.comp59066_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:44 scaffold_23.686591-688813.comp59066_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:32 scaffold_23.686591-688813.comp59066_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:41 scaffold_23.686591-688813.comp59066_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:54 scaffold_23.686591-688975.comp59066_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:39 scaffold_23.686591-688975.comp59066_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:56 scaffold_23.686591-688975.comp59066_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:40 scaffold_23.686591-688975.comp59066_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:46 scaffold_23.686591-688975.comp59066_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:45 scaffold_23.686591-688975.comp59066_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:49 scaffold_23.686979-688813.comp59066_c0_seq136.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:51 scaffold_23.686979-688813.comp59066_c0_seq139.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:39 scaffold_23.686979-688975.comp59066_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:51 scaffold_23.686979-688975.comp59066_c0_seq137.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:54 scaffold_23.686979-688975.comp59066_c0_seq138.est_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 07:56 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scaffold_23.690234-691062.comp58228_c7_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 06:49 scaffold_23.69062-69744.comp433_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 08:03 scaffold_23.692420-694948.comp51249_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 08:03 scaffold_23.694556-695181.comp839860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 scaffold_23.695279-710945.gnl%7CAmel_4%2E5%7CGB49172-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072421.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072422.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0290562.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304412.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304413.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 08:03 scaffold_23.696083-696661.comp59447_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 08:03 scaffold_23.696083-696714.comp59447_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 08:03 scaffold_23.696083-696748.comp59447_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:03 scaffold_23.696083-696759.comp59447_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 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dstandag biol 957K Nov 8 08:01 scaffold_23.6.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 30K Nov 8 06:23 scaffold_23.6.drosophila.rb.out -rw-r--r-- 1 dstandag biol 4.8M Nov 8 12:05 scaffold_23.6.final.section -rw-r--r-- 1 dstandag biol 2.7M Nov 8 07:25 scaffold_23.6.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 1.2M Nov 8 07:59 scaffold_23.6.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 5.5M Nov 8 08:02 scaffold_23.6.raw.section -rw-r--r-- 1 dstandag biol 562K Nov 8 06:24 scaffold_23.6.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.70076-70676.comp16610_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0089425.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0290563.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0304411.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.70266-70881.comp1005591_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.71180-72221.comp36225_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:03 scaffold_23.712367-714691.gnl%7CAmel_4%2E5%7CGB49161-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 08:03 scaffold_23.712520-713560.comp54814_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:03 scaffold_23.712520-713766.comp54814_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 scaffold_23.712609-713560.comp54814_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.712609-713766.comp54814_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:50 scaffold_23.716125-720215.comp58983_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:04 scaffold_23.716125-720215.comp58983_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:47 scaffold_23.716125-720215.comp58983_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:46 scaffold_23.716125-720215.comp58983_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:45 scaffold_23.716125-720215.comp58983_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:51 scaffold_23.716125-720215.comp58983_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720215.comp58983_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.716125-720215.comp58983_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:06 scaffold_23.716125-720215.comp58983_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:53 scaffold_23.716125-720628.comp58983_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:03 scaffold_23.716125-720628.comp58983_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-720628.comp58983_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:48 scaffold_23.716125-720628.comp58983_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:51 scaffold_23.716125-720628.comp58983_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:06 scaffold_23.716125-720628.comp58983_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720628.comp58983_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720628.comp58983_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720628.comp58983_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:50 scaffold_23.716125-720628.comp58983_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:05 scaffold_23.716125-720628.comp58983_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721166.comp58983_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:07 scaffold_23.716125-721166.comp58983_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:03 scaffold_23.716125-721166.comp58983_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:05 scaffold_23.716125-721166.comp58983_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:51 scaffold_23.716125-721166.comp58983_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:08 scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:46 scaffold_23.716125-721460.comp58983_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721460.comp58983_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:45 scaffold_23.716125-721460.comp58983_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:53 scaffold_23.716125-721460.comp58983_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-721460.comp58983_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:48 scaffold_23.716125-721460.comp58983_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:44 scaffold_23.716125-721460.comp58983_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:52 scaffold_23.716125-721460.comp58983_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-721720.comp58983_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:46 scaffold_23.716125-721720.comp58983_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:45 scaffold_23.716125-721720.comp58983_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 08:06 scaffold_23.716125-721720.comp58983_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:48 scaffold_23.716125-721720.comp58983_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:47 scaffold_23.716125-721720.comp58983_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:53 scaffold_23.716125-721720.comp58983_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:45 scaffold_23.716125-722098.comp58983_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:48 scaffold_23.716125-722098.comp58983_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:53 scaffold_23.716125-722098.comp58983_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:50 scaffold_23.716125-722098.comp58983_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:05 scaffold_23.716125-722098.comp58983_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-722098.comp58983_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:47 scaffold_23.716125-722098.comp58983_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-722098.comp58983_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:46 scaffold_23.716125-722428.comp58983_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:08 scaffold_23.716125-722428.comp58983_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:49 scaffold_23.716125-722428.comp58983_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:53 scaffold_23.716125-722428.comp58983_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:06 scaffold_23.716125-722428.comp58983_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:05 scaffold_23.716125-722428.comp58983_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:47 scaffold_23.716125-722428.comp58983_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-722428.comp58983_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 08:04 scaffold_23.716125-722428.comp58983_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:50 scaffold_23.716125-722757.comp58983_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:05 scaffold_23.716125-722757.comp58983_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:52 scaffold_23.716125-722757.comp58983_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722757.comp58983_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:47 scaffold_23.716125-723330.comp58983_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:05 scaffold_23.716125-723330.comp58983_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:04 scaffold_23.716125-723330.comp58983_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:44 scaffold_23.716125-723330.comp58983_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:51 scaffold_23.716125-723330.comp58983_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:48 scaffold_23.716125-723330.comp58983_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:07 scaffold_23.716125-723330.comp58983_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:45 scaffold_23.716125-723330.comp58983_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 10:47 scaffold_23.716125-725421.comp58983_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:46 scaffold_23.716125-725421.comp58983_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:05 scaffold_23.716125-725421.comp58983_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:04 scaffold_23.716125-725421.comp58983_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:45 scaffold_23.716125-725421.comp58983_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:49 scaffold_23.716125-725421.comp58983_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:49 scaffold_23.716125-728040.comp58983_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:48 scaffold_23.716125-728040.comp58983_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:47 scaffold_23.716125-728040.comp58983_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:06 scaffold_23.716125-728040.comp58983_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:04 scaffold_23.716125-728040.comp58983_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 06:55 scaffold_23.7171-17933.gnl%7CAmel_4%2E5%7CGB46618-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070125.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070126.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070127.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070128.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291468.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291469.p_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 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dstandag biol 3.2K Nov 8 10:53 scaffold_23.728443-729727.comp45774_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.729783-730395.comp2904457_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 10:53 scaffold_23.730057-730704.comp1503238_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:49 scaffold_23.73016-73676.comp16138_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 scaffold_23.731277-731906.comp1893859_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.733065-733673.comp3350191_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.73345-73945.comp16138_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 10:53 scaffold_23.734599-735763.comp1287295_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.73525-74446.comp9823_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 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-rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0290962.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303730.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303731.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:03 scaffold_23.748248-752313.gnl%7CAmel_4%2E5%7CGB49163-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:49 scaffold_23.75148-75896.comp276986_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:56 scaffold_23.751890-761021.comp49210_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:55 scaffold_23.751890-761021.comp49210_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:54 scaffold_23.751890-761021.comp49210_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:03 scaffold_23.752357-755378.gnl%7CAmel_4%2E5%7CGB49169-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K 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11:03 scaffold_23.772644-773319.gnl%7CDmel_r5%2E47%7CFBpp0075479.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773322.gnl%7CAmel_4%2E5%7CGB48430-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773325.gnl%7CDmel_r5%2E47%7CFBpp0077688.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773328.gnl%7CDmel_r5%2E47%7CFBpp0071844.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773349.gnl%7CAmel_4%2E5%7CGB40139-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772647-773280.gnl%7CDmel_r5%2E47%7CFBpp0072463.p_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 06:49 scaffold_23.77438-78155.comp13284_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 10:57 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Name: scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 Type: application/octet-stream Size: 4811 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 27 15:39:18 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:39:18 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Hello Carson, Just to confirm, Is there a script that would filter gene models at specific AED score. Alternatively if I were to do this within maker with regards to parameters in maker_opts.ctl file I would have to provide my predicted genes gff3 file to model_gff and set AED_threshold at desired threshold? Thanks and regards, Parul Kudtarkar > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From parulk at caltech.edu Tue Nov 27 15:41:12 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:41:12 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Message-ID: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From dence at genetics.utah.edu Tue Nov 27 15:55:49 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 27 Nov 2012 22:55:49 +0000 Subject: [maker-devel] AED score In-Reply-To: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: Hi Parul, I think the way you described (with the maker_opts.ctl file) is how you want to proceed. You still need to give the genome too. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] Sent: Tuesday, November 27, 2012 3:41 PM To: Parul Kudtarkar Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] AED score Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Tue Nov 27 15:59:22 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:59:22 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: <3841.131.215.15.234.1354057162.squirrel@webmail.caltech.edu> Thanks for quick response Daniel, I'll do it through maker. > Hi Parul, > > I think the way you described (with the maker_opts.ctl file) is how you > want to proceed. You still need to give the genome too. > > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar > [parulk at caltech.edu] > Sent: Tuesday, November 27, 2012 3:41 PM > To: Parul Kudtarkar > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] AED score > > Also, are there any other parameters that are required when filtering > based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >> parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>> may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>> 20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>> how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From kapeelc at gmail.com Tue Nov 27 18:23:12 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Tue, 27 Nov 2012 18:23:12 -0700 Subject: [maker-devel] Maker error message Message-ID: Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Nov 27 18:38:33 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 01:38:33 +0000 Subject: [maker-devel] Maker error message In-Reply-To: References: Message-ID: Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Nov 27 20:39:56 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 27 Nov 2012 22:39:56 -0500 Subject: [maker-devel] AED score In-Reply-To: Message-ID: Use the AED_threshold option in the maker_opts.ctl file if you just want to restrict final gene models to close matches directly within maker. On the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset for SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. Thanks, Carson On 12-11-27 5:55 PM, "Daniel Ence" wrote: >Hi Parul, > >I think the way you described (with the maker_opts.ctl file) is how you >want to proceed. You still need to give the genome too. > >Daniel > > >Daniel Ence >Graduate Student >Eccles Institute of Human Genetics >University of Utah >15 North 2030 East, Room 2100 >Salt Lake City, UT 84112-5330 >________________________________________ >From: maker-devel-bounces at yandell-lab.org >[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >Sent: Tuesday, November 27, 2012 3:41 PM >To: Parul Kudtarkar >Cc: maker-devel at yandell-lab.org >Subject: Re: [maker-devel] AED score > >Also, are there any other parameters that are required when filtering >based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >>parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>>may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>>20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>>how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From dence at genetics.utah.edu Wed Nov 28 12:25:22 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 19:25:22 +0000 Subject: [maker-devel] Maker error message In-Reply-To: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Hi Kapeel,? Please keep this discussion on the maker-devel group, so we can get everyone's input to help resolve this issue with maker.? Can you sen me the maker_opts file that you were using? The options that might be relevant include the libraries you were giving repeatrunner and repeatmasker. Thanks, Daniel? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: kapeelc at gmail.com [kapeelc at gmail.com] Sent: Wednesday, November 28, 2012 11:39 AM To: Daniel Ence Subject: Re: Maker error message Hi Daniel, Here is the output around the error: j_size:94 current j:76 j_size:94 current j:77 j_size:94 current j:78 j_size:94 current j:79 j_size:94 current j:80 j_size:94 current j:81 j_size:94 current j:82 j_size:94 current j:83 j_size:94 current j:84 j_size:94 current j:85 j_size:94 current j:86 j_size:94 current j:87 j_size:94 current j:88 j_size:94 current j:89 j_size:94 current j:90 j_size:94 current j:91 j_size:94 current j:92 j_size:94 current j:93 ...finished clustering. re reading repeat masker report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out re reading blast report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner deleted:1 hits in cluster::shadow_cluster... DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 --Next Contig-- Processing run.log file... Maker is now finished!!! For RepeatMasker I am using wublast as the search engine. The run log had this: LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 DIED RANK 0 DIED COUNT 2 Is there way to skip the the failed chunk and move forward?? Thanks Kapeel Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Quoted from: http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html From kapeelc at gmail.com Wed Nov 28 13:15:13 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Wed, 28 Nov 2012 13:15:13 -0700 Subject: [maker-devel] Maker error message In-Reply-To: References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get > everyone's input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that > might be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out > re reading blast report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're > running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html > -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4830 bytes Desc: not available URL: From carsonhh at gmail.com Thu Nov 29 07:22:42 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:22:42 -0500 Subject: [maker-devel] AED score In-Reply-To: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Message-ID: There are certain characteristics that are apparent in this contig. First it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many of them to align spuriously which produces very short gene models that are more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial bias to get back very short and incomplete models. How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as well as get an estimate of fragmentation as one of the statistics produced is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), and if they are distantly related to other annotated species few proteins may align to the contigs because the introns in the alignments tend to be so long and exons so short that it pushes down the significance scores too much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. Thanks, Carson On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >Dear Carson and Daniel, > >Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 >genes with AED score less than 0.75. However there were no genes predicted >in the output file(see attached file Scaffold1_out). I have also attached >the maker_opts.ctl. Could you please advice on this. > >Thanks and regards, >Parul Kudtarkar > >> Use the AED_threshold option in the maker_opts.ctl file if you just want >> to restrict final gene models to close matches directly within maker. >>On >> the other hand, if you are trying to build a dataset for training gene >> predictors, use the maker2zff script for generating a filtered dataset >>for >> SNAP training. There are a number of filters available. Just call the >> script once without parameters to see the options. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >> >>>Hi Parul, >>> >>>I think the way you described (with the maker_opts.ctl file) is how you >>>want to proceed. You still need to give the genome too. >>> >>>Daniel >>> >>> >>>Daniel Ence >>>Graduate Student >>>Eccles Institute of Human Genetics >>>University of Utah >>>15 North 2030 East, Room 2100 >>>Salt Lake City, UT 84112-5330 >>>________________________________________ >>>From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>>[parulk at caltech.edu] >>>Sent: Tuesday, November 27, 2012 3:41 PM >>>To: Parul Kudtarkar >>>Cc: maker-devel at yandell-lab.org >>>Subject: Re: [maker-devel] AED score >>> >>>Also, are there any other parameters that are required when filtering >>>based on AED score? >>> >>>> Hello Carson, >>>> >>>> Just to confirm, Is there a script that would filter gene models at >>>> specific AED score. >>>> Alternatively if I were to do this within maker with regards to >>>>parameters >>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>> file to model_gff and set AED_threshold at desired threshold? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>>> worst >>>>> as >>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>> require better matching to the evidence by setting it closer to 0. >>>>>You >>>>> can >>>>> also try to increase protein homology evidence as some of your calls >>>>>may >>>>> be split genes due to lack of evidence linking them. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>>Dear Maker community, >>>>>> >>>>>>For gene-prediction I get training data-set from evidence based >>>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>>predictions, followed by boot-strapping. I would typically expect >>>>>>20-30K >>>>>>genes however I am getting 8 times the expected gene count indicating >>>>>> too >>>>>>many false positives. Is there a way to further refine these >>>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>>how >>>>>>to go about this? >>>>>> >>>>>>Thanks and regards, >>>>>>Parul Kudtarkar >>>>>> >>>>>>-- >>>>>>Scientific Programmer >>>>>>Center for Computational Regulatory Genomics >>>>>>Beckman Institute, >>>>>>California Institute of Technology >>>>>>http://www.spbase.org >>>>>> >>>>>> >>>>>>_______________________________________________ >>>>>>maker-devel mailing list >>>>>>maker-devel at box290.bluehost.com >>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o >>>>>>rg >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 07:52:25 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:52:25 -0500 Subject: [maker-devel] Maker error message In-Reply-To: Message-ID: There should normally be more error message than that. The module used to capture the error returns the string "Died" without an end line character when there is a problem capturing the STDERR of the failure (and I see that phrase here), so could you run this again and see if it produces a different message the second time. Also I'm going to send you instructions on download the development version of MAKER in a separate message (off list). It is easier for me to make changes and have you test them immediately that way. Also there are already some bug fixes in the devel version so it's good to rule those out. Thanks, Carson From: Kapeel Chougule Date: Wednesday, 28 November, 2012 3:15 PM To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Maker error message Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get everyone's > input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that might > be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific > .out > re reading blast report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2 > Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 28 14:40:51 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 28 Nov 2012 13:40:51 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Dear Carson and Daniel, Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 genes with AED score less than 0.75. However there were no genes predicted in the output file(see attached file Scaffold1_out). I have also attached the maker_opts.ctl. Could you please advice on this. Thanks and regards, Parul Kudtarkar > Use the AED_threshold option in the maker_opts.ctl file if you just want > to restrict final gene models to close matches directly within maker. On > the other hand, if you are trying to build a dataset for training gene > predictors, use the maker2zff script for generating a filtered dataset for > SNAP training. There are a number of filters available. Just call the > script once without parameters to see the options. > > Thanks, > Carson > > > > > On 12-11-27 5:55 PM, "Daniel Ence" wrote: > >>Hi Parul, >> >>I think the way you described (with the maker_opts.ctl file) is how you >>want to proceed. You still need to give the genome too. >> >>Daniel >> >> >>Daniel Ence >>Graduate Student >>Eccles Institute of Human Genetics >>University of Utah >>15 North 2030 East, Room 2100 >>Salt Lake City, UT 84112-5330 >>________________________________________ >>From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>[parulk at caltech.edu] >>Sent: Tuesday, November 27, 2012 3:41 PM >>To: Parul Kudtarkar >>Cc: maker-devel at yandell-lab.org >>Subject: Re: [maker-devel] AED score >> >>Also, are there any other parameters that are required when filtering >>based on AED score? >> >>> Hello Carson, >>> >>> Just to confirm, Is there a script that would filter gene models at >>> specific AED score. >>> Alternatively if I were to do this within maker with regards to >>>parameters >>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>> file to model_gff and set AED_threshold at desired threshold? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>> worst >>>> as >>>> it is a distance metric. You can use the AED_threshold parameter to >>>> require better matching to the evidence by setting it closer to 0. You >>>> can >>>> also try to increase protein homology evidence as some of your calls >>>>may >>>> be split genes due to lack of evidence linking them. >>>> >>>> --Carson >>>> >>>> >>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Dear Maker community, >>>>> >>>>>For gene-prediction I get training data-set from evidence based >>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>predictions, followed by boot-strapping. I would typically expect >>>>>20-30K >>>>>genes however I am getting 8 times the expected gene count indicating >>>>> too >>>>>many false positives. Is there a way to further refine these >>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>how >>>>>to go about this? >>>>> >>>>>Thanks and regards, >>>>>Parul Kudtarkar >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1.gff Type: application/octet-stream Size: 594161 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1_out.gff Type: application/octet-stream Size: 371507 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4560 bytes Desc: not available URL: From mikael.durling at slu.se Thu Nov 29 09:20:10 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Thu, 29 Nov 2012 16:20:10 +0000 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids Message-ID: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Hello all, I'm running Maker (2.26 / r956 from svn) with a previous run in the input as maker_gff. However, the maker mpi ranks quit stop one after another with the following error messages. prepare section files Gathering GFF3 input into hits - chunk:3 ERROR: Non-unique top level ID for While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. --> rank=4, hostname=my-mgrid2 ERROR: Failed while prepare section files ERROR: Chunk failed at level:12, tier_type:2 FAILED CONTIG:scf_89936 In the end no ranks are running, but maker doesn't quit. Checking the maker_gff input, I do find duplicated ids, as this sample: scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.082870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.082870 but not for the scaffold found in the error message above. Are those two errors unrelated? If I run maker without providing a maker_gff the run works fine. Any input on this issue would be appreciated as I would like the reannotation to work in order to carry forward human readable names. cheers, Mikael ------------------------------------- Mikael Brandstr?m Durling, PhD Assistant Professor Sveriges lantbruksuniversitet Swedish University of Agricultural Sciences Uppsala BioCenter Dept of Forest Mycology and Plant Pathology Box 7026, 75007 Uppsala Visiting address: Almas All? 5 Telefon: 018-671503 mikael.durling at slu.se, www.slu.se/mykopat From carsonhh at gmail.com Thu Nov 29 09:23:39 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 11:23:39 -0500 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Message-ID: You can get the fixed version by doing svn update inside the maker directory. I will be changing the download version to 2.27 on yandell0lab.org, probably this weekend. Thanks, Carson On 12-11-29 11:20 AM, "Mikael Brandstr?m Durling" wrote: >Hello all, > >I'm running Maker (2.26 / r956 from svn) with a previous run in the input >as maker_gff. However, the maker mpi ranks quit stop one after another >with the following error messages. > >prepare section files >Gathering GFF3 input into hits - chunk:3 >ERROR: Non-unique top level ID for >While this is technically legal in GFF3, it usually >indicates a poorly fomatted GFF3 file (perhaps you >tried to merge two GFF3 files without accounting for >unique IDs). MAKER will not handle these correctly. > >--> rank=4, hostname=my-mgrid2 >ERROR: Failed while prepare section files >ERROR: Chunk failed at level:12, tier_type:2 >FAILED CONTIG:scf_89936 > >In the end no ranks are running, but maker doesn't quit. > >Checking the maker_gff input, I do find duplicated ids, as this sample: > >scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158 >:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 >scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.0 >82870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.08287 >0 > >but not for the scaffold found in the error message above. Are those two >errors unrelated? > >If I run maker without providing a maker_gff the run works fine. > >Any input on this issue would be appreciated as I would like the >reannotation to work in order to carry forward human readable names. > >cheers, >Mikael > > > > >------------------------------------- >Mikael Brandstr?m Durling, PhD >Assistant Professor > >Sveriges lantbruksuniversitet >Swedish University of Agricultural Sciences > >Uppsala BioCenter >Dept of Forest Mycology and Plant Pathology >Box 7026, 75007 Uppsala >Visiting address: Almas All? 5 >Telefon: 018-671503 >mikael.durling at slu.se, www.slu.se/mykopat > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Thu Nov 29 17:31:40 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Thu, 29 Nov 2012 16:31:40 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Thanks for the guidance Carson, total contig size is 330,611 with N50 of 39.17kb. I agree we have short ESTs. So this is the possible reason when filtering based on AED score 0.75 there are no gene models predicted despite the model_gff file has few genes with scores less than 0.75? Thanks and regards, Parul Kudtarkar > There are certain characteristics that are apparent in this contig. First > it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many > of them to align spuriously which produces very short gene models that are > more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add > more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models > almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial > bias to get back very short and incomplete models. > > How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as > well as get an estimate of fragmentation as one of the statistics produced > is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter > and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. > > If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), > and if they are distantly related to other annotated species few proteins > may align to the contigs because the introns in the alignments tend to be > so long and exons so short that it pushes down the significance scores too > much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. > > Thanks, > Carson > > > > On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: > >>Dear Carson and Daniel, >>Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >> 5 >>genes with AED score less than 0.75. However there were no genes >> predicted >>in the output file(see attached file Scaffold1_out). I have also attached >>the maker_opts.ctl. Could you please advice on this. >>Thanks and regards, >>Parul Kudtarkar >>> Use the AED_threshold option in the maker_opts.ctl file if you just want >>> to restrict final gene models to close matches directly within maker. >>>On >>> the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset >>>for >>> SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. >>> Thanks, >>> Carson >>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>Hi Parul, >>>>I think the way you described (with the maker_opts.ctl file) is how you >>>>want to proceed. You still need to give the genome too. >>>>Daniel >>>>Daniel Ence >>>>Graduate Student >>>>Eccles Institute of Human Genetics >>>>University of Utah >>>>15 North 2030 East, Room 2100 >>>>Salt Lake City, UT 84112-5330 >>>>________________________________________ >>>>From: maker-devel-bounces at yandell-lab.org >>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] >>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>To: Parul Kudtarkar >>>>Cc: maker-devel at yandell-lab.org >>>>Subject: Re: [maker-devel] AED score >>>>Also, are there any other parameters that are required when filtering based on AED score? >>>>> Hello Carson, >>>>> Just to confirm, Is there a script that would filter gene models at specific AED score. >>>>> Alternatively if I were to do this within maker with regards to >>>>>parameters >>>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>>> file to model_gff and set AED_threshold at desired threshold? Thanks and regards, >>>>> Parul Kudtarkar >>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>>>>> as >>>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>You >>>>>> can >>>>>> also try to increase protein homology evidence as some of your calls >>>>>>may >>>>>> be split genes due to lack of evidence linking them. >>>>>> --Carson >>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>Dear Maker community, >>>>>>>For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K >>>>>>>genes however I am getting 8 times the expected gene count >>>>>>> indicating >>>>>>> too >>>>>>>many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes >>>>>>>how >>>>>>>to go about this? >>>>>>>Thanks and regards, >>>>>>>Parul Kudtarkar >>>>>>>-- >>>>>>>Scientific Programmer >>>>>>>Center for Computational Regulatory Genomics >>>>>>>Beckman Institute, >>>>>>>California Institute of Technology >>>>>>>http://www.spbase.org >>>>>>>_______________________________________________ >>>>>>>maker-devel mailing list >>>>>>>maker-devel at box290.bluehost.com >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o rg >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org _______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 18:39:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 20:39:31 -0500 Subject: [maker-devel] AED score In-Reply-To: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Message-ID: Wow 330,000 is a lot. a large portion of genes are likely to be partial at best. You should seriously consider using mRNAseq to capture those by using maker's est_gff option to pass in results from cufflinks or trinity. Also I wouldn't even try to annotate contigs less than 10kb in size, just have maker skip them by setting the min_contig filter in the maker_opts.ctl file. Thanks, Carson On 12-11-29 7:31 PM, "Parul Kudtarkar" wrote: >Thanks for the guidance Carson, total contig size is 330,611 with N50 of >39.17kb. I agree we have short ESTs. So this is the possible reason when >filtering based on AED score 0.75 there are no gene models predicted >despite the model_gff file has few genes with scores less than 0.75? > >Thanks and regards, >Parul Kudtarkar > >> There are certain characteristics that are apparent in this contig. >First >> it seems to be repeat rich with a very low gene density. You also have >very short ESTs, and because of the lengths you are probably getting >many >> of them to align spuriously which produces very short gene models that >are >> more than likely false positives or at the very least just a piece of a >gene. I would turn off est2genome as a predictor for this reason unless >you can get longer EST assemblies (i.e. From mRNAseq). Your protein >alignments also seem to be few and far between. You probably need to >add >> more proteins from a couple of related species, and you might consider >using protein2genome rather than est2genome as a predictor if you are >still working to generate a training set. Also est2genome produced >models >> almost always have an AED score near 0 so mixing est2genome with the >AED_threshold with such limited protein support does create an >artificial >> bias to get back very short and incomplete models. >> >> How many contigs do you have in total and what is the N50 value for the >assembly? If you have a large number of very short contigs, you will get >very inflated gene counts because you get genes split across contigs and >many contigs tend t be subtle rearrangements of other contigs just >assembled in a slightly different way (so you can get bits and pieces of >the same genes just rearranged). This scenario is another confounding >factor if using the est2genome predictor with short ESTs. I would >recommend running CEGMA to get an estimate for the genome completeness >as >> well as get an estimate of fragmentation as one of the statistics >produced >> is a percent of genes that are found complete (end to end) vs those that >are partial. CEGMA identifies house keeping genes that tend to be >shorter >> and less intron rich than other genes in the genome, so if CEGMA gives a >high partial percentage and a low complete percentage, then this pattern >can be expected to be even more exaggerated for other genes in the >genome. >> >> If your genome is highly fragmented or proteins do not align well then >there are other strategies. For example, some vertebrate genomes end up >having extremely fragmented assemblies (on the order of 100,000 >contigs), >> and if they are distantly related to other annotated species few >proteins >> may align to the contigs because the introns in the alignments tend to >be >> so long and exons so short that it pushes down the significance scores >too >> much. In those cases heavy mRNAseq seems to be the best if not only way >to get enough evidence to stitch gene models together. >> >> Thanks, >> Carson >> >> >> >> On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson and Daniel, >>>Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >>> 5 >>>genes with AED score less than 0.75. However there were no genes >>> predicted >>>in the output file(see attached file Scaffold1_out). I have also >attached >>>the maker_opts.ctl. Could you please advice on this. >>>Thanks and regards, >>>Parul Kudtarkar >>>> Use the AED_threshold option in the maker_opts.ctl file if you just >>>>want >>>> to restrict final gene models to close matches directly within maker. >>>>On >>>> the other hand, if you are trying to build a dataset for training gene >predictors, use the maker2zff script for generating a filtered dataset >>>>for >>>> SNAP training. There are a number of filters available. Just call the >script once without parameters to see the options. >>>> Thanks, >>>> Carson >>>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>>Hi Parul, >>>>>I think the way you described (with the maker_opts.ctl file) is how >you >>>>>want to proceed. You still need to give the genome too. >>>>>Daniel >>>>>Daniel Ence >>>>>Graduate Student >>>>>Eccles Institute of Human Genetics >>>>>University of Utah >>>>>15 North 2030 East, Room 2100 >>>>>Salt Lake City, UT 84112-5330 >>>>>________________________________________ >>>>>From: maker-devel-bounces at yandell-lab.org >>>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >>>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>>To: Parul Kudtarkar >>>>>Cc: maker-devel at yandell-lab.org >>>>>Subject: Re: [maker-devel] AED score >>>>>Also, are there any other parameters that are required when filtering >based on AED score? >>>>>> Hello Carson, >>>>>> Just to confirm, Is there a script that would filter gene models at >specific AED score. >>>>>> Alternatively if I were to do this within maker with regards to >>>>>>parameters >>>>>> in maker_opts.ctl file I would have to provide my predicted genes >>>>>>gff3 >>>>>> file to model_gff and set AED_threshold at desired threshold? >Thanks and regards, >>>>>> Parul Kudtarkar >>>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >worst >>>>>>> as >>>>>>> it is a distance metric. You can use the AED_threshold parameter >to >>>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>>You >>>>>>> can >>>>>>> also try to increase protein homology evidence as some of your >calls >>>>>>>may >>>>>>> be split genes due to lack of evidence linking them. >>>>>>> --Carson >>>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>>Dear Maker community, >>>>>>>>For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect >20-30K >>>>>>>>genes however I am getting 8 times the expected gene count >>>>>>>> indicating >>>>>>>> too >>>>>>>>many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if >yes >>>>>>>>how >>>>>>>>to go about this? >>>>>>>>Thanks and regards, >>>>>>>>Parul Kudtarkar >>>>>>>>-- >>>>>>>>Scientific Programmer >>>>>>>>Center for Computational Regulatory Genomics >>>>>>>>Beckman Institute, >>>>>>>>California Institute of Technology >>>>>>>>http://www.spbase.org >>>>>>>>_______________________________________________ >>>>>>>>maker-devel mailing list >>>>>>>>maker-devel at box290.bluehost.com >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab >>>>>>>>.o >rg >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > > > From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 02:20:19 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 01:20:19 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. Message-ID: Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 03:01:46 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 02:01:46 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: References: Message-ID: Hi Carson, when I tried running genemark as below, I see the *.lst files (protein & nuc fasta) produced. But no gtf2 at all... And no gms.log files at all. Any ideas? /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p 0 -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -a Enmo_susu.11.fsa Thanks, Gowthaman ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org] Sent: Sunday, November 04, 2012 1:20 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Chunk failed at level 6 error.. Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 07:18:24 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:18:24 -0500 Subject: [maker-devel] Conensus gene model In-Reply-To: <1640.131.215.15.234.1351728273.squirrel@webmail.caltech.edu> Message-ID: The way models are generated, it really doesn't so much matter where the protein alignments came from. Basically the protein alignment is just creating a region of potential CDS. MAKER than gives that region as a hint to the gene predictors, but the gene predictors really make the call on how to finally structure the gene based on their training sets. You can short circuit this by using the protein2genome option as a separate run with only your primary proteins. MAKER will then try and turn those protein alignments directly into genes. Results from that run can sometimes be useful for generating training sets as well, or can be passed back into MAKER as pred_gff so MAKEr has the option to turn those into models as an alternative to the models produced by the ab initio predictors. --Carson On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: >Hi Jason, thanks for directions on generating training-set for augustus. >Also as alignment evidence if we are providing protein sequences from the >primary organism as well as other closely related species is there an >option to give the primary protein file precedence over others? >At the moment I have all the proteins(from primary organism as well as >related species) into a single file as protein option in maker_opts.ctl > >Thanks and regards, >Parul Kudtarkar > >> Paul - >> >> I think I've posted on this before here if you are asking how to go from >> SNAP training to Augustus training. >> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >> >> I do this type of training a lot - here some pointers. >> >> I often train by generating models using cegma on the genome and get >>these >> 400 or so good models as my training set. when I have EST or RNA-Seq I >> use PASA to generate the best set of annotations. >> >> For CEGMA - then I run this script that comes with MAKER: >> cegma2zff output.cegma.gff genome.fa >> >> Then I follow the SNAP directions >> >> fathom genome.ann genome.dna -categorize 1000 >> fathom uni.ann uni.dna -export 1000 -plus >> mkdir MYGENOME >> cd MYGENOME >> forge ../export.ann ../export.dna --OPTIONS >> cd ../MYGENOME >> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >> >> I then also make the augustus training data like this running in the >> directory that has the export.ann and export.dna files: >> perl gene_prediction/zff2augustus_gbk.pl > train.gb >> >> using this script: >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>ff2augustus_gbk.pl >> >> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>and >> best models from PASA and incorporate all these data in to my SNAP >> training set, and then export again back to gbk for the augustus >>training. >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>asatraining2zff.pl >> >> Then you just need to run the Augustus training (autoAugTrain.pl) on the >> train.gb file. >> >> Jason >> >> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar wrote: >> >>> Hello Carson and maker community, >>> >>> Thank you very much for your guidelines on using the maker-pipeline. >>> Yes, >>> green sea urchin genome that we are trying to annotate. >>> We are running the on scaffolds and most of these scaffolds are small >>>in >>> size(very first genome assembly). We would typically expect 20,000 >>>genes >>> in this genome. So we are running maker using EST and proteins from the >>> genome and out-groups to generate training dataset for SNAP and >>> Augustus. >>> Depending on the resulting predictions we may bootstrap the predicted >>> genes once again using EST and proteins. >>> >>> Do you have any further suggestions? Also could you point how to >>>convert >>> training set generated for SNAP to be used as training set for Augustus >>> as >>> well? Would maker give equal weightage to SNAP and Augustus predictions >>> for generating gene model? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> One thing you seem to be missing is protein evidence. >>>> >>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>> recommend adding all proteins from the Strongylocentrotus purpuratus >>> genome, then throw in another Deuterstome of your choice. Perhaps you >>> should also add a couple of outgroup organisms like Nematostella >>> vectensis >>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>> adding >>> to many protostome outgroups (i.e. C. elegans and Drosophila) because a >>> big part of their evolution is gene loss (so distant cnidaria often >>> match >>>> deuterstomes better than most protostomes do). >>>> >>>> You could take the maker results when protein data is included and use >>> it >>>> to retrain SNAP again. >>>> >>>> Even a 22 kb contig is still really short. Is this genome primarily >>> constituted by short contigs like this? I would recommend running >>>CEGMA >>> once on this genome to get an appropriate estimate of how recoverable >>> the >>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>> Cegma >>>> will give you an estimate for genome completeness as well as estimates >>> of >>>> what percentage of genes will be found in their entirety and what >>> percent >>>> will be partial genes. This is important to do if your genome is >>> fragmented as it will give you a reasonable expectation of what you can >>> expected to recover (as short contigs don't annotate very well - you >>> tend >>>> to loose a lot). >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>> >>>>> Hi Carson, >>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>as >>>>> 3 >>> exons EST alignments. Could you please recommend additional training. >>>We >>> are currently running maker on the entire contig set and eventually >>> merge >>>>> all the gff3 contig predictions. The using suggested >>>>>parameter/methods >>> we >>>>> would like to get a consensus gene-set with minimal false >>>>> positives/negatives. >>>>> Thanks, >>>>> Parul >>>>>> The contig in question is really too small to get much out of it >>>>>> (only 5 >>>>> kb). There was only one single exon EST alignments and a couple of >>> predictions with no evidence support. Anything smaller than 10 kb is >>> mostly useless for annotation purposes. You would really need a few >>> 100kb >>>>>> length or longer contigs to glean enough information for optimizing >>>>>> your >>>>> parameters. >>>>>> The general suggestions for any maker run are to use proteins from a >>>>> closely related organism or a couple of closely related organisms for >>>>> the >>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>> for >>>>> certain eukaryotes that have a bias for single exon transcripts (i.e. >>>>> some >>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>> initio >>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>> positives). >>>>>> Additional training would really depend on what your other contigs >>> look >>>>> like. Do you have any large contigs? I could look at one of those >>>>> and >>> give suggestions but the provided contig is just too short to glean >>> much. >>>>>> Thanks, >>>>>> Carson >>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>> Hello, >>>>>>> Please advice on the aforementioned query? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> ---------------------------- Original Message >>>>>>> ---------------------------- >>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>> From: "Parul Kudtarkar" >>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>> To: maker-devel at yandell-lab.org >>>>>>> >>>>>>>-------------------------------------------------------------------- >>>>>>>---- >>> -- >>>>> Hi, >>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>est,protein >>>>>>> and >>>>> contig file), agustus,genemarkE(we ran it outside maker and have gff3 >>>>>>> file >>>>>>> as input). The output that we get is combination of various >>>>>>> gene-predictors and evidences. I have attached sample result file. >>> What >>>>> would you recommend to get consensus result set? Bootstrapping the >>> resulting gff3 file (rerunning maker)? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 07:36:08 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:36:08 -0500 Subject: [maker-devel] Strange error at blastn step In-Reply-To: Message-ID: Sorry for the slow reply. I've been way for most of the last week. Could you do two more things before running another test. Update again to the latest development version, also set TMP to a non-NFS location like /tmp. Thanks, Carson From: Daniel Standage Date: Monday, 29 October, 2012 8:43 AM To: Carson Holt Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Strange error at blastn step I just ran svn update and tried again with the development version of Maker. Same long list of errors as in the last message. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Oct 29, 2012 at 9:39 AM, Daniel Standage wrote: > Carson, > > I was able to run the first svn update before the test job ran, but I didn't > get the message about this second update until after it has already executed > and failed. I got about 372 lines of such. > >> STATUS: Parsing control files... >> STATUS: Processing and indexing input FASTA files... >> STATUS: Setting up database for any GFF3 input... >> A data structure will be created for you at: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_datastore >> >> To access files for individual sequences use the datastore index: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_master_datastore_index.log >> >> STATUS: Now running MAKER... >> WARNING: Cannot find >scaffold_0, trying to re-index the fasta. >> stop here: scaffold_0 >> ERROR: Fasta index error >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 239. >> Process::MpiChunk::_prepare('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 73 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c808b0)', 'HASH(0x3c8ec40)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 79 >> Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x3c71f30)') >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 56 >> Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x3c80640)', 0, >> 'Process::MpiChunk') called at >> /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 627 >> --> rank=NA, hostname=c4 >> ERROR: Failed in tier preparation >> WARNING: You must always set a rank before running MpiTiers >> FATAL: argument `seq_id` does not exist in MpiTier object >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 86. >> >> Process::MpiChunk::_initialize_vars('Process::MpiChunk=HASH(0x3cc93d0)', >> 'HASH(0x3cc9400)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 47 >> Process::MpiChunk::new('Process::MpiChunk', 'HASH(0x3c80820)', 0, 0) >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 407 >> Process::MpiChunk::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f498)', 'HASH(0x3cc8f20)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 3811 >> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x3c8b300)', 'load', >> 'HASH(0x3c80820)', 0, 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 310 >> Process::MpiChunk::_loader('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0, 0, 'Process::MpiTiers=HASH(0x3c71f30)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 364 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f9c0)', 'HASH(0x3c8fb28)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 375 > > I'll try the next update and run the test again. I see a lot of references in > there to MPI, and just thought I would make it clear that although I am > running in a cluster environment, I am using the default serial version of > Maker, not the parallel MPI version. > > Also, after this failed, I tried changing the TMP directory so that it was > located on the same NFS mount as the scratch disk to which the output was > written. This did not seem to have any affect, and I saw the same issues with > the EST sequences unable to be found. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Fri, Oct 26, 2012 at 6:59 PM, Carson Holt wrote: >> >> >> From: Carson Holt >> Date: Friday, 26 October, 2012 6:10 PM >> To: Daniel Standage >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> I've been going over the indexing code using different scenarios and I may >> have isolated a candidate for what is causing this. Could you do one more >> 'svn update' inside the maker devel directory before running a test job? >> >> Thanks, >> Carson >> >> From: Daniel Standage >> Date: Friday, 26 October, 2012 2:29 PM >> To: Carson Holt >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> Got this from the compute node. Looks like native disk space to me. >> >> [dstandag at mason ~] df /tmp >> Filesystem 1K-blocks Used Available Use% Mounted on >> /dev/sda1 478573472 12319684 441943620 3% /tmp >> >> Installing a bundle of Perl prereqs for development version, will try that >> soon. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Fri, Oct 26, 2012 at 2:24 PM, Carson Holt wrote: >>> Ok. Try the developer release and see if it still happens. >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>> Date: Friday, 26 October, 2012 2:19 PM >>> >>> To: Carson Holt >>> Cc: "maker-devel at yandell-lab.org" >>> >>> Subject: Re: [maker-devel] Strange error at blastn step >>> >>> Unfortunately, the job is no longer running and as a result I cannot connect >>> to the compute nodes as I could while it was running. On the interactive >>> node, it looks like it's real disk, although it looks like there are some >>> tmpfs mounts. >>> >>> [dstandag at mason src] df /tmp >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> [dstandag at mason src] df >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> login_x86_64 16497564 3077352 13420212 19% / >>> tmpfs 16497564 0 16497564 0% /dev/shm >>> tmpfs 10240 0 10240 0% /var/tmp >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> AFS 9000000 0 9000000 0% /afs >>> bl-nas1:/vol/hd00 3435973856 1775658144 1660315712 52% /N/hd00 >>> bl-nas1:/vol/hd01 3435973856 1684116928 1751856928 50% /N/hd01 >>> bl-nas2:/vol/hd02 3435973856 1856598656 1579375200 55% /N/hd02 >>> bl-nas2:/vol/hd03 3435973856 2747626240 688347616 80% /N/hd03 >>> bl-nas1:/vol/hdln 81920 3424 78496 5% /N/u >>> bl-nas2:/vol/soft 1258291200 837003424 421287776 67% /N/soft >>> bl-nas1:/vol/logs 419430400 67163328 352267072 17% /N/logs >>> ... >>> ... >>> >>> I'll see if I can launch another short job and verify this on the compute >>> nodes. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Fri, Oct 26, 2012 at 2:14 PM, Carson Holt wrote: >>>> The command 'df /tmp' will tell you whether /tmp is a tmpfs mount >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Friday, 26 October, 2012 2:12 PM >>>> To: Carson Holt >>>> Cc: "maker-devel at yandell-lab.org" >>>> >>>> Subject: Re: [maker-devel] Strange error at blastn step >>>> >>>> It looks like /tmp is indeed being used: the files I played with were under >>>> /tmp/maker_1YQF9o. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Fri, Oct 26, 2012 at 2:09 PM, Carson Holt wrote: >>>>> Check to see where /tmp is located? Some clusters have it set up as a >>>>> tmpfs directory and I have had problems with fasta indexes running from >>>>> tmpfs mounts in the past. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Friday, 26 October, 2012 2:05 PM >>>>> To: Carson Holt >>>>> >>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>> >>>>> The maker working directory is in a cluster environment with shared >>>>> scratch space (I'm guessing NFS-mounted). I didn't change the temp >>>>> directory setting, so it should be the local default (/tmp). >>>>> >>>>> I'll give the dev version a shot. Thanks. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Fri, Oct 26, 2012 at 1:57 PM, Carson Holt wrote: >>>>>> Could you try this development version and tell me if the error still >>>>>> happens? >>>>>> >>>>>> Use this command to download --> >>>>>> <> >>>>>> >>>>>> Username: <> >>>>>> Password: <> >>>>>> >>>>>> Are you running in an NFS mounted directory or are you resetting TMP to a >>>>>> different location? >>>>>> >>>>>> Thanks, >>>>>> Carson >>>>>> >>>>>> >>>>>> From: Daniel Standage >>>>>> Date: Friday, 26 October, 2012 1:52 PM >>>>>> To: Maker Mailing List >>>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>>> >>>>>> I have since installed Maker on a different machine and tried it out. The >>>>>> test run completed successfully, but as I commenced with the full genome >>>>>> annotation, I have noticed the following error popping up frequently. >>>>>> >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.8.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-10 hits >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.9.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-6 hits >>>>>>> WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta. >>>>>>> stop here:comp59088_c1_seq7 >>>>>>> ERROR: Fasta index error >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while polishig ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 14 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_0 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> --Next Contig-- >>>>>>> >>>>>>> #--------------------------------------------------------------------- >>>>>>> Now starting the contig!! >>>>>>> SeqID: scaffold_1 >>>>>>> Length: 5805686 >>>>>>> #--------------------------------------------------------------------- >>>>>> >>>>>> My first thought based on the message is that blastdbcmd could not find >>>>>> the sequence in the database. I verified this was the case--I could not >>>>>> extract sequence comp59088_c1_seq7 from the database Maker had created >>>>>> under /tmp. However, after removing the index files and re-running >>>>>> makeblastdb with the -parse_seqids option set, blastdbcmd successfully >>>>>> extracted the sequence. >>>>>> >>>>>> I was initially happy with this finding, but upon closer inspection it >>>>>> looks like Maker does not use blastdbcmd to extract sequences, but rather >>>>>> its own internal code. Therefore I'm still not sure where the problem is >>>>>> and how I might fix it. Any insights? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> -- >>>>>> Daniel S. Standage >>>>>> Ph.D. Candidate >>>>>> Bioinformatics and Computational Biology Program >>>>>> Department of Genetics, Development, and Cell Biology >>>>>> Iowa State University >>>>>> >>>>>> >>>>>> >>>>>> On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage >>>>>> wrote: >>>>>>> Greetings! >>>>>>> >>>>>>> I am doing a test run of my Maker setup on a new machine, annotating a >>>>>>> pretty short contig (about 3kb). However, there seems to be a hiccup >>>>>>> during the blastn stage. This is the terminal message. >>>>>>> >>>>>>> #--------- command -------------# >>>>>>> Widget::blastn: >>>>>>> /share/home/01854/standage/local/bin/blastn -db >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Ef >>>>>>> asta.mpi.10.7 -query >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0 >>>>>>> -num_alignments 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend >>>>>>> 3 -word_size 15 -reward 1 -penalty -3 -gapopen 3 -dbsize 1000 -searchsp >>>>>>> 500000000 -num_threads 16 -lcase_masking -dust yes -soft_masking true >>>>>>> -show_gis -out >>>>>>> /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker >>>>>>> .output/maker.bogus_datastore/scaffold_866/theVoid.scaffold_866/scaffold >>>>>>> _866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrini >>>>>>> ty%2ETrimmomatic%2Efasta.mpi.10.7.blastn >>>>>>> #-------------------------------# >>>>>>> deleted:0 hits >>>>>>> ERROR: Could not obtain lock to format database >>>>>>> >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while doing blastn of ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 8 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_866 >>>>>>> >>>>>>> Several blastn steps appeared to have completed successfully to this one >>>>>>> failing. Any ideas what could be causing this? >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> -- >>>>>>> Daniel S. Standage >>>>>>> Ph.D. Candidate >>>>>>> Bioinformatics and Computational Biology Program >>>>>>> Department of Genetics, Development, and Cell Biology >>>>>>> Iowa State University >>>>>>> >>>>>> >>>>>> _______________________________________________ maker-devel mailing list >>>>>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinf >>>>>> o/maker-devel_yandell-lab.org >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 5 07:41:57 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:41:57 -0500 Subject: [maker-devel] gff3_preds2models script In-Reply-To: <3207.131.215.15.234.1350942378.squirrel@webmail.caltech.edu> Message-ID: The gff3_preds2models doesn't support the shared ID method for model assembly. You will need to create a parent match feature and child match_part features (each with a unique ID and Parent= attribute). You can find examples in the GFF3 specification here --> http://www.sequenceontology.org/gff3.shtml Thanks, Carson On 12-10-22 5:46 PM, "Parul Kudtarkar" wrote: >Hello, > >I want to add gene structure(gene/mRNA/exon) to gff3 file. I am using >gff3_preds2models for this purpose. However I get following error >**WARNING: No top level feature found for ID WHL22.100252 >I have attached the sample input gff3 file and the list of ids > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 08:08:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 10:08:36 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt , Maker Mailing List Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 08:14:18 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:14:18 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List < > maker-devel at yandell-lab.org> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PdomMaker9.e44232.bz2 Type: application/x-bzip2 Size: 5881 bytes Desc: not available URL: From parulk at caltech.edu Mon Nov 5 14:40:46 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 5 Nov 2012 13:40:46 -0800 (PST) Subject: [maker-devel] Conensus gene model In-Reply-To: References: Message-ID: <4116.131.215.15.234.1352151646.squirrel@webmail.caltech.edu> Dear Carson, Thanks you very much, this is helpful. > The way models are generated, it really doesn't so much matter where the > protein alignments came from. Basically the protein alignment is just > creating a region of potential CDS. MAKER than gives that region as a > hint to the gene predictors, but the gene predictors really make the call > on how to finally structure the gene based on their training sets. You > can short circuit this by using the protein2genome option as a separate > run with only your primary proteins. MAKER will then try and turn those > protein alignments directly into genes. Results from that run can > sometimes be useful for generating training sets as well, or can be passed > back into MAKER as pred_gff so MAKEr has the option to turn those into > models as an alternative to the models produced by the ab initio > predictors. > > --Carson > > > On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: > >>Hi Jason, thanks for directions on generating training-set for augustus. >>Also as alignment evidence if we are providing protein sequences from the >>primary organism as well as other closely related species is there an >>option to give the primary protein file precedence over others? >>At the moment I have all the proteins(from primary organism as well as >>related species) into a single file as protein option in maker_opts.ctl >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Paul - >>> >>> I think I've posted on this before here if you are asking how to go >>> from >>> SNAP training to Augustus training. >>> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >>> >>> I do this type of training a lot - here some pointers. >>> >>> I often train by generating models using cegma on the genome and get >>>these >>> 400 or so good models as my training set. when I have EST or RNA-Seq I >>> use PASA to generate the best set of annotations. >>> >>> For CEGMA - then I run this script that comes with MAKER: >>> cegma2zff output.cegma.gff genome.fa >>> >>> Then I follow the SNAP directions >>> >>> fathom genome.ann genome.dna -categorize 1000 >>> fathom uni.ann uni.dna -export 1000 -plus >>> mkdir MYGENOME >>> cd MYGENOME >>> forge ../export.ann ../export.dna --OPTIONS >>> cd ../MYGENOME >>> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >>> >>> I then also make the augustus training data like this running in the >>> directory that has the export.ann and export.dna files: >>> perl gene_prediction/zff2augustus_gbk.pl > train.gb >>> >>> using this script: >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>>ff2augustus_gbk.pl >>> >>> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>>and >>> best models from PASA and incorporate all these data in to my SNAP >>> training set, and then export again back to gbk for the augustus >>>training. >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>>asatraining2zff.pl >>> >>> Then you just need to run the Augustus training (autoAugTrain.pl) on >>> the >>> train.gb file. >>> >>> Jason >>> >>> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar >>> wrote: >>> >>>> Hello Carson and maker community, >>>> >>>> Thank you very much for your guidelines on using the maker-pipeline. >>>> Yes, >>>> green sea urchin genome that we are trying to annotate. >>>> We are running the on scaffolds and most of these scaffolds are small >>>>in >>>> size(very first genome assembly). We would typically expect 20,000 >>>>genes >>>> in this genome. So we are running maker using EST and proteins from >>>> the >>>> genome and out-groups to generate training dataset for SNAP and >>>> Augustus. >>>> Depending on the resulting predictions we may bootstrap the predicted >>>> genes once again using EST and proteins. >>>> >>>> Do you have any further suggestions? Also could you point how to >>>>convert >>>> training set generated for SNAP to be used as training set for >>>> Augustus >>>> as >>>> well? Would maker give equal weightage to SNAP and Augustus >>>> predictions >>>> for generating gene model? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> One thing you seem to be missing is protein evidence. >>>>> >>>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>>> recommend adding all proteins from the Strongylocentrotus purpuratus >>>> genome, then throw in another Deuterstome of your choice. Perhaps you >>>> should also add a couple of outgroup organisms like Nematostella >>>> vectensis >>>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>>> adding >>>> to many protostome outgroups (i.e. C. elegans and Drosophila) because >>>> a >>>> big part of their evolution is gene loss (so distant cnidaria often >>>> match >>>>> deuterstomes better than most protostomes do). >>>>> >>>>> You could take the maker results when protein data is included and >>>>> use >>>> it >>>>> to retrain SNAP again. >>>>> >>>>> Even a 22 kb contig is still really short. Is this genome primarily >>>> constituted by short contigs like this? I would recommend running >>>>CEGMA >>>> once on this genome to get an appropriate estimate of how recoverable >>>> the >>>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>>> Cegma >>>>> will give you an estimate for genome completeness as well as >>>>> estimates >>>> of >>>>> what percentage of genes will be found in their entirety and what >>>> percent >>>>> will be partial genes. This is important to do if your genome is >>>> fragmented as it will give you a reasonable expectation of what you >>>> can >>>> expected to recover (as short contigs don't annotate very well - you >>>> tend >>>>> to loose a lot). >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>> Hi Carson, >>>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>>as >>>>>> 3 >>>> exons EST alignments. Could you please recommend additional training. >>>>We >>>> are currently running maker on the entire contig set and eventually >>>> merge >>>>>> all the gff3 contig predictions. The using suggested >>>>>>parameter/methods >>>> we >>>>>> would like to get a consensus gene-set with minimal false >>>>>> positives/negatives. >>>>>> Thanks, >>>>>> Parul >>>>>>> The contig in question is really too small to get much out of it >>>>>>> (only 5 >>>>>> kb). There was only one single exon EST alignments and a couple of >>>> predictions with no evidence support. Anything smaller than 10 kb is >>>> mostly useless for annotation purposes. You would really need a few >>>> 100kb >>>>>>> length or longer contigs to glean enough information for optimizing >>>>>>> your >>>>>> parameters. >>>>>>> The general suggestions for any maker run are to use proteins from >>>>>>> a >>>>>> closely related organism or a couple of closely related organisms >>>>>> for >>>>>> the >>>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>>> for >>>>>> certain eukaryotes that have a bias for single exon transcripts >>>>>> (i.e. >>>>>> some >>>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>>> initio >>>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>>> positives). >>>>>>> Additional training would really depend on what your other contigs >>>> look >>>>>> like. Do you have any large contigs? I could look at one of those >>>>>> and >>>> give suggestions but the provided contig is just too short to glean >>>> much. >>>>>>> Thanks, >>>>>>> Carson >>>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>>> Hello, >>>>>>>> Please advice on the aforementioned query? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>>> From: "Parul Kudtarkar" >>>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>>> To: maker-devel at yandell-lab.org >>>>>>>> >>>>>>>>-------------------------------------------------------------------- >>>>>>>>---- >>>> -- >>>>>> Hi, >>>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>>est,protein >>>>>>>> and >>>>>> contig file), agustus,genemarkE(we ran it outside maker and have >>>>>> gff3 >>>>>>>> file >>>>>>>> as input). The output that we get is combination of various >>>>>>>> gene-predictors and evidences. I have attached sample result file. >>>> What >>>>>> would you recommend to get consensus result set? Bootstrapping the >>>> resulting gff3 file (rerunning maker)? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Wed Nov 7 07:00:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 09:00:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line for a > few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on > native disk space, and relaunched. I have attached the output of the job that > failed in <5 minutes. It looks pretty similar to the errors I got the last > time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 08:05:45 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:05:45 -0500 Subject: [maker-devel] Maker issues Message-ID: Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker.log Type: application/octet-stream Size: 48916 bytes Desc: not available URL: From daniel.standage at gmail.com Wed Nov 7 07:30:11 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 09:30:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > >> Thanks. Could you also run with the --debug flag set on the command line >> for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt , Maker Mailing List < >> maker-devel at yandell-lab.org> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory >> is on native disk space, and relaunched. I have attached the output of the >> job that failed in <5 minutes. It looks pretty similar to the errors I got >> the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 08:29:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 10:29:34 -0500 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: Message-ID: Sorry for the slow reply. I'm not on a long drive, but I am away this week. Could you send me the genemark hmm file and one of the contigs that fails. Thanks, Carson On 12-11-04 3:20 AM, "Gowthaman Ramasamy" wrote: >Hi Carson, >As it happens, I am sorry to bother you again on a weekend. Here is my >hoping that you are not on a long drive this time. > >I am running genemark prokaryote via maker on a genome with 36 >chromosomes. All but two finishes well. > >On those two, i am not able to find anything unusual. Following is the >error message i see. Could you please point to me what could be the >possible source of these errors. Thanks verymuch in advance... > >Widget::genemark: >/depot/perl-5.12.1/bin/perl >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gm >hmm_wrap -m >./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokar >yotic%2Emod_hmm%2Emod.genemark >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/query.fasta >#-------------------------------# >substr outside of string at >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMac >hine.pm line 223. > >FATAL ERROR >ERROR: Failed while preparing masked sequence and ab-inits!! > >ERROR: Chunk failed at level 6 >!! >FAILED CONTIG:Enmo_susu.05 > > >Thanks once again, >Gowthaman From daniel.standage at gmail.com Wed Nov 7 09:43:17 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 11:43:17 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed *loalize* to *localize* and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >> fasta indexer is broken. I have an open bug I am trying to resolve with >> the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >> >>> Thanks. Could you also run with the --debug flag set on the command line >>> for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List < >>> maker-devel at yandell-lab.org> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory >>> is on native disk space, and relaunched. I have attached the output of the >>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>> the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 09:46:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 11:46:31 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Looked good for a while, but came across this error. > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > > > > --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is > repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live >> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >> indexer is broken. I have an open bug I am trying to resolve with the >> Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> Thanks. Could you also run with the --debug flag set on the command line for >>> a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List >>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory is >>> on native disk space, and relaunched. I have attached the output of the job >>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>> last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Thu Nov 8 07:32:59 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 09:32:59 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > > It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to > *localize* and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >> and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>> fasta indexer is broken. I have an open bug I am trying to resolve with >>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List < >>>> maker-devel at yandell-lab.org> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>> errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Thu Nov 8 07:47:20 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Thu, 8 Nov 2012 14:47:20 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Hi Daniel, is it possible you have some proteins in your EST files? '------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw' Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [daniel.standage at gmail.com] Sent: Thursday, November 08, 2012 7:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From daniel.standage at gmail.com Thu Nov 8 08:48:52 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 10:48:52 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> References: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Message-ID: Based on Mark's suggestion, I took a look at the EST files. Luckily there is no protein sequence contamination. [dstandag at mason Transcriptome] grep -v '^>' Pdom.Trinity.Trimmomatic.fasta | grep -o . | sort | uniq -c 79400764 A 39834991 C 40702954 G 77980105 T [dstandag at mason Transcriptome] grep -v '^>' Pmet.Trinity.R.fasta | grep -o . | sort | uniq -c 18294708 A 9108213 C 9449127 G 17756470 T -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Thu, Nov 8, 2012 at 9:47 AM, Mark Yandell wrote: > Hi Daniel, > > is it possible you have some proteins in your EST files? > > '------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw' > > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [ > daniel.standage at gmail.com] > Sent: Thursday, November 08, 2012 7:32 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 08:02:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:02:21 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.make r.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold _7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffo ld_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58 983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 > --maxintron 10000 --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq37.for.716125-723330.0.fasta at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. ...as well as one occurrence of this error. > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869 > 077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sca > ffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar > --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7 > /theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm > :86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is >> repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl live >>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >>> indexer is broken. I have an open bug I am trying to resolve with the >>> Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> Thanks. Could you also run with the --debug flag set on the command line >>>> for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List >>>> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP directory is >>>> on native disk space, and relaunched. I have attached the output of the job >>>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>>> last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 08:13:38 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:13:38 -0500 Subject: [maker-devel] Query on genemark results In-Reply-To: Message-ID: The previous bug was a complete lack of GeneMark results in the GFF3, not just a lack of consensus models from GeneMark. It is possible to get no consensus models from GeneMark if they score poorly. Send me the GFF3 results of your larger contigs and I can review it and tell you if any models are being improperly categorized. Thanks, Carson On 12-10-28 1:50 PM, "kokwei" wrote: >Hi, > >I have the same problems as posted by Andr? Gomes on 10/4/10. I still >have the same problems even though using the current available version >of maker (maker 2.1 and maker 2.26 beta version). > >I have tried to do the gene prediction on eukaryotic genome using 3 >ab-initio gene predictors (SNAP, Augustus and GeneMark-ES) using Maker. >From the fasta_merge output, I have 3 separate files of gene models >($prefix.all.maker.augustus_masked.proteins.fasta, >$prefix.all.maker.snap_masked.proteins.fasta and >$prefix.all.maker.genemark.proteins.fasta) and one >$prefix.all.maker.proteins.fasta (I presume this should be the consensus >gene models from 3 predictors' results, right?). > > From the consensus gene models file, I don't see even one result from >genemark but all from snap/augustus only. Is that normal? >Also from the file naming and gene model label in final gff file, it's >showing that genemark is not masked like those of augustus and snap? Is >that true? Why only augustus and snap masked but not genemark? Please >assist and thanks for your helps. > >Kok Wei > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From mikael.durling at slu.se Tue Nov 13 06:57:36 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 13 Nov 2012 13:57:36 +0000 Subject: [maker-devel] NULs in master_datastore_index.log Message-ID: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Hello, In order to work around locking problems with SQLite, I tried running (latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason it seems maker does not detect the automounted volumes as being nfs mounted?). Running over NFSv4 makes SQLite happy, but then another problem popped up. It seems ds_utility.pm happens to write simultaneously to the datastore_index from several MPI ranks, which in my case results in stretches of NULs in the datastore file. This seems to result in maker trying to analyse the same contig simultaneously on two different MPI ranks. (I get rank failure notices on the output twice for the same rank, and maker complaining that the same GFF3 ID appears more than once). Any hints on how this can be handled? It appears as I should have installed and run maker on some other cluster without NFS mounted volumes to save myself a lot of hassles. Thanks in advance, Mikael From carsonhh at gmail.com Tue Nov 13 07:12:58 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 13 Nov 2012 09:12:58 -0500 Subject: [maker-devel] NULs in master_datastore_index.log In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Message-ID: Locks for not running contigs are a separate thing from the datastore index. They are handled by file locks in the directory for each contig. For the datastore index, it can be subject to race conditions if two processes happen to write an output string at the exact same time, but can be rebuilt in less than 2 min at the end of your job using the -dsindex flag. The failure notices you are getting might be because of the configuration of the NFS mount. MAKER will check the locks it creates several times while running a given contig to see if the lock was broken, and if it was then that contig will fail producing an error. This will happen before it does any activity that might conflict with the other active run of that contig by another process, so the process that broke the lock should continue without issue somewhere else, but you will get a trail of messages in the error log and maybe some ugliness in the datastore index. You can try altering the flags set for the NFS mount, or just set the retry count really high. You will have to run maker -dsindex once your MPI job finishes to get the datastore index log back in order on completion, but that only takes a couple of minutes to rebuild. --Carson On 12-11-13 8:57 AM, "Mikael Brandstr?m Durling" wrote: >Hello, > >In order to work around locking problems with SQLite, I tried running >(latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason >it seems maker does not detect the automounted volumes as being nfs >mounted?). Running over NFSv4 makes SQLite happy, but then another >problem popped up. It seems ds_utility.pm happens to write simultaneously >to the datastore_index from several MPI ranks, which in my case results >in stretches of NULs in the datastore file. This seems to result in maker >trying to analyse the same contig simultaneously on two different MPI >ranks. (I get rank failure notices on the output twice for the same rank, >and maker complaining that the same GFF3 ID appears more than once). > >Any hints on how this can be handled? > >It appears as I should have installed and run maker on some other cluster >without NFS mounted volumes to save myself a lot of hassles. > >Thanks in advance, >Mikael > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From es9 at sanger.ac.uk Thu Nov 15 03:20:56 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 10:20:56 +0000 Subject: [maker-devel] Augustus training within Maker Message-ID: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Hi, Could you please confirm something for me: If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. To achieve this, do I need to change anything in maker_opts.ctl or do I leave augustus_species= #Augustus gene prediction species model as is, or should it be edited for the 2nd run? Many thanks Eleanor -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From dsth at ebi.ac.uk Thu Nov 15 04:14:31 2012 From: dsth at ebi.ac.uk (Daniel Hughes) Date: Thu, 15 Nov 2012 11:14:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: heya, Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus > species config folder of gene parameters, then Augustus runs using this > data alone. > I understand that with a second Maker run Augustus retrains using the > BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I > leave > augustus_species= #Augustus gene prediction species model > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. dan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Thu Nov 15 04:34:09 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 11:34:09 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this Ele On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > heya, > > Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. > I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I leave > augustus_species= #Augustus gene prediction species model > > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. > > dan. > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 16 07:19:47 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 16 Nov 2012 09:19:47 -0500 Subject: [maker-devel] segmentation fault (core dumped) for maker running In-Reply-To: Message-ID: The correct file to update in Bioperl is /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm not Bioperl.pm, but technically you only have to fix whichever .pm file loads last. So if it's working then don't worry about it because one of the files fixed by the first command are loading after /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm. Thanks, Carson From: Hung Chih-Ming Date: Thursday, 15 November, 2012 2:02 AM To: Carson Holt Cc: Subject: segmentation fault (core dumped) for maker running Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ymwur1 at gmail.com Thu Nov 15 00:02:55 2012 From: ymwur1 at gmail.com (Hung Chih-Ming) Date: Thu, 15 Nov 2012 15:02:55 +0800 Subject: [maker-devel] segmentation fault (core dumped) for maker running Message-ID: Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Fri Nov 16 17:37:53 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri, 16 Nov 2012 17:37:53 -0700 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Message-ID: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Dan is correct about the workings of the hint based communication between MAKER and the gene predictors - and just to clarify further. MAKER never 're-trains' Augustus or any of the other gene predictors. Many people will retrain the gene predictors between iterative MAKER runs, but this is a manual (and for Augustus non-trivial) step. B On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this > > Ele > > > On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > >> heya, >> >> Could you please confirm something for me: >> >> If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. >> I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. >> >> To achieve this, do I need to change anything in maker_opts.ctl or do I leave >> augustus_species= #Augustus gene prediction species model >> >> >> AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. >> >> dan. >> >> >> > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Sat Nov 17 03:42:31 2012 From: es9 at sanger.ac.uk (es9) Date: Sat, 17 Nov 2012 10:42:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Message-ID: Thank you to you both for clarifying this ... I was get a smidge confused and reading previous posts I can see the answer had already been asked and replied to. Next time I will cruise the archives before posting! Regards, Eleanor > Dan is correct about the workings of the hint based communication > between MAKER and the gene predictors - and just to clarify further. > MAKER never 're-trains' Augustus or any of the other gene predictors. > Many people will retrain the gene predictors between iterative MAKER > runs, but this is a manual (and for Augustus non-trivial) step. > > B > > On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > >> Aha - that makes sense, so with every run Augustus is run with the >> BLAST hints available, thanks for clarifying this >> >> Ele >> >> On 15 Nov 2012, at 11:14, Daniel Hughes wrote: >> >>> heya, >>> >>>> Could you please confirm something for me: >>>> >>>> If with the first Maker run you provide the location of the >>>> Augustus species config folder of gene parameters, then Augustus >>>> runs using this data alone. >>>> I understand that with a second Maker run Augustus retrains >>>> using the BLAST evidence from the 1st run. >>>> >>>> To achieve this, do I need to change anything in maker_opts.ctl >>>> or do I leave >>>> augustus_species= #Augustus gene prediction species model >>> >>> AFAIK maker runs augustus, blast etc., as sort of raw compute >>> stages in the earlier tier_types, the results of these stages e.g. >>> protein alignments etc., are then 'synthesised' into 'hints' >>> (early tier_type 3) that are provided to ab initio predicters >>> capable of taking external 'hints' - such as augustus - that are >>> used to generate the final models (after further adjustmnets wrt., >>> utrs etc.). that is to say i think what you mean by first and >>> second maker runs are actually internal usage of ab initios that >>> occur at different stages of any single maker run and you should >>> be shielded from this. >>> >>> dan. >> >> -- The Wellcome Trust Sanger Institute is operated by Genome >> Research Limited, a charity registered in England with number >> 1021457 and a company registered in England with number 2742969, >> whose registered office is 215 Euston Road, London, NW1 2BE. >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com [1] >> > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > Links: > ------ > [1] mailto:maker-devel at box290.bluehost.com -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From parulk at caltech.edu Tue Nov 20 16:35:34 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:35:34 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction Message-ID: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Hello, I am running SNAP, Augustus and genemark(genemarkE results were calculated externally and gff3 file was provided to option pred_gff). However the resulting gff3 source field does not mention if the prediction were derived from SNAP, Augustus or genemark. I have attached the configuration file. Also is there any option where were could have priority for SNAP predictions? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4631 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 20 16:39:42 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:39:42 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> References: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Message-ID: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Hello, Just found that for Scaffold of larger size it does explicitly specify the prediction source. Thanks, Parul > Hello, > > I am running SNAP, Augustus and genemark(genemarkE results were calculated > externally and gff3 file was provided to option pred_gff). However the > resulting gff3 source field does not mention if the prediction were > derived from SNAP, Augustus or genemark. I have attached the > configuration file. Also is there any option where were could have > priority for SNAP predictions? > > Thanks and regards, > Parul Kudtarkar > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From barry.utah at gmail.com Tue Nov 20 20:21:47 2012 From: barry.utah at gmail.com (Barry Moore) Date: Tue, 20 Nov 2012 20:21:47 -0700 Subject: [maker-devel] email about Maker In-Reply-To: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> References: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> Message-ID: Hi Jorge, These would be two different proteins identified on the same scaffold. The numbers don't have any meaning other than that the genes are numbered sequentially and so these two genes would be adjacent to each other. If you have access to the GFF3 file produced by Maker for this genome you should see those two IDs with adjacent but different coordinates as well. B On Nov 19, 2012, at 10:48 AM, Jorge Ibarra wrote: > Dear Dr Moore > > I have a quick question about Maker and I'd appreciate if you could answer that to me. I downloaded two protein sequences predicted by Maker with the following indentifiers: > > >maker_scaffold_7-snap-gene-1.23-mRNA-1 Glucosylceramidase > >maker_scaffold_7-snap-gene-1.24-mRNA-1 Glucosylceramidase > > The only thing that varies in the two sequences identifiers are the number 1.23 and 1.24, and I was wondering what this numbers mean. Their sequence are also really similar (96%). > > I wonder if these sequences represent two genes in the same scaffold (scaffold_7) or if they are two slightly different predictions of the same gene. > > So my question is what do those numbers (1.23 and 1.24) represent in Maker? > > Thank you. > > Jorge Ibarra > PhD student Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 07:25:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 09:25:36 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Message-ID: Is it possible that you just picked a contig that didn't have any pred_gff entries for snap and augustus the first time? The predictions you pass through should be of type match/match_part and will have the source as pred_gff:snap or pred_gff:augustus. Could you check and let me know or send me an example of entries from a contig you passed through and the results you are seeing? No. there is no priority given to one prediction over the other. They are choses based on evidence overlap similarity. Thanks, Carson On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >Hello, > >Just found that for Scaffold of larger size it does explicitly specify the >prediction source. > >Thanks, >Parul > >> Hello, >> >> I am running SNAP, Augustus and genemark(genemarkE results were >>calculated >> externally and gff3 file was provided to option pred_gff). However the >> resulting gff3 source field does not mention if the prediction were >> derived from SNAP, Augustus or genemark. I have attached the >> configuration file. Also is there any option where were could have >> priority for SNAP predictions? >> >> Thanks and regards, >> Parul Kudtarkar >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From benayoun at stanford.edu Wed Nov 21 11:45:55 2012 From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=) Date: Wed, 21 Nov 2012 10:45:55 -0800 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Message-ID: Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department *BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 13:58:05 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 15:58:05 -0500 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? In-Reply-To: Message-ID: There are many ways of doing this. You can run everything separately and then copy all GFF3 files into a common folder and use the gff3_merge script that comes with maker to combine them. Alternatively you can run maker with the -g and -base options. This allows you to specify a new genome on the command line and the base name of the directory to write to. Using those flags you can swap in a different contig file while maintaining the same output directory for your job as a whole. Just run maker at the end of the run using the original fasta and the -dsindex flag, to sync the datastore index file so it is complete if you do this option. To split out contigs of interest you can also use the fasta_tool that comes with maker and use the -grep_header or ?select flags to indicate which contigs to retrieve. --Carson From: B?r?nice Benayoun Date: Wednesday, 21 November, 2012 1:45 PM To: Cc: Dario Riccardo Valenzano Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 21 14:15:00 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 21 Nov 2012 13:15:00 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Dear Carson, That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb which is very small). I have attached a Scaffold of 1.5kb with no predictions and another Scaffold of 28kb. It is of course expected that we would not get any gene-prediction for small size Scaffolds. For next maker run would you recommend bootstrap to reduce false positives? Thanks and regards, Parul Kudtarkar > Is it possible that you just picked a contig that didn't have any pred_gff > entries for snap and augustus the first time? The predictions you pass > through should be of type match/match_part and will have the source as > pred_gff:snap or pred_gff:augustus. Could you check and let me know or > send me an example of entries from a contig you passed through and the > results you are seeing? > > No. there is no priority given to one prediction over the other. They are > choses based on evidence overlap similarity. > > Thanks, > Carson > > > > > On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: > >>Hello, >> >>Just found that for Scaffold of larger size it does explicitly specify >> the >>prediction source. >> >>Thanks, >>Parul >> >>> Hello, >>> >>> I am running SNAP, Augustus and genemark(genemarkE results were >>>calculated >>> externally and gff3 file was provided to option pred_gff). However the >>> resulting gff3 source field does not mention if the prediction were >>> derived from SNAP, Augustus or genemark. I have attached the >>> configuration file. Also is there any option where were could have >>> priority for SNAP predictions? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold118825.gff Type: application/octet-stream Size: 1719 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold20.gff Type: application/octet-stream Size: 377514 bytes Desc: not available URL: From carsonhh at gmail.com Sun Nov 25 15:55:32 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 17:55:32 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Message-ID: I see both augustus and snap derived predictions (match/match_part) with augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that were derived from these predictions. There are no predictions from genemark. Is that what you were expecting? If not could you specify how it varies. With respect to bootstrapping, it really depends how well trained your gene predictors are. In general only one round of bootstrapping may be necessary after newly training a gene predictor. Thanks, Carson On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >Dear Carson, > >That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >which is very small). I have attached a Scaffold of 1.5kb with no >predictions and another Scaffold of 28kb. It is of course expected that we >would not get any gene-prediction for small size Scaffolds. > >For next maker run would you recommend bootstrap to reduce false >positives? > >Thanks and regards, >Parul Kudtarkar > >> Is it possible that you just picked a contig that didn't have any >>pred_gff >> entries for snap and augustus the first time? The predictions you pass >> through should be of type match/match_part and will have the source as >> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >> send me an example of entries from a contig you passed through and the >> results you are seeing? >> >> No. there is no priority given to one prediction over the other. They >>are >> choses based on evidence overlap similarity. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >> >>>Hello, >>> >>>Just found that for Scaffold of larger size it does explicitly specify >>> the >>>prediction source. >>> >>>Thanks, >>>Parul >>> >>>> Hello, >>>> >>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>calculated >>>> externally and gff3 file was provided to option pred_gff). However the >>>> resulting gff3 source field does not mention if the prediction were >>>> derived from SNAP, Augustus or genemark. I have attached the >>>> configuration file. Also is there any option where were could have >>>> priority for SNAP predictions? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Sun Nov 25 21:10:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 23:10:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more detail > to the errors in the development version if you do an 'svn update'. Then you > will know the system specific reason why close or opened failed. For the > other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1 > 869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, > there are some intermittent issues. I've seen a couple occurrences of the > following error... > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq101.for.716125-721460.0.fasta -t >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 >> --maxintron 10000 --showcigar --percent 20 > >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq37.for.716125-723330.0.fasta at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > > ...as well as one occurrence of this error. > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker >> .output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.186 >> 9077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >> affold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >> --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_ >> 7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.p >> m:86 >> STACK: Widget::exonerate::est2genome::assemble >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:82 >> STACK: polisher::exonerate::est::polish >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:44 >> STACK: GI::to_polisher >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:166>> 3 >> STACK: Process::MpiChunk::run >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling uri_escape at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling File::Path::mkpath at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> >>> >>> >>> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to >> localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps and >>> is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl live >>>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command line >>>>> for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List >>>>> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP directory >>>>> is on native disk space, and relaunched. I have attached the output of the >>>>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>>>> the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Sun Nov 25 21:56:31 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 26 Nov 2012 04:56:31 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> good detective work there Carson! Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] Sent: Sunday, November 25, 2012 9:10 PM To: Daniel Standage Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage > Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From cjfields at illinois.edu Sun Nov 25 22:33:52 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 05:33:52 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { if ( $str =~ m/U/i ) { $alphabet = 'rna'; } else { $alphabet = 'dna'; } } else { $alphabet = 'protein'; } Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. chris On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > good detective work there Carson! > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] > Sent: Sunday, November 25, 2012 9:10 PM > To: Daniel Standage > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. > That is why you get --> > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > > You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. > > Thanks, > Carson > > > > From: Daniel Standage > > Date: Friday, 23 November, 2012 3:06 PM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Thanks for your reply, and sorry for my delayed response. > > I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 > STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 > STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: > 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: > Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From daniel.standage at gmail.com Mon Nov 26 04:08:56 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 26 Nov 2012 06:08:56 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thanks for the responses from everybody! The genomic sequence I am annotating is coming directly from AllPaths-LG, which I've noticed retains as much ambiguity as possible--thus the seldom seen ambiguity nucleotides which in this case seem to outnumber the resolved nucleotides. On one hand, I would hate to lose all the information these ambiguity characters provide by replacing them with Ns, but on the other hand if most tools treat them as such, then it might not make much of a difference. Another option I guess would be to replace ambiguity nucleotides by the most likely explicit nucleotide based solely on sequence composition. This would retain more information than an N, and would at least partially correct. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 26, 2012 at 12:33 AM, Fields, Christopher J < cjfields at illinois.edu> wrote: > This is coming from BioPerl trying to guess the alphabet if one is not > provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just > committed, in fact). It's probably best to explicitly set this when > possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell > wrote: > > > good detective work there Carson! > > > > > > Mark Yandell > > Professor of Human Genetics > > H.A. & Edna Benning Presidential Endowed Chair > > Eccles Institute of Human Genetics > > University of Utah > > 15 North 2030 East, Room 2100 > > Salt Lake City, UT 84112-5330 > > ph:801-587-7707 > > > > ________________________________________ > > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [ > carsonhh at gmail.com] > > Sent: Sunday, November 25, 2012 9:10 PM > > To: Daniel Standage > > Cc: Maker Mailing List > > Subject: Re: [maker-devel] Maker issues > > > > I think the problem is in the sequence of your scaffold. I pulled this > out of the exonerate alignment --> > > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > > > Notice the letters W, K, R, M, etc. While these are technically legal > nucleotides, many external programs, and in this case BioPerl doesn't > handle them well. > > That is why you get --> > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > > > You might want to replace them in your input fasta with the letter 'N' > so they are treated as masked. You will have to delete the mpi_blastdb > directory to let maker rebuild the fasta indexes and you will probably have > to set clean_try=1 in the control files so that MAKER deletes old result > files that contain those characters on the retry. The other error may be > just a snowball effect from the first error, so you should see of it still > happens after fixing the input fasta file. > > > > Thanks, > > Carson > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Friday, 23 November, 2012 3:06 PM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Thanks for your reply, and sorry for my delayed response. > > > > I have attached the first file you requested, but the other two do not > exist. I have attached a listing of the files in that directory. Let me > know if you need anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > > > thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Thursday, 8 November, 2012 9:32 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_23 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_23 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > ...as well as one occurrence of this error. > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > > > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > > q93.est_exonerate.0 > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > > ----------------------------------------------------------- > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_7 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_7 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > I'll let you know if I see anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Typo now fixed on my end too ;-) > > > > Thanks, > > Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Wednesday, 7 November, 2012 11:43 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Looked good for a while, but came across this error. > > > > total clusters:20 now processing 0 > > flattening EST clusters > > doing tblastx of alt-ESTs > > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > > --> rank=NA, hostname=c4 > > ERROR: Failed while doing tblastx of alt-ESTs > > ERROR: Chunk failed at level:4, tier_type:2 > > FAILED CONTIG:scaffold_58 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_58 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > > > --Next Contig-- > > > > It seems pretty clear that there is a typo in GI.pm. I changed loalize > to localize and relaunched. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < > daniel.standage at gmail.com> wrote: > > Done. > > > > Test job has successfully cleared the preliminary Fasta indexing steps > and is repeat masking. I'll let you know if there are any problems. Thanks! > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > > > Thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:14 AM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Debug output attached (bzip2 compressed). > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > > > --Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:05 AM > > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > > Subject: Maker issues > > > > Carson, > > > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > > > > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Nov 26 09:53:59 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 26 Nov 2012 16:53:59 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thank you for the commit to Bioperl. I'll can also manipulate the alphabet value in the object hash right before calling the revcomp method, it's not the most elegant solution but the seq object creation is insulated from my control so I can't set it there --> Bio::Search::HSP::HSPI.pm line 578 I would still recommend losing the ambiguous bases though as they will very likely still cause problems in some downstream application. Thanks, Carson On 12-11-26 12:33 AM, "Fields, Christopher J" wrote: >This is coming from BioPerl trying to guess the alphabet if one is not >provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > >Easy enough to fix to allow for additional ambiguous nucleotides (just >committed, in fact). It's probably best to explicitly set this when >possible, though; it is a guess, after all. > >chris > >On Nov 25, 2012, at 10:56 PM, Mark Yandell >wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>[carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this >>out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal >>nucleotides, many external programs, and in this case BioPerl doesn't >>handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' >>so they are treated as masked. You will have to delete the mpi_blastdb >>directory to let maker rebuild the fasta indexes and you will probably >>have to set clean_try=1 in the control files so that MAKER deletes old >>result files that contain those characters on the retry. The other >>error may be just a snowball effect from the first error, so you should >>see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage >>> >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not >>exist. I have attached a listing of the files in that directory. Let me >>know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>> wrote: >> The first error is an IO error with your system. I've added some more >>detail to the errors in the development version if you do an 'svn >>update'. Then you will know the system specific reason why close or >>opened failed. For the other error, could you send me this file --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/sc >>affold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta >> >> And this one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. >>However, there are some intermittent issues. I've seen a couple >>occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta -t >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq37.for.716125-723330.0.fasta at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pd >> >>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for >>.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> >>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastor >>e/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>--showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> >>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaff >>old_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_in >>fo.pm:86 >> STACK: Widget::exonerate::est2genome::assemble >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:82 >> STACK: polisher::exonerate::est::polish >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:44 >> STACK: GI::to_polisher >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:1663 >> STACK: Process::MpiChunk::run >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:335 >> STACK: Process::MpiChunk::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:351 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>> wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >>> >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>> wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >>and is repeat masking. I'll let you know if there are any problems. >>Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>> wrote: >> 1.006902 Bio::Root::Version >>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>It's fasta indexer is broken. I have an open bug I am trying to resolve >>with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>> wrote: >> Thanks. Could you also run with the --debug flag set on the command >>line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker >>Mailing List >>> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP >>directory is on native disk space, and relaunched. I have attached the >>output of the job that failed in <5 minutes. It looks pretty similar to >>the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From parulk at caltech.edu Mon Nov 26 12:21:23 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 11:21:23 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Hello Carson, Thanks for the feedback.Genemark was run outside maker and the resulting gff3 file was provided as option to pred_gff. What would the source in the gff3 of maker result state of the predictions where made from pred_gff? Thanks and regards, Parul Kudtarkar > I see both augustus and snap derived predictions (match/match_part) with > augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that > were derived from these predictions. There are no predictions from > genemark. Is that what you were expecting? If not could you specify how > it varies. > > With respect to bootstrapping, it really depends how well trained your > gene predictors are. In general only one round of bootstrapping may be > necessary after newly training a gene predictor. > > Thanks, > Carson > > > > On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: > >>Dear Carson, >> >>That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >>which is very small). I have attached a Scaffold of 1.5kb with no >>predictions and another Scaffold of 28kb. It is of course expected that >> we >>would not get any gene-prediction for small size Scaffolds. >> >>For next maker run would you recommend bootstrap to reduce false >>positives? >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Is it possible that you just picked a contig that didn't have any >>>pred_gff >>> entries for snap and augustus the first time? The predictions you pass >>> through should be of type match/match_part and will have the source as >>> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >>> send me an example of entries from a contig you passed through and the >>> results you are seeing? >>> >>> No. there is no priority given to one prediction over the other. They >>>are >>> choses based on evidence overlap similarity. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>> >>>>Hello, >>>> >>>>Just found that for Scaffold of larger size it does explicitly specify >>>> the >>>>prediction source. >>>> >>>>Thanks, >>>>Parul >>>> >>>>> Hello, >>>>> >>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>calculated >>>>> externally and gff3 file was provided to option pred_gff). However >>>>> the >>>>> resulting gff3 source field does not mention if the prediction were >>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>> configuration file. Also is there any option where were could have >>>>> priority for SNAP predictions? >>>>> >>>>> Thanks and regards, >>>>> Parul Kudtarkar >>>>> >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From jason.stajich at gmail.com Mon Nov 26 14:32:42 2012 From: jason.stajich at gmail.com (Jason Stajich) Date: Mon, 26 Nov 2012 13:32:42 -0800 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: right - you can explicitly set the alphabet to 'dna' when building a sequence object but I don't know if this down in MAKER code that is tripping up? Jason On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" wrote: > This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage > >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: >> The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta >> >> And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 >> STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 >> STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 >> STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 >> STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage > >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: >> 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: >> Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker Mailing List > >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Jason Stajich jason.stajich at gmail.com jason at bioperl.org From parulk at caltech.edu Mon Nov 26 14:35:48 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 13:35:48 -0800 (PST) Subject: [maker-devel] AED score Message-ID: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Dear Maker community, For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K genes however I am getting 8 times the expected gene count indicating too many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes how to go about this? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Mon Nov 26 14:37:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:37:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The sequence object is being created well down into BioPerl (outside of my control), but I think I can explicitly set the alphabet to 'dna' by modifying the existing object just before calling the revcomp method to get around that. Thanks, Carson On 12-11-26 4:32 PM, "Jason Stajich" wrote: >right - you can explicitly set the alphabet to 'dna' when building a >sequence object but I don't know if this down in MAKER code that is >tripping up? > >Jason >On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" > wrote: > >> This is coming from BioPerl trying to guess the alphabet if one is not >>provided. The specific spot: >> >> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >> if ( $str =~ m/U/i ) { >> $alphabet = 'rna'; >> } else { >> $alphabet = 'dna'; >> } >> } else { >> $alphabet = 'protein'; >> } >> >> Easy enough to fix to allow for additional ambiguous nucleotides (just >>committed, in fact). It's probably best to explicitly set this when >>possible, though; it is a guess, after all. >> >> chris >> >> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>wrote: >> >>> good detective work there Carson! >>> >>> >>> Mark Yandell >>> Professor of Human Genetics >>> H.A. & Edna Benning Presidential Endowed Chair >>> Eccles Institute of Human Genetics >>> University of Utah >>> 15 North 2030 East, Room 2100 >>> Salt Lake City, UT 84112-5330 >>> ph:801-587-7707 >>> >>> ________________________________________ >>> From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>[carsonhh at gmail.com] >>> Sent: Sunday, November 25, 2012 9:10 PM >>> To: Daniel Standage >>> Cc: Maker Mailing List >>> Subject: Re: [maker-devel] Maker issues >>> >>> I think the problem is in the sequence of your scaffold. I pulled >>>this out of the exonerate alignment --> >>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>> >>> Notice the letters W, K, R, M, etc. While these are technically legal >>>nucleotides, many external programs, and in this case BioPerl doesn't >>>handle them well. >>> That is why you get --> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> >>> You might want to replace them in your input fasta with the letter 'N' >>>so they are treated as masked. You will have to delete the mpi_blastdb >>>directory to let maker rebuild the fasta indexes and you will probably >>>have to set clean_try=1 in the control files so that MAKER deletes old >>>result files that contain those characters on the retry. The other >>>error may be just a snowball effect from the first error, so you should >>>see of it still happens after fixing the input fasta file. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Friday, 23 November, 2012 3:06 PM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Thanks for your reply, and sorry for my delayed response. >>> >>> I have attached the first file you requested, but the other two do not >>>exist. I have attached a listing of the files in that directory. Let me >>>know if you need anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> wrote: >>> The first error is an IO error with your system. I've added some more >>>detail to the errors in the development version if you do an 'svn >>>update'. Then you will know the system specific reason why close or >>>opened failed. For the other error, could you send me this file --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>> >>> This one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta >>> >>> And this one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta >>> >>> thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Thursday, 8 November, 2012 9:32 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Scaling up to whole-genome annotation, things seem to be going well. >>>However, there are some intermittent issues. I've seen a couple >>>occurrences of the following error... >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> couldn't close >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>60. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_23 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_23 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> ...as well as one occurrence of this error. >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pd >>> >>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>> >>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>--showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>> >>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>> q93.est_exonerate.0 >>> #-------------------------------# >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>> STACK: Bio::PrimarySeqI::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>> STACK: Bio::LocatableSeq::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>nfo.pm:86 >>> STACK: Widget::exonerate::est2genome::assemble >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:686 >>> STACK: Widget::exonerate::est2genome::parse >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:961 >>> STACK: polisher::exonerate::est::e_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:82 >>> STACK: polisher::exonerate::est::polish >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:44 >>> STACK: GI::to_polisher >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>> STACK: GI::polish_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>> STACK: Process::MpiChunk::_go >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:1663 >>> STACK: Process::MpiChunk::run >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:335 >>> STACK: Process::MpiChunk::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:351 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_7 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_7 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> I'll let you know if I see anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> wrote: >>> Thanks. Typo now fixed on my end too ;-) >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Wednesday, 7 November, 2012 11:43 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Looked good for a while, but came across this error. >>> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> >>> --Next Contig-- >>> >>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>to localize and relaunched. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>>and is repeat masking. I'll let you know if there are any problems. >>>Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> wrote: >>> 1.006902 Bio::Root::Version >>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>It's fasta indexer is broken. I have an open bug I am trying to >>>resolve with the Bioperl developers, but for now use the CPAN version >>>of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> wrote: >>> Thanks. Could you also run with the --debug flag set on the command >>>line for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt >, Maker >>>Mailing List >>>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP >>>directory is on native disk space, and relaunched. I have attached the >>>output of the job that failed in <5 minutes. It looks pretty similar to >>>the errors I got the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >Jason Stajich >jason.stajich at gmail.com >jason at bioperl.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 14:46:48 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:46:48 -0500 Subject: [maker-devel] AED score In-Reply-To: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Message-ID: AED score with 1 are the ones you don't want. 0 is best and 1 is worst as it is a distance metric. You can use the AED_threshold parameter to require better matching to the evidence by setting it closer to 0. You can also try to increase protein homology evidence as some of your calls may be split genes due to lack of evidence linking them. --Carson On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >Dear Maker community, > >For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect 20-30K >genes however I am getting 8 times the expected gene count indicating too >many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if yes how >to go about this? > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 14:48:18 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:48:18 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Message-ID: They should show up as genemark or pred_gff:genemark. Could you verify that the input file from genemark indeed contained predictions that should have been on this contig as not all contigs may have calls from genemark? --Carson On 12-11-26 2:21 PM, "Parul Kudtarkar" wrote: >Hello Carson, > >Thanks for the feedback.Genemark was run outside maker and the resulting >gff3 file was provided as option to pred_gff. What would the source in the >gff3 of maker result state of the predictions where made from pred_gff? > >Thanks and regards, >Parul Kudtarkar > >> I see both augustus and snap derived predictions (match/match_part) with >> augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that >> were derived from these predictions. There are no predictions from >> genemark. Is that what you were expecting? If not could you specify how >> it varies. >> >> With respect to bootstrapping, it really depends how well trained your >> gene predictors are. In general only one round of bootstrapping may be >> necessary after newly training a gene predictor. >> >> Thanks, >> Carson >> >> >> >> On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson, >>> >>>That is correct. There were no pred_gff for smaller size >>>Scaffolds(~1.5kb >>>which is very small). I have attached a Scaffold of 1.5kb with no >>>predictions and another Scaffold of 28kb. It is of course expected that >>> we >>>would not get any gene-prediction for small size Scaffolds. >>> >>>For next maker run would you recommend bootstrap to reduce false >>>positives? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>> Is it possible that you just picked a contig that didn't have any >>>>pred_gff >>>> entries for snap and augustus the first time? The predictions you >>>>pass >>>> through should be of type match/match_part and will have the source as >>>> pred_gff:snap or pred_gff:augustus. Could you check and let me know >>>>or >>>> send me an example of entries from a contig you passed through and the >>>> results you are seeing? >>>> >>>> No. there is no priority given to one prediction over the other. They >>>>are >>>> choses based on evidence overlap similarity. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Hello, >>>>> >>>>>Just found that for Scaffold of larger size it does explicitly specify >>>>> the >>>>>prediction source. >>>>> >>>>>Thanks, >>>>>Parul >>>>> >>>>>> Hello, >>>>>> >>>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>>calculated >>>>>> externally and gff3 file was provided to option pred_gff). However >>>>>> the >>>>>> resulting gff3 source field does not mention if the prediction were >>>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>>> configuration file. Also is there any option where were could have >>>>>> priority for SNAP predictions? >>>>>> >>>>>> Thanks and regards, >>>>>> Parul Kudtarkar >>>>>> >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > From cjfields at illinois.edu Mon Nov 26 14:55:04 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 21:55:04 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> That makes sense. The change I made should also allow these sequences to 'just work', but this would of course require a BioPerl update. We could also make that change within BioPerl if needed if we know where it might be; it seems in this case a returned sequence should be 'dna' if the application is exonerate. chris On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > The sequence object is being created well down into BioPerl (outside of my > control), but I think I can explicitly set the alphabet to 'dna' by > modifying the existing object just before calling the revcomp method to > get around that. > > Thanks, > Carson > > > On 12-11-26 4:32 PM, "Jason Stajich" wrote: > >> right - you can explicitly set the alphabet to 'dna' when building a >> sequence object but I don't know if this down in MAKER code that is >> tripping up? >> >> Jason >> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >> wrote: >> >>> This is coming from BioPerl trying to guess the alphabet if one is not >>> provided. The specific spot: >>> >>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>> if ( $str =~ m/U/i ) { >>> $alphabet = 'rna'; >>> } else { >>> $alphabet = 'dna'; >>> } >>> } else { >>> $alphabet = 'protein'; >>> } >>> >>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>> committed, in fact). It's probably best to explicitly set this when >>> possible, though; it is a guess, after all. >>> >>> chris >>> >>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>> wrote: >>> >>>> good detective work there Carson! >>>> >>>> >>>> Mark Yandell >>>> Professor of Human Genetics >>>> H.A. & Edna Benning Presidential Endowed Chair >>>> Eccles Institute of Human Genetics >>>> University of Utah >>>> 15 North 2030 East, Room 2100 >>>> Salt Lake City, UT 84112-5330 >>>> ph:801-587-7707 >>>> >>>> ________________________________________ >>>> From: maker-devel-bounces at yandell-lab.org >>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>> [carsonhh at gmail.com] >>>> Sent: Sunday, November 25, 2012 9:10 PM >>>> To: Daniel Standage >>>> Cc: Maker Mailing List >>>> Subject: Re: [maker-devel] Maker issues >>>> >>>> I think the problem is in the sequence of your scaffold. I pulled >>>> this out of the exonerate alignment --> >>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>> >>>> Notice the letters W, K, R, M, etc. While these are technically legal >>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>> handle them well. >>>> That is why you get --> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> >>>> You might want to replace them in your input fasta with the letter 'N' >>>> so they are treated as masked. You will have to delete the mpi_blastdb >>>> directory to let maker rebuild the fasta indexes and you will probably >>>> have to set clean_try=1 in the control files so that MAKER deletes old >>>> result files that contain those characters on the retry. The other >>>> error may be just a snowball effect from the first error, so you should >>>> see of it still happens after fixing the input fasta file. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Friday, 23 November, 2012 3:06 PM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Thanks for your reply, and sorry for my delayed response. >>>> >>>> I have attached the first file you requested, but the other two do not >>>> exist. I have attached a listing of the files in that directory. Let me >>>> know if you need anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> > wrote: >>>> The first error is an IO error with your system. I've added some more >>>> detail to the errors in the development version if you do an 'svn >>>> update'. Then you will know the system specific reason why close or >>>> opened failed. For the other error, could you send me this file --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>> >>>> This one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta >>>> >>>> And this one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>> >>>> thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Thursday, 8 November, 2012 9:32 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Scaling up to whole-genome annotation, things seem to be going well. >>>> However, there are some intermittent issues. I've seen a couple >>>> occurrences of the following error... >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> couldn't close >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>> 60. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> ...as well as one occurrence of this error. >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pd >>>> >>>> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>> >>>> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>> --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>> >>>> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>> q93.est_exonerate.0 >>>> #-------------------------------# >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>> STACK: Bio::PrimarySeqI::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>>> STACK: Bio::LocatableSeq::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>> nfo.pm:86 >>>> STACK: Widget::exonerate::est2genome::assemble >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:686 >>>> STACK: Widget::exonerate::est2genome::parse >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:961 >>>> STACK: polisher::exonerate::est::e_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:82 >>>> STACK: polisher::exonerate::est::polish >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:44 >>>> STACK: GI::to_polisher >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>> STACK: GI::polish_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>> STACK: Process::MpiChunk::_go >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:1663 >>>> STACK: Process::MpiChunk::run >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:335 >>>> STACK: Process::MpiChunk::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:351 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> I'll let you know if I see anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> > wrote: >>>> Thanks. Typo now fixed on my end too ;-) >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Looked good for a while, but came across this error. >>>> >>>> total clusters:20 now processing 0 >>>> flattening EST clusters >>>> doing tblastx of alt-ESTs >>>> Undefined subroutine &GI::loalize_file called at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while doing tblastx of alt-ESTs >>>> ERROR: Chunk failed at level:4, tier_type:2 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> >>>> --Next Contig-- >>>> >>>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>> to localize and relaunched. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> > wrote: >>>> Done. >>>> >>>> Test job has successfully cleared the preliminary Fasta indexing steps >>>> and is repeat masking. I'll let you know if there are any problems. >>>> Thanks! >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> > wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>> It's fasta indexer is broken. I have an open bug I am trying to >>>> resolve with the Bioperl developers, but for now use the CPAN version >>>> of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> > wrote: >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt >, Maker >>>> Mailing List >>>> > >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to >>>> the errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > From carsonhh at gmail.com Mon Nov 26 15:07:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 17:07:46 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> Message-ID: The seq object is being create in Bio::Search::HSP::HSPI.pm line 578 which itself is several layers deep into BioPerl after creation of a Bio::Search::Hit object. I think explicitly setting the alphabet would require modifications to a number of modules that create hits from Bio::SearchIO so that the alphabet gets stored early on, but that seems like a lot of work and could break any number of things along the way. The current change should allow BioPerl to guess right. After all the upstream code did explicitly call revcomp, so it obviously thinks that the sequence can be reverse complimented, so BioPerl is now just verifying that the alphabet matches legal characters, even if it is an unlikely match. --Carson On 12-11-26 4:55 PM, "Fields, Christopher J" wrote: >That makes sense. The change I made should also allow these sequences to >'just work', but this would of course require a BioPerl update. > >We could also make that change within BioPerl if needed if we know where >it might be; it seems in this case a returned sequence should be 'dna' if >the application is exonerate. > >chris > >On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > >> The sequence object is being created well down into BioPerl (outside of >>my >> control), but I think I can explicitly set the alphabet to 'dna' by >> modifying the existing object just before calling the revcomp method to >> get around that. >> >> Thanks, >> Carson >> >> >> On 12-11-26 4:32 PM, "Jason Stajich" wrote: >> >>> right - you can explicitly set the alphabet to 'dna' when building a >>> sequence object but I don't know if this down in MAKER code that is >>> tripping up? >>> >>> Jason >>> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >>> wrote: >>> >>>> This is coming from BioPerl trying to guess the alphabet if one is not >>>> provided. The specific spot: >>>> >>>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>>> if ( $str =~ m/U/i ) { >>>> $alphabet = 'rna'; >>>> } else { >>>> $alphabet = 'dna'; >>>> } >>>> } else { >>>> $alphabet = 'protein'; >>>> } >>>> >>>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>>> committed, in fact). It's probably best to explicitly set this when >>>> possible, though; it is a guess, after all. >>>> >>>> chris >>>> >>>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>>> >>>> wrote: >>>> >>>>> good detective work there Carson! >>>>> >>>>> >>>>> Mark Yandell >>>>> Professor of Human Genetics >>>>> H.A. & Edna Benning Presidential Endowed Chair >>>>> Eccles Institute of Human Genetics >>>>> University of Utah >>>>> 15 North 2030 East, Room 2100 >>>>> Salt Lake City, UT 84112-5330 >>>>> ph:801-587-7707 >>>>> >>>>> ________________________________________ >>>>> From: maker-devel-bounces at yandell-lab.org >>>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>>> [carsonhh at gmail.com] >>>>> Sent: Sunday, November 25, 2012 9:10 PM >>>>> To: Daniel Standage >>>>> Cc: Maker Mailing List >>>>> Subject: Re: [maker-devel] Maker issues >>>>> >>>>> I think the problem is in the sequence of your scaffold. I pulled >>>>> this out of the exonerate alignment --> >>>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>>> >>>>> Notice the letters W, K, R, M, etc. While these are technically >>>>>legal >>>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>>> handle them well. >>>>> That is why you get --> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> >>>>> You might want to replace them in your input fasta with the letter >>>>>'N' >>>>> so they are treated as masked. You will have to delete the >>>>>mpi_blastdb >>>>> directory to let maker rebuild the fasta indexes and you will >>>>>probably >>>>> have to set clean_try=1 in the control files so that MAKER deletes >>>>>old >>>>> result files that contain those characters on the retry. The other >>>>> error may be just a snowball effect from the first error, so you >>>>>should >>>>> see of it still happens after fixing the input fasta file. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Friday, 23 November, 2012 3:06 PM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Thanks for your reply, and sorry for my delayed response. >>>>> >>>>> I have attached the first file you requested, but the other two do >>>>>not >>>>> exist. I have attached a listing of the files in that directory. Let >>>>>me >>>>> know if you need anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>>> > wrote: >>>>> The first error is an IO error with your system. I've added some >>>>>more >>>>> detail to the errors in the development version if you do an 'svn >>>>> update'. Then you will know the system specific reason why close or >>>>> opened failed. For the other error, could you send me this file --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_ >>>>>7/ >>>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>>> >>>>> This one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta >>>>> >>>>> And this one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>>> >>>>> thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Thursday, 8 November, 2012 9:32 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Scaling up to whole-genome annotation, things seem to be going well. >>>>> However, there are some intermittent issues. I've seen a couple >>>>> occurrences of the following error... >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> couldn't close >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm >>>>>line >>>>> 60. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> ...as well as one occurrence of this error. >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> maker.output/maker.pd >>>>> >>>>> >>>>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93. >>>>>fo >>>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>>> >>>>> >>>>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datas >>>>>to >>>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>>> --showcigar --percent 20 > >>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>>> >>>>> >>>>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >>>>>af >>>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>>> q93.est_exonerate.0 >>>>> #-------------------------------# >>>>> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> STACK: Error::throw >>>>> STACK: Bio::Root::Root::throw >>>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>>> STACK: Bio::PrimarySeqI::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:38 >>>>>1 >>>>> STACK: Bio::LocatableSeq::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:5 >>>>>77 >>>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice >>>>>_i >>>>> nfo.pm:86 >>>>> STACK: Widget::exonerate::est2genome::assemble >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:686 >>>>> STACK: Widget::exonerate::est2genome::parse >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:961 >>>>> STACK: polisher::exonerate::est::e_exonerate >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:82 >>>>> STACK: polisher::exonerate::est::polish >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:44 >>>>> STACK: GI::to_polisher >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>>> STACK: GI::polish_exonerate >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>>> STACK: Process::MpiChunk::_go >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:1663 >>>>> STACK: Process::MpiChunk::run >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:335 >>>>> STACK: Process::MpiChunk::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:351 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>>> ----------------------------------------------------------- >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> I'll let you know if I see anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Typo now fixed on my end too ;-) >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Looked good for a while, but came across this error. >>>>> >>>>> total clusters:20 now processing 0 >>>>> flattening EST clusters >>>>> doing tblastx of alt-ESTs >>>>> Undefined subroutine &GI::loalize_file called at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>2648. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while doing tblastx of alt-ESTs >>>>> ERROR: Chunk failed at level:4, tier_type:2 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> >>>>> --Next Contig-- >>>>> >>>>> It seems pretty clear that there is a typo in GI.pm. I changed >>>>>loalize >>>>> to localize and relaunched. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>>> > wrote: >>>>> Done. >>>>> >>>>> Test job has successfully cleared the preliminary Fasta indexing >>>>>steps >>>>> and is repeat masking. I'll let you know if there are any problems. >>>>> Thanks! >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>>> > wrote: >>>>> 1.006902 Bio::Root::Version >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.p >>>>>m >>>>> >>>>> One thing I noticed, in the debug output is that you are using >>>>>Bioperl >>>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>>> It's fasta indexer is broken. I have an open bug I am trying to >>>>> resolve with the Bioperl developers, but for now use the CPAN version >>>>> of Bioperl. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:14 AM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Debug output attached (bzip2 compressed). >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt >, >>>>>Maker >>>>> Mailing List >>>>> > >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached >>>>>the >>>>> output of the job that failed in <5 minutes. It looks pretty similar >>>>>to >>>>> the errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> maker-devel mailing list >>>>> maker-devel at box290.bluehost.com >>>>> >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > From parulk at caltech.edu Mon Nov 26 15:15:58 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 14:15:58 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <2223.131.215.15.234.1353968158.squirrel@webmail.caltech.edu> Dear Carson, Thanks, I retrain/rerun using better AED score to filter false negatives. > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From daniel.standage at gmail.com Fri Nov 23 13:06:34 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Fri, 23 Nov 2012 15:06:34 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> >> It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to >> *localize* and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < >> daniel.standage at gmail.com> wrote: >> >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>> and is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List < >>>>> maker-devel at yandell-lab.org> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached the >>>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>>> errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... 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-rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303233.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303234.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303235.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038212.gnl%7CAmel_4%2E5%7CGB40495-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB40142-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB53378-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038224.gnl%7CAmel_4%2E5%7CGB43258-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:19 scaffold_23.1037324-1038248.gnl%7CAmel_4%2E5%7CGB48486-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 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Nov 8 06:55 scaffold_23.11767-15264.gnl%7CDmel_r5%2E47%7CFBpp0079114.p_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:20 scaffold_23.1177210-1187515.comp55832_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 06:57 scaffold_23.118600-121630.comp56223_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:05 scaffold_23.119493-121535.gnl%7CAmel_4%2E5%7CGB42515-PA.p_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0080719.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0085457.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:24 scaffold_23.11.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 33K Nov 8 06:28 scaffold_23.11.drosophila.rb.out -rw-r--r-- 1 dstandag biol 469K Nov 8 12:05 scaffold_23.11.final.section -rw-r--r-- 1 dstandag biol 198K Nov 8 11:19 scaffold_23.11.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 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-rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:25 scaffold_23.1239438-1240065.comp58697_c2_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:25 scaffold_23.1240020-1240577.comp51041_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:58 scaffold_23.125651-126606.comp51692_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:57 scaffold_23.126190-129712.comp51692_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:58 scaffold_23.126190-129712.comp51692_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:05 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dstandag biol 5.4K Nov 8 07:05 scaffold_23.129450-131047.gnl%7CAmel_4%2E5%7CGB47192-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 11:35 scaffold_23.1296927-1297434.gnl%7CAmel_4%2E5%7CGB43383-PA.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:29 scaffold_23.12.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 24K Nov 8 06:29 scaffold_23.12.drosophila.rb.out -rw-r--r-- 1 dstandag biol 343K Nov 8 12:05 scaffold_23.12.final.section -rw-r--r-- 1 dstandag biol 119K Nov 8 11:24 scaffold_23.12.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 104K Nov 8 11:28 scaffold_23.12.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 41K Nov 8 07:09 scaffold_23.1-2.raw.section -rw-r--r-- 1 dstandag biol 344K Nov 8 11:29 scaffold_23.12.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:29 scaffold_23.12.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1307615-1308418.comp1419599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 26K Nov 8 11:35 scaffold_23.1308043-1330696.gnl%7CAmel_4%2E5%7CGB48919-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1308162-1309528.comp44341_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302629.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302630.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302631.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1330258.gnl%7CDmel_r5%2E47%7CFBpp0302633.p_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:30 scaffold_23.1309128-1310251.comp26811_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 11:30 scaffold_23.1309844-1319042.comp55832_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:58 scaffold_23.131077-131586.comp59045_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 132K Nov 8 11:40 scaffold_23.13-14.raw.section -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1316714-1317272.comp1218705_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:59 scaffold_23.131685-132925.comp58909_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:59 scaffold_23.131685-134704.comp58909_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 8.3K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 11:30 scaffold_23.1318842-1326844.comp55832_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 11:30 scaffold_23.1318842-1329152.comp55832_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 11:30 scaffold_23.1318842-1331426.comp55832_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 06:58 scaffold_23.132429-133368.comp59433_c2_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1325517-1326265.comp1845494_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:59 scaffold_23.132575-133077.comp59433_c2_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 06:59 scaffold_23.132639-133189.comp59433_c2_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:58 scaffold_23.132947-134704.comp58909_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:59 scaffold_23.132947-134801.comp58909_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 11:30 scaffold_23.1331331-1332259.comp40535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:59 scaffold_23.133194-134178.comp58909_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 11:30 scaffold_23.1331948-1333303.comp32761_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1333133-1334007.comp56864_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1333600-1334315.comp56864_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 11:30 scaffold_23.1333918-1335419.comp56864_c3_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1335705.comp56864_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1337728.comp56864_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:35 scaffold_23.1334768-1337724.gnl%7CAmel_4%2E5%7CGB48917-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:05 scaffold_23.133512-135390.gnl%7CAmel_4%2E5%7CGB45366-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1335366-1335970.comp1729875_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:30 scaffold_23.1336887-1337499.comp1746631_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:00 scaffold_23.133757-134452.comp58909_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1340213-1340817.comp3166415_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1341145-1341745.comp2137934_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1341790-1342546.comp2308491_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:58 scaffold_23.134716-136043.comp58909_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:30 scaffold_23.1351224-1351773.comp56864_c3_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1351855-1352444.comp49157_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:30 scaffold_23.1352403-1353237.comp50400_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 11:30 scaffold_23.1352824-1354274.comp50400_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1353863-1354457.comp32051_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:30 scaffold_23.1354103-1354916.comp32051_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 11:30 scaffold_23.1354495-1355883.comp28788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:30 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scaffold_23.1361370-1362023.comp63024_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1361962-1362628.comp56945_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 11:30 scaffold_23.1362208-1364017.comp56945_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1363621-1364241.comp56945_c15_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1363824-1364656.comp56945_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:30 scaffold_23.1364241-1365534.comp56945_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 11:30 scaffold_23.1365475-1366354.comp58627_c6_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1365475-1367018.comp58627_c6_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 11:30 scaffold_23.1366668-1368555.comp58344_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1369001-1370345.comp57731_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1369932-1370651.comp57731_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.137055-137860.comp53917_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1370982-1372429.comp58968_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 scaffold_23.1372006-1372825.comp56955_c2_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 11:30 scaffold_23.1373883-1375967.comp53188_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:00 scaffold_23.137439-138464.comp53917_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1376023-1376568.comp58089_c12_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:35 scaffold_23.1389507.1410090.0.comp58089_c6_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 scaffold_23.1389801-1390543.comp47217_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 07:00 scaffold_23.138981-140060.comp58679_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1389854-1390711.comp47217_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 11:36 scaffold_23.1390291-1390966.comp47217_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 11:36 scaffold_23.1390743-1392000.comp58289_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1391945-1392597.comp58289_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 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-rw-r--r-- 1 dstandag biol 5.4K Nov 8 11:36 scaffold_23.1397553-1399112.comp58089_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.139809-140616.comp39902_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1398718-1399314.comp58089_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1398899-1399721.comp58089_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:36 scaffold_23.1399307-1400290.comp58089_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 11:36 scaffold_23.1399900-1400941.comp58089_c17_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 58K Nov 8 11:35 scaffold_23.13.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 34K Nov 8 06:30 scaffold_23.13.drosophila.rb.out -rw-r--r-- 1 dstandag biol 1.5M Nov 8 12:05 scaffold_23.13.final.section -rw-r--r-- 1 dstandag biol 364K Nov 8 11:29 scaffold_23.13.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 430K Nov 8 11:33 scaffold_23.13.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 1.4M Nov 8 11:35 scaffold_23.13.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:30 scaffold_23.13.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1400609-1401459.comp55139_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1401269-1402022.comp55139_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1401609-1402216.comp55139_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:36 scaffold_23.1402425-1403729.comp53666_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:00 scaffold_23.140332-144653.comp32064_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1403482-1404578.comp48783_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1404302-1405136.comp56313_c10_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1404714-1405577.comp56313_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1404752-1405577.comp56313_c9_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1405378-1406432.comp58905_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406035-1406617.comp58905_c6_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406210-1406799.comp57287_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 11:36 scaffold_23.1406210-1408214.comp57287_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409289.comp57287_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409306.comp57287_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1408987-1409890.comp55527_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:36 scaffold_23.1409724-1410684.comp53099_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410284-1410885.comp53099_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1410463-1411098.comp53099_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410682-1411329.comp53099_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411082-1411787.comp53099_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:40 scaffold_23.1411196-1420373.gnl%7CAmel_4%2E5%7CGB48913-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1411769-1412299.comp53730_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411806-1412343.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 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2.1K Nov 8 11:46 scaffold_23.1628188-1628869.comp53690_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1628995-1629629.comp1757695_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:46 scaffold_23.1629447-1630245.comp2225268_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:51 scaffold_23.1630078-1640599.gnl%7CAmel_4%2E5%7CGB48912-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1633935-1634941.comp469996_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1634612-1635227.comp1032535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:46 scaffold_23.1634842-1635615.comp9891_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:46 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06:46 scaffold_23.47976-52664.comp57565_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481059-481744.comp5788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:15 scaffold_23.481631-482286.comp31314_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481869-482552.comp1406842_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K 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-rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:22 scaffold_23.4.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503515-504045.comp57130_c2_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503604-504201.comp59180_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:20 scaffold_23.503604-504204.comp59180_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.503604-504276.comp59180_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:20 scaffold_23.503604-504336.comp59180_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:20 scaffold_23.503654-504201.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:20 scaffold_23.503654-504350.comp59180_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503699-504221.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 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2.2K Nov 8 07:20 scaffold_23.570506-571138.comp58475_c5_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:47 scaffold_23.57128-61415.comp57935_c3_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 07:20 scaffold_23.577559-578709.comp58715_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 07:20 scaffold_23.577559-578885.comp58715_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.578520-579331.comp17262_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:20 scaffold_23.579634-580662.comp19872_c0_seq1.est_exonerate -rw-r--r-- 1 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dstandag biol 4.5K Nov 8 07:20 scaffold_23.588308-588965.comp58681_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:20 scaffold_23.588513-589494.comp58681_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:21 scaffold_23.588513-589516.comp58681_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:26 scaffold_23.589528-590438.comp56568_c1_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 07:26 scaffold_23.590043-590860.comp56568_c1_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:26 scaffold_23.590182-590860.comp56568_c1_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CAmel_4%2E5%7CGB42672-PA.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0291239.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0293789.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 08:01 scaffold_23.590687-592189.gnl%7CDmel_r5%2E47%7CFBpp0071071.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0081035.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303794.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303795.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303796.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590885-592138.gnl%7CAmel_4%2E5%7CGB44981-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590894-591937.gnl%7CAmel_4%2E5%7CGB44980-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590909-591693.gnl%7CDmel_r5%2E47%7CFBpp0083755.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:26 scaffold_23.591776-592368.comp42067_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.592659-593271.comp59308_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.592659-593380.comp59308_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:26 scaffold_23.592965-593648.comp48548_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.593120-593648.comp48548_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:26 scaffold_23.593237-593841.comp59308_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.594070-594730.comp1421803_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:26 scaffold_23.599941-600713.comp58738_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 47K Nov 8 07:25 scaffold_23.5.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 49K Nov 8 06:22 scaffold_23.5.drosophila.rb.out -rw-r--r-- 1 dstandag biol 917K Nov 8 12:05 scaffold_23.5.final.section -rw-r--r-- 1 dstandag biol 730K Nov 8 07:19 scaffold_23.5.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 416K Nov 8 07:23 scaffold_23.5.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 976K Nov 8 07:25 scaffold_23.5.raw.section -rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:23 scaffold_23.5.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.600393-600917.comp59155_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:26 scaffold_23.600937-601763.comp1225959_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 08:01 scaffold_23.604967-608877.gnl%7CAmel_4%2E5%7CGB43104-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.606823-608989.comp51953_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:26 scaffold_23.608733-612437.comp56721_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:27 scaffold_23.608733-612437.comp56721_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609085-612369.gnl%7CAmel_4%2E5%7CGB54556-PA.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0070184.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303734.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303735.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0071164.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0304872.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.61000-61642.comp57935_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:01 scaffold_23.612645-614365.gnl%7CAmel_4%2E5%7CGB43132-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.612828-614317.gnl%7CDmel_r5%2E47%7CFBpp0074633.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.613400-614111.gnl%7CDmel_r5%2E47%7CFBpp0075906.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:26 scaffold_23.614151-614876.comp1433111_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:27 scaffold_23.614490-616677.comp62542_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615220-616300.gnl%7CDmel_r5%2E47%7CFBpp0080690.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615229-616300.gnl%7CAmel_4%2E5%7CGB48404-PA.p_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 07:30 scaffold_23.616573-622123.comp53298_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 06:55 scaffold_23.61662-63231.gnl%7CAmel_4%2E5%7CGB47823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:01 scaffold_23.617032-621897.gnl%7CAmel_4%2E5%7CGB43186-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.617361-621707.gnl%7CDmel_r5%2E47%7CFBpp0078372.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 06:49 scaffold_23.62025-63600.comp57576_c4_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 scaffold_23.62037-63192.gnl%7CDmel_r5%2E47%7CFBpp0070204.p_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 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-rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:27 scaffold_23.622010-624802.comp57205_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 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dstandag biol 9.8K Nov 8 07:27 scaffold_23.622010-625026.comp57205_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:30 scaffold_23.622010-625026.comp57205_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:28 scaffold_23.622010-625026.comp57205_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:30 scaffold_23.622010-625178.comp57205_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:27 scaffold_23.622010-625178.comp57205_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 scaffold_23.622010-625178.comp57205_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 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-rw-r--r-- 1 dstandag biol 6.9K Nov 8 08:01 scaffold_23.635723-637373.gnl%7CDmel_r5%2E47%7CFBpp0082101.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:30 scaffold_23.637770-638562.comp42460_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:30 scaffold_23.638373-640543.comp40473_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649502.gnl%7CAmel_4%2E5%7CGB43214-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649511.gnl%7CDmel_r5%2E47%7CFBpp0292225.p_exonerate -rw-r--r-- 1 dstandag biol 27K Nov 8 08:01 scaffold_23.638434-649538.gnl%7CAmel_4%2E5%7CGB45049-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.638434-649601.gnl%7CDmel_r5%2E47%7CFBpp0288420.p_exonerate -rw-r--r-- 1 dstandag biol 55K Nov 8 08:01 scaffold_23.638434-650174.gnl%7CAmel_4%2E5%7CGB49952-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638437-649103.gnl%7CAmel_4%2E5%7CGB42359-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638440-647567.gnl%7CAmel_4%2E5%7CGB55144-PA.p_exonerate -rw-r--r-- 1 dstandag biol 28K Nov 8 08:01 scaffold_23.638440-649430.gnl%7CDmel_r5%2E47%7CFBpp0293284.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638443-649532.gnl%7CAmel_4%2E5%7CGB42373-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.63987-64717.comp59376_c14_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 07:30 scaffold_23.640205-641458.comp934535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.641067-641742.comp17454_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 08:01 scaffold_23.641259-642288.gnl%7CAmel_4%2E5%7CGB41007-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K Nov 8 07:30 scaffold_23.641345-642764.comp17454_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:30 scaffold_23.642369-643170.comp1226599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.642760-643453.comp3200316_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.64294-84968.comp42086_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:01 scaffold_23.645509-646340.gnl%7CAmel_4%2E5%7CGB49823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.647483-648154.comp3284778_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:55 scaffold_23.649-1243.gnl%7CDmel_r5%2E47%7CFBpp0290776.p_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:01 scaffold_23.649971-651261.gnl%7CAmel_4%2E5%7CGB49951-PA.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:30 scaffold_23.651850-655866.comp56215_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 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Nov 8 08:02 scaffold_23.659787-662130.gnl%7CDmel_r5%2E47%7CFBpp0293463.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075012.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075013.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0073292.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:02 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0290751.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0304481.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659802-662082.gnl%7CDmel_r5%2E47%7CFBpp0075772.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659802-662088.gnl%7CDmel_r5%2E47%7CFBpp0293948.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662097.gnl%7CAmel_4%2E5%7CGB47477-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662121.gnl%7CAmel_4%2E5%7CGB41363-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662139.gnl%7CAmel_4%2E5%7CGB43707-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662290.gnl%7CAmel_4%2E5%7CGB51586-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662299.gnl%7CAmel_4%2E5%7CGB49425-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0089153.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0290826.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304233.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304234.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0305596.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659808-662094.gnl%7CAmel_4%2E5%7CGB52193-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CAmel_4%2E5%7CGB47284-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0076890.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0085042.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB44431-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB49047-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083843.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083906.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659817-662079.gnl%7CAmel_4%2E5%7CGB46102-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0073585.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0082346.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0305521.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:31 scaffold_23.664598-665339.comp57441_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.664951-665488.comp59321_c5_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 06:55 scaffold_23.66506-67079.gnl%7CAmel_4%2E5%7CGB47837-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088318.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088319.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088320.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089257.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089258.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0288398.p_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:31 scaffold_23.665135-665802.comp285497_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 07:31 scaffold_23.665399-666883.comp53689_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.666469-667197.comp53689_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.667162-667951.comp52180_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:31 scaffold_23.667162-671428.comp52180_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 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dstandag biol 3.3K Nov 8 07:31 scaffold_23.667978-669042.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 07:31 scaffold_23.668017-669001.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 07:31 scaffold_23.668059-668959.comp59180_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.668936-669683.comp382769_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.66912-67979.comp5946_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:31 scaffold_23.669726-671764.comp52180_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 06:49 scaffold_23.67030-67979.comp5946_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:31 scaffold_23.671029-677447.comp52180_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.671054-671764.comp52180_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.671886-672575.comp57527_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671901-672561.comp57527_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672538.comp57527_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672575.comp57527_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41577-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41578-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB46989-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB50263-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.672098-672598.comp59502_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:31 scaffold_23.672970-673610.comp59089_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 07:31 scaffold_23.673324-674422.comp53293_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:31 scaffold_23.673999-677447.comp52180_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076415.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076416.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302862.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302863.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302864.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0081016.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0304068.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.675963-676551.comp408860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:31 scaffold_23.677207-677898.comp772804_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 06:49 scaffold_23.67721-68472.comp350940_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.677525-678233.comp53322_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 scaffold_23.677908-678920.comp53322_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:31 scaffold_23.677908-679249.comp53322_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.9K Nov 8 07:31 scaffold_23.678839-682919.comp32442_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:31 scaffold_23.679979-680866.comp36035_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 07:31 scaffold_23.679979-681267.comp36035_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.1M Nov 8 11:03 scaffold_23.6-7.raw.section -rw-r--r-- 1 dstandag biol 1.8K Nov 8 07:31 scaffold_23.680259-680866.comp36035_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.680259-681267.comp36035_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 08:02 scaffold_23.680843-682232.gnl%7CAmel_4%2E5%7CGB50275-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 08:02 scaffold_23.680846-682172.gnl%7CDmel_r5%2E47%7CFBpp0070979.p_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:50 scaffold_23.682524-683916.comp33074_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:44 scaffold_23.683503-684184.comp59066_c0_seq140.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:46 scaffold_23.683503-688813.comp59066_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:35 scaffold_23.683503-688813.comp59066_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:53 scaffold_23.683503-688813.comp59066_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:50 scaffold_23.683503-688813.comp59066_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:33 scaffold_23.683503-688813.comp59066_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:55 scaffold_23.683503-688813.comp59066_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:37 scaffold_23.683503-688813.comp59066_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:36 scaffold_23.683503-688813.comp59066_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:44 scaffold_23.683503-688813.comp59066_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683763-688813.comp59066_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683882-688813.comp59066_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:36 scaffold_23.683882-688813.comp59066_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:48 scaffold_23.683882-688813.comp59066_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:51 scaffold_23.683882-688813.comp59066_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:56 scaffold_23.683882-688813.comp59066_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:47 scaffold_23.683882-688813.comp59066_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:32 scaffold_23.683882-688813.comp59066_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:42 scaffold_23.683882-688813.comp59066_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:49 scaffold_23.683882-688813.comp59066_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:50 scaffold_23.683882-688813.comp59066_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:35 scaffold_23.683988-688813.comp59066_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:32 scaffold_23.684333-688813.comp59066_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:49 scaffold_23.684333-688813.comp59066_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:51 scaffold_23.684333-688813.comp59066_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:52 scaffold_23.684333-688813.comp59066_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:54 scaffold_23.684333-688813.comp59066_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:33 scaffold_23.684333-688813.comp59066_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:44 scaffold_23.684333-688813.comp59066_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:39 scaffold_23.684333-688813.comp59066_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:43 scaffold_23.684333-688975.comp59066_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:53 scaffold_23.684333-688975.comp59066_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:45 scaffold_23.684333-688975.comp59066_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:55 scaffold_23.684333-688975.comp59066_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721817.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721839.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 12K Nov 8 07:56 scaffold_23.684971-688813.comp59066_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.684971-688813.comp59066_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.684971-688813.comp59066_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:42 scaffold_23.684971-688813.comp59066_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:37 scaffold_23.684971-688975.comp59066_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:41 scaffold_23.684971-688975.comp59066_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.684975-688813.comp59066_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:39 scaffold_23.684975-688813.comp59066_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.684975-688813.comp59066_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.684975-688813.comp59066_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:45 scaffold_23.684975-688975.comp59066_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:53 scaffold_23.684975-688975.comp59066_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq2%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 12K Nov 8 07:38 scaffold_23.685264-688813.comp59066_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.685264-688813.comp59066_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.685264-688813.comp59066_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685264-688813.comp59066_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685264-688813.comp59066_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:52 scaffold_23.685264-688813.comp59066_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:32 scaffold_23.685264-688813.comp59066_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685264-688813.comp59066_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:37 scaffold_23.685264-688975.comp59066_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.685264-688975.comp59066_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685264-688975.comp59066_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685334-688813.comp59066_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685334-688813.comp59066_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685334-688813.comp59066_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:48 scaffold_23.685334-688813.comp59066_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685334-688813.comp59066_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:49 scaffold_23.685334-688813.comp59066_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685334-688975.comp59066_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:46 scaffold_23.685334-688975.comp59066_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.685334-688975.comp59066_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.68540-69483.comp433_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 11:02 scaffold_23.685479.720745.0.gnl%7CAmel_4%2E5%7CGB49172-PA%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072421%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072422%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0290562%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304412%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304413%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304414%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 11K Nov 8 07:44 scaffold_23.685588-688813.comp59066_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685588-688813.comp59066_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:33 scaffold_23.685588-688813.comp59066_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:51 scaffold_23.685588-688813.comp59066_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:32 scaffold_23.685588-688813.comp59066_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:49 scaffold_23.685588-688813.comp59066_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:52 scaffold_23.685801-688813.comp59066_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:41 scaffold_23.685801-688813.comp59066_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:44 scaffold_23.685801-688813.comp59066_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:42 scaffold_23.685801-688813.comp59066_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:46 scaffold_23.685801-688813.comp59066_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:54 scaffold_23.685801-688813.comp59066_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:51 scaffold_23.685801-688813.comp59066_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:45 scaffold_23.685801-688975.comp59066_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:42 scaffold_23.685801-688975.comp59066_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:32 scaffold_23.685801-688975.comp59066_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:37 scaffold_23.685801-688975.comp59066_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:38 scaffold_23.686019-688813.comp59066_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:37 scaffold_23.686019-688813.comp59066_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 07:52 scaffold_23.686019-688813.comp59066_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:42 scaffold_23.686019-688813.comp59066_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:45 scaffold_23.686019-688975.comp59066_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:56 scaffold_23.686019-688975.comp59066_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:32 scaffold_23.686019-688975.comp59066_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:55 scaffold_23.686019-688975.comp59066_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:52 scaffold_23.686019-688975.comp59066_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:43 scaffold_23.686506-688813.comp59066_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686506-688813.comp59066_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:48 scaffold_23.686506-688813.comp59066_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:38 scaffold_23.686506-688813.comp59066_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:54 scaffold_23.686506-688813.comp59066_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:34 scaffold_23.686506-688813.comp59066_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:44 scaffold_23.686506-688813.comp59066_c0_seq135.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:35 scaffold_23.686506-688975.comp59066_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:51 scaffold_23.686506-688975.comp59066_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:43 scaffold_23.686506-688975.comp59066_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:38 scaffold_23.686506-688975.comp59066_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:51 scaffold_23.686591-688813.comp59066_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686591-688813.comp59066_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:44 scaffold_23.686591-688813.comp59066_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:32 scaffold_23.686591-688813.comp59066_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:41 scaffold_23.686591-688813.comp59066_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:54 scaffold_23.686591-688975.comp59066_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:39 scaffold_23.686591-688975.comp59066_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:56 scaffold_23.686591-688975.comp59066_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:40 scaffold_23.686591-688975.comp59066_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:46 scaffold_23.686591-688975.comp59066_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:45 scaffold_23.686591-688975.comp59066_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:49 scaffold_23.686979-688813.comp59066_c0_seq136.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:51 scaffold_23.686979-688813.comp59066_c0_seq139.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:39 scaffold_23.686979-688975.comp59066_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:51 scaffold_23.686979-688975.comp59066_c0_seq137.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:54 scaffold_23.686979-688975.comp59066_c0_seq138.est_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 07:56 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scaffold_23.690234-691062.comp58228_c7_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 06:49 scaffold_23.69062-69744.comp433_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 08:03 scaffold_23.692420-694948.comp51249_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 08:03 scaffold_23.694556-695181.comp839860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 scaffold_23.695279-710945.gnl%7CAmel_4%2E5%7CGB49172-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072421.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072422.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0290562.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304412.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304413.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 08:03 scaffold_23.696083-696661.comp59447_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 08:03 scaffold_23.696083-696714.comp59447_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 08:03 scaffold_23.696083-696748.comp59447_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:03 scaffold_23.696083-696759.comp59447_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 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dstandag biol 957K Nov 8 08:01 scaffold_23.6.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 30K Nov 8 06:23 scaffold_23.6.drosophila.rb.out -rw-r--r-- 1 dstandag biol 4.8M Nov 8 12:05 scaffold_23.6.final.section -rw-r--r-- 1 dstandag biol 2.7M Nov 8 07:25 scaffold_23.6.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 1.2M Nov 8 07:59 scaffold_23.6.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 5.5M Nov 8 08:02 scaffold_23.6.raw.section -rw-r--r-- 1 dstandag biol 562K Nov 8 06:24 scaffold_23.6.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.70076-70676.comp16610_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0089425.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0290563.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0304411.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.70266-70881.comp1005591_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.71180-72221.comp36225_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:03 scaffold_23.712367-714691.gnl%7CAmel_4%2E5%7CGB49161-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 08:03 scaffold_23.712520-713560.comp54814_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:03 scaffold_23.712520-713766.comp54814_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 scaffold_23.712609-713560.comp54814_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.712609-713766.comp54814_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:50 scaffold_23.716125-720215.comp58983_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:04 scaffold_23.716125-720215.comp58983_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:47 scaffold_23.716125-720215.comp58983_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:46 scaffold_23.716125-720215.comp58983_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:45 scaffold_23.716125-720215.comp58983_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:51 scaffold_23.716125-720215.comp58983_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720215.comp58983_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.716125-720215.comp58983_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:06 scaffold_23.716125-720215.comp58983_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:53 scaffold_23.716125-720628.comp58983_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:03 scaffold_23.716125-720628.comp58983_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-720628.comp58983_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:48 scaffold_23.716125-720628.comp58983_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:51 scaffold_23.716125-720628.comp58983_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:06 scaffold_23.716125-720628.comp58983_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720628.comp58983_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720628.comp58983_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720628.comp58983_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:50 scaffold_23.716125-720628.comp58983_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:05 scaffold_23.716125-720628.comp58983_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721166.comp58983_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:07 scaffold_23.716125-721166.comp58983_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:03 scaffold_23.716125-721166.comp58983_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:05 scaffold_23.716125-721166.comp58983_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:51 scaffold_23.716125-721166.comp58983_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:08 scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:46 scaffold_23.716125-721460.comp58983_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721460.comp58983_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:45 scaffold_23.716125-721460.comp58983_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:53 scaffold_23.716125-721460.comp58983_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-721460.comp58983_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:48 scaffold_23.716125-721460.comp58983_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:44 scaffold_23.716125-721460.comp58983_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:52 scaffold_23.716125-721460.comp58983_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-721720.comp58983_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:46 scaffold_23.716125-721720.comp58983_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:45 scaffold_23.716125-721720.comp58983_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 08:06 scaffold_23.716125-721720.comp58983_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:48 scaffold_23.716125-721720.comp58983_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:47 scaffold_23.716125-721720.comp58983_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:53 scaffold_23.716125-721720.comp58983_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:45 scaffold_23.716125-722098.comp58983_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:48 scaffold_23.716125-722098.comp58983_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:53 scaffold_23.716125-722098.comp58983_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:50 scaffold_23.716125-722098.comp58983_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:05 scaffold_23.716125-722098.comp58983_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-722098.comp58983_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:47 scaffold_23.716125-722098.comp58983_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-722098.comp58983_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:46 scaffold_23.716125-722428.comp58983_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:08 scaffold_23.716125-722428.comp58983_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:49 scaffold_23.716125-722428.comp58983_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:53 scaffold_23.716125-722428.comp58983_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:06 scaffold_23.716125-722428.comp58983_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:05 scaffold_23.716125-722428.comp58983_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:47 scaffold_23.716125-722428.comp58983_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-722428.comp58983_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 08:04 scaffold_23.716125-722428.comp58983_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:50 scaffold_23.716125-722757.comp58983_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:05 scaffold_23.716125-722757.comp58983_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:52 scaffold_23.716125-722757.comp58983_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722757.comp58983_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:47 scaffold_23.716125-723330.comp58983_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:05 scaffold_23.716125-723330.comp58983_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:04 scaffold_23.716125-723330.comp58983_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:44 scaffold_23.716125-723330.comp58983_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:51 scaffold_23.716125-723330.comp58983_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:48 scaffold_23.716125-723330.comp58983_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:07 scaffold_23.716125-723330.comp58983_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:45 scaffold_23.716125-723330.comp58983_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 10:47 scaffold_23.716125-725421.comp58983_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:46 scaffold_23.716125-725421.comp58983_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:05 scaffold_23.716125-725421.comp58983_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:04 scaffold_23.716125-725421.comp58983_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:45 scaffold_23.716125-725421.comp58983_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:49 scaffold_23.716125-725421.comp58983_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:49 scaffold_23.716125-728040.comp58983_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:48 scaffold_23.716125-728040.comp58983_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:47 scaffold_23.716125-728040.comp58983_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:06 scaffold_23.716125-728040.comp58983_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:04 scaffold_23.716125-728040.comp58983_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 06:55 scaffold_23.7171-17933.gnl%7CAmel_4%2E5%7CGB46618-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070125.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070126.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070127.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070128.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291468.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291469.p_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 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dstandag biol 3.2K Nov 8 10:53 scaffold_23.728443-729727.comp45774_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.729783-730395.comp2904457_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 10:53 scaffold_23.730057-730704.comp1503238_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:49 scaffold_23.73016-73676.comp16138_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 scaffold_23.731277-731906.comp1893859_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.733065-733673.comp3350191_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.73345-73945.comp16138_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 10:53 scaffold_23.734599-735763.comp1287295_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.73525-74446.comp9823_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 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-rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0290962.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303730.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303731.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:03 scaffold_23.748248-752313.gnl%7CAmel_4%2E5%7CGB49163-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:49 scaffold_23.75148-75896.comp276986_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:56 scaffold_23.751890-761021.comp49210_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:55 scaffold_23.751890-761021.comp49210_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:54 scaffold_23.751890-761021.comp49210_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:03 scaffold_23.752357-755378.gnl%7CAmel_4%2E5%7CGB49169-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K 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11:03 scaffold_23.772644-773319.gnl%7CDmel_r5%2E47%7CFBpp0075479.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773322.gnl%7CAmel_4%2E5%7CGB48430-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773325.gnl%7CDmel_r5%2E47%7CFBpp0077688.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773328.gnl%7CDmel_r5%2E47%7CFBpp0071844.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773349.gnl%7CAmel_4%2E5%7CGB40139-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772647-773280.gnl%7CDmel_r5%2E47%7CFBpp0072463.p_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 06:49 scaffold_23.77438-78155.comp13284_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 10:57 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Name: scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 Type: application/octet-stream Size: 4812 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 27 15:39:18 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:39:18 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Hello Carson, Just to confirm, Is there a script that would filter gene models at specific AED score. Alternatively if I were to do this within maker with regards to parameters in maker_opts.ctl file I would have to provide my predicted genes gff3 file to model_gff and set AED_threshold at desired threshold? Thanks and regards, Parul Kudtarkar > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From parulk at caltech.edu Tue Nov 27 15:41:12 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:41:12 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Message-ID: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From dence at genetics.utah.edu Tue Nov 27 15:55:49 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 27 Nov 2012 22:55:49 +0000 Subject: [maker-devel] AED score In-Reply-To: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: Hi Parul, I think the way you described (with the maker_opts.ctl file) is how you want to proceed. You still need to give the genome too. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] Sent: Tuesday, November 27, 2012 3:41 PM To: Parul Kudtarkar Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] AED score Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Tue Nov 27 15:59:22 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:59:22 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: <3841.131.215.15.234.1354057162.squirrel@webmail.caltech.edu> Thanks for quick response Daniel, I'll do it through maker. > Hi Parul, > > I think the way you described (with the maker_opts.ctl file) is how you > want to proceed. You still need to give the genome too. > > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar > [parulk at caltech.edu] > Sent: Tuesday, November 27, 2012 3:41 PM > To: Parul Kudtarkar > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] AED score > > Also, are there any other parameters that are required when filtering > based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >> parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>> may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>> 20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>> how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From kapeelc at gmail.com Tue Nov 27 18:23:12 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Tue, 27 Nov 2012 18:23:12 -0700 Subject: [maker-devel] Maker error message Message-ID: Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Nov 27 18:38:33 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 01:38:33 +0000 Subject: [maker-devel] Maker error message In-Reply-To: References: Message-ID: Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Nov 27 20:39:56 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 27 Nov 2012 22:39:56 -0500 Subject: [maker-devel] AED score In-Reply-To: Message-ID: Use the AED_threshold option in the maker_opts.ctl file if you just want to restrict final gene models to close matches directly within maker. On the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset for SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. Thanks, Carson On 12-11-27 5:55 PM, "Daniel Ence" wrote: >Hi Parul, > >I think the way you described (with the maker_opts.ctl file) is how you >want to proceed. You still need to give the genome too. > >Daniel > > >Daniel Ence >Graduate Student >Eccles Institute of Human Genetics >University of Utah >15 North 2030 East, Room 2100 >Salt Lake City, UT 84112-5330 >________________________________________ >From: maker-devel-bounces at yandell-lab.org >[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >Sent: Tuesday, November 27, 2012 3:41 PM >To: Parul Kudtarkar >Cc: maker-devel at yandell-lab.org >Subject: Re: [maker-devel] AED score > >Also, are there any other parameters that are required when filtering >based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >>parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>>may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>>20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>>how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From dence at genetics.utah.edu Wed Nov 28 12:25:22 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 19:25:22 +0000 Subject: [maker-devel] Maker error message In-Reply-To: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Hi Kapeel,? Please keep this discussion on the maker-devel group, so we can get everyone's input to help resolve this issue with maker.? Can you sen me the maker_opts file that you were using? The options that might be relevant include the libraries you were giving repeatrunner and repeatmasker. Thanks, Daniel? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: kapeelc at gmail.com [kapeelc at gmail.com] Sent: Wednesday, November 28, 2012 11:39 AM To: Daniel Ence Subject: Re: Maker error message Hi Daniel, Here is the output around the error: j_size:94 current j:76 j_size:94 current j:77 j_size:94 current j:78 j_size:94 current j:79 j_size:94 current j:80 j_size:94 current j:81 j_size:94 current j:82 j_size:94 current j:83 j_size:94 current j:84 j_size:94 current j:85 j_size:94 current j:86 j_size:94 current j:87 j_size:94 current j:88 j_size:94 current j:89 j_size:94 current j:90 j_size:94 current j:91 j_size:94 current j:92 j_size:94 current j:93 ...finished clustering. re reading repeat masker report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out re reading blast report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner deleted:1 hits in cluster::shadow_cluster... DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 --Next Contig-- Processing run.log file... Maker is now finished!!! For RepeatMasker I am using wublast as the search engine. The run log had this: LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 DIED RANK 0 DIED COUNT 2 Is there way to skip the the failed chunk and move forward?? Thanks Kapeel Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Quoted from: http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html From kapeelc at gmail.com Wed Nov 28 13:15:13 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Wed, 28 Nov 2012 13:15:13 -0700 Subject: [maker-devel] Maker error message In-Reply-To: References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get > everyone's input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that > might be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out > re reading blast report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're > running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html > -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4831 bytes Desc: not available URL: From carsonhh at gmail.com Thu Nov 29 07:22:42 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:22:42 -0500 Subject: [maker-devel] AED score In-Reply-To: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Message-ID: There are certain characteristics that are apparent in this contig. First it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many of them to align spuriously which produces very short gene models that are more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial bias to get back very short and incomplete models. How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as well as get an estimate of fragmentation as one of the statistics produced is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), and if they are distantly related to other annotated species few proteins may align to the contigs because the introns in the alignments tend to be so long and exons so short that it pushes down the significance scores too much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. Thanks, Carson On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >Dear Carson and Daniel, > >Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 >genes with AED score less than 0.75. However there were no genes predicted >in the output file(see attached file Scaffold1_out). I have also attached >the maker_opts.ctl. Could you please advice on this. > >Thanks and regards, >Parul Kudtarkar > >> Use the AED_threshold option in the maker_opts.ctl file if you just want >> to restrict final gene models to close matches directly within maker. >>On >> the other hand, if you are trying to build a dataset for training gene >> predictors, use the maker2zff script for generating a filtered dataset >>for >> SNAP training. There are a number of filters available. Just call the >> script once without parameters to see the options. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >> >>>Hi Parul, >>> >>>I think the way you described (with the maker_opts.ctl file) is how you >>>want to proceed. You still need to give the genome too. >>> >>>Daniel >>> >>> >>>Daniel Ence >>>Graduate Student >>>Eccles Institute of Human Genetics >>>University of Utah >>>15 North 2030 East, Room 2100 >>>Salt Lake City, UT 84112-5330 >>>________________________________________ >>>From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>>[parulk at caltech.edu] >>>Sent: Tuesday, November 27, 2012 3:41 PM >>>To: Parul Kudtarkar >>>Cc: maker-devel at yandell-lab.org >>>Subject: Re: [maker-devel] AED score >>> >>>Also, are there any other parameters that are required when filtering >>>based on AED score? >>> >>>> Hello Carson, >>>> >>>> Just to confirm, Is there a script that would filter gene models at >>>> specific AED score. >>>> Alternatively if I were to do this within maker with regards to >>>>parameters >>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>> file to model_gff and set AED_threshold at desired threshold? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>>> worst >>>>> as >>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>> require better matching to the evidence by setting it closer to 0. >>>>>You >>>>> can >>>>> also try to increase protein homology evidence as some of your calls >>>>>may >>>>> be split genes due to lack of evidence linking them. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>>Dear Maker community, >>>>>> >>>>>>For gene-prediction I get training data-set from evidence based >>>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>>predictions, followed by boot-strapping. I would typically expect >>>>>>20-30K >>>>>>genes however I am getting 8 times the expected gene count indicating >>>>>> too >>>>>>many false positives. Is there a way to further refine these >>>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>>how >>>>>>to go about this? >>>>>> >>>>>>Thanks and regards, >>>>>>Parul Kudtarkar >>>>>> >>>>>>-- >>>>>>Scientific Programmer >>>>>>Center for Computational Regulatory Genomics >>>>>>Beckman Institute, >>>>>>California Institute of Technology >>>>>>http://www.spbase.org >>>>>> >>>>>> >>>>>>_______________________________________________ >>>>>>maker-devel mailing list >>>>>>maker-devel at box290.bluehost.com >>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o >>>>>>rg >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 07:52:25 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:52:25 -0500 Subject: [maker-devel] Maker error message In-Reply-To: Message-ID: There should normally be more error message than that. The module used to capture the error returns the string "Died" without an end line character when there is a problem capturing the STDERR of the failure (and I see that phrase here), so could you run this again and see if it produces a different message the second time. Also I'm going to send you instructions on download the development version of MAKER in a separate message (off list). It is easier for me to make changes and have you test them immediately that way. Also there are already some bug fixes in the devel version so it's good to rule those out. Thanks, Carson From: Kapeel Chougule Date: Wednesday, 28 November, 2012 3:15 PM To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Maker error message Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get everyone's > input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that might > be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific > .out > re reading blast report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2 > Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 28 14:40:51 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 28 Nov 2012 13:40:51 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Dear Carson and Daniel, Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 genes with AED score less than 0.75. However there were no genes predicted in the output file(see attached file Scaffold1_out). I have also attached the maker_opts.ctl. Could you please advice on this. Thanks and regards, Parul Kudtarkar > Use the AED_threshold option in the maker_opts.ctl file if you just want > to restrict final gene models to close matches directly within maker. On > the other hand, if you are trying to build a dataset for training gene > predictors, use the maker2zff script for generating a filtered dataset for > SNAP training. There are a number of filters available. Just call the > script once without parameters to see the options. > > Thanks, > Carson > > > > > On 12-11-27 5:55 PM, "Daniel Ence" wrote: > >>Hi Parul, >> >>I think the way you described (with the maker_opts.ctl file) is how you >>want to proceed. You still need to give the genome too. >> >>Daniel >> >> >>Daniel Ence >>Graduate Student >>Eccles Institute of Human Genetics >>University of Utah >>15 North 2030 East, Room 2100 >>Salt Lake City, UT 84112-5330 >>________________________________________ >>From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>[parulk at caltech.edu] >>Sent: Tuesday, November 27, 2012 3:41 PM >>To: Parul Kudtarkar >>Cc: maker-devel at yandell-lab.org >>Subject: Re: [maker-devel] AED score >> >>Also, are there any other parameters that are required when filtering >>based on AED score? >> >>> Hello Carson, >>> >>> Just to confirm, Is there a script that would filter gene models at >>> specific AED score. >>> Alternatively if I were to do this within maker with regards to >>>parameters >>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>> file to model_gff and set AED_threshold at desired threshold? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>> worst >>>> as >>>> it is a distance metric. You can use the AED_threshold parameter to >>>> require better matching to the evidence by setting it closer to 0. You >>>> can >>>> also try to increase protein homology evidence as some of your calls >>>>may >>>> be split genes due to lack of evidence linking them. >>>> >>>> --Carson >>>> >>>> >>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Dear Maker community, >>>>> >>>>>For gene-prediction I get training data-set from evidence based >>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>predictions, followed by boot-strapping. I would typically expect >>>>>20-30K >>>>>genes however I am getting 8 times the expected gene count indicating >>>>> too >>>>>many false positives. Is there a way to further refine these >>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>how >>>>>to go about this? >>>>> >>>>>Thanks and regards, >>>>>Parul Kudtarkar >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1.gff Type: application/octet-stream Size: 594162 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1_out.gff Type: application/octet-stream Size: 371508 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4561 bytes Desc: not available URL: From mikael.durling at slu.se Thu Nov 29 09:20:10 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Thu, 29 Nov 2012 16:20:10 +0000 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids Message-ID: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Hello all, I'm running Maker (2.26 / r956 from svn) with a previous run in the input as maker_gff. However, the maker mpi ranks quit stop one after another with the following error messages. prepare section files Gathering GFF3 input into hits - chunk:3 ERROR: Non-unique top level ID for While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. --> rank=4, hostname=my-mgrid2 ERROR: Failed while prepare section files ERROR: Chunk failed at level:12, tier_type:2 FAILED CONTIG:scf_89936 In the end no ranks are running, but maker doesn't quit. Checking the maker_gff input, I do find duplicated ids, as this sample: scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.082870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.082870 but not for the scaffold found in the error message above. Are those two errors unrelated? If I run maker without providing a maker_gff the run works fine. Any input on this issue would be appreciated as I would like the reannotation to work in order to carry forward human readable names. cheers, Mikael ------------------------------------- Mikael Brandstr?m Durling, PhD Assistant Professor Sveriges lantbruksuniversitet Swedish University of Agricultural Sciences Uppsala BioCenter Dept of Forest Mycology and Plant Pathology Box 7026, 75007 Uppsala Visiting address: Almas All? 5 Telefon: 018-671503 mikael.durling at slu.se, www.slu.se/mykopat From carsonhh at gmail.com Thu Nov 29 09:23:39 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 11:23:39 -0500 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Message-ID: You can get the fixed version by doing svn update inside the maker directory. I will be changing the download version to 2.27 on yandell0lab.org, probably this weekend. Thanks, Carson On 12-11-29 11:20 AM, "Mikael Brandstr?m Durling" wrote: >Hello all, > >I'm running Maker (2.26 / r956 from svn) with a previous run in the input >as maker_gff. However, the maker mpi ranks quit stop one after another >with the following error messages. > >prepare section files >Gathering GFF3 input into hits - chunk:3 >ERROR: Non-unique top level ID for >While this is technically legal in GFF3, it usually >indicates a poorly fomatted GFF3 file (perhaps you >tried to merge two GFF3 files without accounting for >unique IDs). MAKER will not handle these correctly. > >--> rank=4, hostname=my-mgrid2 >ERROR: Failed while prepare section files >ERROR: Chunk failed at level:12, tier_type:2 >FAILED CONTIG:scf_89936 > >In the end no ranks are running, but maker doesn't quit. > >Checking the maker_gff input, I do find duplicated ids, as this sample: > >scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158 >:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 >scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.0 >82870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.08287 >0 > >but not for the scaffold found in the error message above. Are those two >errors unrelated? > >If I run maker without providing a maker_gff the run works fine. > >Any input on this issue would be appreciated as I would like the >reannotation to work in order to carry forward human readable names. > >cheers, >Mikael > > > > >------------------------------------- >Mikael Brandstr?m Durling, PhD >Assistant Professor > >Sveriges lantbruksuniversitet >Swedish University of Agricultural Sciences > >Uppsala BioCenter >Dept of Forest Mycology and Plant Pathology >Box 7026, 75007 Uppsala >Visiting address: Almas All? 5 >Telefon: 018-671503 >mikael.durling at slu.se, www.slu.se/mykopat > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Thu Nov 29 17:31:40 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Thu, 29 Nov 2012 16:31:40 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Thanks for the guidance Carson, total contig size is 330,611 with N50 of 39.17kb. I agree we have short ESTs. So this is the possible reason when filtering based on AED score 0.75 there are no gene models predicted despite the model_gff file has few genes with scores less than 0.75? Thanks and regards, Parul Kudtarkar > There are certain characteristics that are apparent in this contig. First > it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many > of them to align spuriously which produces very short gene models that are > more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add > more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models > almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial > bias to get back very short and incomplete models. > > How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as > well as get an estimate of fragmentation as one of the statistics produced > is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter > and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. > > If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), > and if they are distantly related to other annotated species few proteins > may align to the contigs because the introns in the alignments tend to be > so long and exons so short that it pushes down the significance scores too > much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. > > Thanks, > Carson > > > > On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: > >>Dear Carson and Daniel, >>Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >> 5 >>genes with AED score less than 0.75. However there were no genes >> predicted >>in the output file(see attached file Scaffold1_out). I have also attached >>the maker_opts.ctl. Could you please advice on this. >>Thanks and regards, >>Parul Kudtarkar >>> Use the AED_threshold option in the maker_opts.ctl file if you just want >>> to restrict final gene models to close matches directly within maker. >>>On >>> the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset >>>for >>> SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. >>> Thanks, >>> Carson >>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>Hi Parul, >>>>I think the way you described (with the maker_opts.ctl file) is how you >>>>want to proceed. You still need to give the genome too. >>>>Daniel >>>>Daniel Ence >>>>Graduate Student >>>>Eccles Institute of Human Genetics >>>>University of Utah >>>>15 North 2030 East, Room 2100 >>>>Salt Lake City, UT 84112-5330 >>>>________________________________________ >>>>From: maker-devel-bounces at yandell-lab.org >>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] >>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>To: Parul Kudtarkar >>>>Cc: maker-devel at yandell-lab.org >>>>Subject: Re: [maker-devel] AED score >>>>Also, are there any other parameters that are required when filtering based on AED score? >>>>> Hello Carson, >>>>> Just to confirm, Is there a script that would filter gene models at specific AED score. >>>>> Alternatively if I were to do this within maker with regards to >>>>>parameters >>>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>>> file to model_gff and set AED_threshold at desired threshold? Thanks and regards, >>>>> Parul Kudtarkar >>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>>>>> as >>>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>You >>>>>> can >>>>>> also try to increase protein homology evidence as some of your calls >>>>>>may >>>>>> be split genes due to lack of evidence linking them. >>>>>> --Carson >>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>Dear Maker community, >>>>>>>For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K >>>>>>>genes however I am getting 8 times the expected gene count >>>>>>> indicating >>>>>>> too >>>>>>>many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes >>>>>>>how >>>>>>>to go about this? >>>>>>>Thanks and regards, >>>>>>>Parul Kudtarkar >>>>>>>-- >>>>>>>Scientific Programmer >>>>>>>Center for Computational Regulatory Genomics >>>>>>>Beckman Institute, >>>>>>>California Institute of Technology >>>>>>>http://www.spbase.org >>>>>>>_______________________________________________ >>>>>>>maker-devel mailing list >>>>>>>maker-devel at box290.bluehost.com >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o rg >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org _______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 18:39:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 20:39:31 -0500 Subject: [maker-devel] AED score In-Reply-To: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Message-ID: Wow 330,000 is a lot. a large portion of genes are likely to be partial at best. You should seriously consider using mRNAseq to capture those by using maker's est_gff option to pass in results from cufflinks or trinity. Also I wouldn't even try to annotate contigs less than 10kb in size, just have maker skip them by setting the min_contig filter in the maker_opts.ctl file. Thanks, Carson On 12-11-29 7:31 PM, "Parul Kudtarkar" wrote: >Thanks for the guidance Carson, total contig size is 330,611 with N50 of >39.17kb. I agree we have short ESTs. So this is the possible reason when >filtering based on AED score 0.75 there are no gene models predicted >despite the model_gff file has few genes with scores less than 0.75? > >Thanks and regards, >Parul Kudtarkar > >> There are certain characteristics that are apparent in this contig. >First >> it seems to be repeat rich with a very low gene density. You also have >very short ESTs, and because of the lengths you are probably getting >many >> of them to align spuriously which produces very short gene models that >are >> more than likely false positives or at the very least just a piece of a >gene. I would turn off est2genome as a predictor for this reason unless >you can get longer EST assemblies (i.e. From mRNAseq). Your protein >alignments also seem to be few and far between. You probably need to >add >> more proteins from a couple of related species, and you might consider >using protein2genome rather than est2genome as a predictor if you are >still working to generate a training set. Also est2genome produced >models >> almost always have an AED score near 0 so mixing est2genome with the >AED_threshold with such limited protein support does create an >artificial >> bias to get back very short and incomplete models. >> >> How many contigs do you have in total and what is the N50 value for the >assembly? If you have a large number of very short contigs, you will get >very inflated gene counts because you get genes split across contigs and >many contigs tend t be subtle rearrangements of other contigs just >assembled in a slightly different way (so you can get bits and pieces of >the same genes just rearranged). This scenario is another confounding >factor if using the est2genome predictor with short ESTs. I would >recommend running CEGMA to get an estimate for the genome completeness >as >> well as get an estimate of fragmentation as one of the statistics >produced >> is a percent of genes that are found complete (end to end) vs those that >are partial. CEGMA identifies house keeping genes that tend to be >shorter >> and less intron rich than other genes in the genome, so if CEGMA gives a >high partial percentage and a low complete percentage, then this pattern >can be expected to be even more exaggerated for other genes in the >genome. >> >> If your genome is highly fragmented or proteins do not align well then >there are other strategies. For example, some vertebrate genomes end up >having extremely fragmented assemblies (on the order of 100,000 >contigs), >> and if they are distantly related to other annotated species few >proteins >> may align to the contigs because the introns in the alignments tend to >be >> so long and exons so short that it pushes down the significance scores >too >> much. In those cases heavy mRNAseq seems to be the best if not only way >to get enough evidence to stitch gene models together. >> >> Thanks, >> Carson >> >> >> >> On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson and Daniel, >>>Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >>> 5 >>>genes with AED score less than 0.75. However there were no genes >>> predicted >>>in the output file(see attached file Scaffold1_out). I have also >attached >>>the maker_opts.ctl. Could you please advice on this. >>>Thanks and regards, >>>Parul Kudtarkar >>>> Use the AED_threshold option in the maker_opts.ctl file if you just >>>>want >>>> to restrict final gene models to close matches directly within maker. >>>>On >>>> the other hand, if you are trying to build a dataset for training gene >predictors, use the maker2zff script for generating a filtered dataset >>>>for >>>> SNAP training. There are a number of filters available. Just call the >script once without parameters to see the options. >>>> Thanks, >>>> Carson >>>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>>Hi Parul, >>>>>I think the way you described (with the maker_opts.ctl file) is how >you >>>>>want to proceed. You still need to give the genome too. >>>>>Daniel >>>>>Daniel Ence >>>>>Graduate Student >>>>>Eccles Institute of Human Genetics >>>>>University of Utah >>>>>15 North 2030 East, Room 2100 >>>>>Salt Lake City, UT 84112-5330 >>>>>________________________________________ >>>>>From: maker-devel-bounces at yandell-lab.org >>>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >>>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>>To: Parul Kudtarkar >>>>>Cc: maker-devel at yandell-lab.org >>>>>Subject: Re: [maker-devel] AED score >>>>>Also, are there any other parameters that are required when filtering >based on AED score? >>>>>> Hello Carson, >>>>>> Just to confirm, Is there a script that would filter gene models at >specific AED score. >>>>>> Alternatively if I were to do this within maker with regards to >>>>>>parameters >>>>>> in maker_opts.ctl file I would have to provide my predicted genes >>>>>>gff3 >>>>>> file to model_gff and set AED_threshold at desired threshold? >Thanks and regards, >>>>>> Parul Kudtarkar >>>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >worst >>>>>>> as >>>>>>> it is a distance metric. You can use the AED_threshold parameter >to >>>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>>You >>>>>>> can >>>>>>> also try to increase protein homology evidence as some of your >calls >>>>>>>may >>>>>>> be split genes due to lack of evidence linking them. >>>>>>> --Carson >>>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>>Dear Maker community, >>>>>>>>For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect >20-30K >>>>>>>>genes however I am getting 8 times the expected gene count >>>>>>>> indicating >>>>>>>> too >>>>>>>>many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if >yes >>>>>>>>how >>>>>>>>to go about this? >>>>>>>>Thanks and regards, >>>>>>>>Parul Kudtarkar >>>>>>>>-- >>>>>>>>Scientific Programmer >>>>>>>>Center for Computational Regulatory Genomics >>>>>>>>Beckman Institute, >>>>>>>>California Institute of Technology >>>>>>>>http://www.spbase.org >>>>>>>>_______________________________________________ >>>>>>>>maker-devel mailing list >>>>>>>>maker-devel at box290.bluehost.com >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab >>>>>>>>.o >rg >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > > > From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 02:20:19 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 01:20:19 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. Message-ID: Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman From gowthaman.ramasamy at seattlebiomed.org Sun Nov 4 03:01:46 2012 From: gowthaman.ramasamy at seattlebiomed.org (Gowthaman Ramasamy) Date: Sun, 4 Nov 2012 02:01:46 -0800 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: References: Message-ID: Hi Carson, when I tried running genemark as below, I see the *.lst files (protein & nuc fasta) produced. But no gtf2 at all... And no gms.log files at all. Any ideas? /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p 0 -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -a Enmo_susu.11.fsa Thanks, Gowthaman ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] On Behalf Of Gowthaman Ramasamy [gowthaman.ramasamy at seattlebiomed.org] Sent: Sunday, November 04, 2012 1:20 AM To: maker-devel at yandell-lab.org Subject: [maker-devel] Chunk failed at level 6 error.. Hi Carson, As it happens, I am sorry to bother you again on a weekend. Here is my hoping that you are not on a long drive this time. I am running genemark prokaryote via maker on a genome with 36 chromosomes. All but two finishes well. On those two, i am not able to find anything unusual. Following is the error message i see. Could you please point to me what could be the possible source of these errors. Thanks verymuch in advance... Widget::genemark: /depot/perl-5.12.1/bin/perl /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gmhmm_wrap -m ./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p /nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokaryotic%2Emod_hmm%2Emod.genemark /autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//theVoid.Enmo_susu.05/query.fasta #-------------------------------# substr outside of string at /nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMachine.pm line 223. FATAL ERROR ERROR: Failed while preparing masked sequence and ab-inits!! ERROR: Chunk failed at level 6 !! FAILED CONTIG:Enmo_susu.05 Thanks once again, Gowthaman _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 07:18:24 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:18:24 -0500 Subject: [maker-devel] Conensus gene model In-Reply-To: <1640.131.215.15.234.1351728273.squirrel@webmail.caltech.edu> Message-ID: The way models are generated, it really doesn't so much matter where the protein alignments came from. Basically the protein alignment is just creating a region of potential CDS. MAKER than gives that region as a hint to the gene predictors, but the gene predictors really make the call on how to finally structure the gene based on their training sets. You can short circuit this by using the protein2genome option as a separate run with only your primary proteins. MAKER will then try and turn those protein alignments directly into genes. Results from that run can sometimes be useful for generating training sets as well, or can be passed back into MAKER as pred_gff so MAKEr has the option to turn those into models as an alternative to the models produced by the ab initio predictors. --Carson On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: >Hi Jason, thanks for directions on generating training-set for augustus. >Also as alignment evidence if we are providing protein sequences from the >primary organism as well as other closely related species is there an >option to give the primary protein file precedence over others? >At the moment I have all the proteins(from primary organism as well as >related species) into a single file as protein option in maker_opts.ctl > >Thanks and regards, >Parul Kudtarkar > >> Paul - >> >> I think I've posted on this before here if you are asking how to go from >> SNAP training to Augustus training. >> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >> >> I do this type of training a lot - here some pointers. >> >> I often train by generating models using cegma on the genome and get >>these >> 400 or so good models as my training set. when I have EST or RNA-Seq I >> use PASA to generate the best set of annotations. >> >> For CEGMA - then I run this script that comes with MAKER: >> cegma2zff output.cegma.gff genome.fa >> >> Then I follow the SNAP directions >> >> fathom genome.ann genome.dna -categorize 1000 >> fathom uni.ann uni.dna -export 1000 -plus >> mkdir MYGENOME >> cd MYGENOME >> forge ../export.ann ../export.dna --OPTIONS >> cd ../MYGENOME >> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >> >> I then also make the augustus training data like this running in the >> directory that has the export.ann and export.dna files: >> perl gene_prediction/zff2augustus_gbk.pl > train.gb >> >> using this script: >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>ff2augustus_gbk.pl >> >> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>and >> best models from PASA and incorporate all these data in to my SNAP >> training set, and then export again back to gbk for the augustus >>training. >> >>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>asatraining2zff.pl >> >> Then you just need to run the Augustus training (autoAugTrain.pl) on the >> train.gb file. >> >> Jason >> >> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar wrote: >> >>> Hello Carson and maker community, >>> >>> Thank you very much for your guidelines on using the maker-pipeline. >>> Yes, >>> green sea urchin genome that we are trying to annotate. >>> We are running the on scaffolds and most of these scaffolds are small >>>in >>> size(very first genome assembly). We would typically expect 20,000 >>>genes >>> in this genome. So we are running maker using EST and proteins from the >>> genome and out-groups to generate training dataset for SNAP and >>> Augustus. >>> Depending on the resulting predictions we may bootstrap the predicted >>> genes once again using EST and proteins. >>> >>> Do you have any further suggestions? Also could you point how to >>>convert >>> training set generated for SNAP to be used as training set for Augustus >>> as >>> well? Would maker give equal weightage to SNAP and Augustus predictions >>> for generating gene model? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> One thing you seem to be missing is protein evidence. >>>> >>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>> recommend adding all proteins from the Strongylocentrotus purpuratus >>> genome, then throw in another Deuterstome of your choice. Perhaps you >>> should also add a couple of outgroup organisms like Nematostella >>> vectensis >>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>> adding >>> to many protostome outgroups (i.e. C. elegans and Drosophila) because a >>> big part of their evolution is gene loss (so distant cnidaria often >>> match >>>> deuterstomes better than most protostomes do). >>>> >>>> You could take the maker results when protein data is included and use >>> it >>>> to retrain SNAP again. >>>> >>>> Even a 22 kb contig is still really short. Is this genome primarily >>> constituted by short contigs like this? I would recommend running >>>CEGMA >>> once on this genome to get an appropriate estimate of how recoverable >>> the >>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>> Cegma >>>> will give you an estimate for genome completeness as well as estimates >>> of >>>> what percentage of genes will be found in their entirety and what >>> percent >>>> will be partial genes. This is important to do if your genome is >>> fragmented as it will give you a reasonable expectation of what you can >>> expected to recover (as short contigs don't annotate very well - you >>> tend >>>> to loose a lot). >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>> >>>>> Hi Carson, >>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>as >>>>> 3 >>> exons EST alignments. Could you please recommend additional training. >>>We >>> are currently running maker on the entire contig set and eventually >>> merge >>>>> all the gff3 contig predictions. The using suggested >>>>>parameter/methods >>> we >>>>> would like to get a consensus gene-set with minimal false >>>>> positives/negatives. >>>>> Thanks, >>>>> Parul >>>>>> The contig in question is really too small to get much out of it >>>>>> (only 5 >>>>> kb). There was only one single exon EST alignments and a couple of >>> predictions with no evidence support. Anything smaller than 10 kb is >>> mostly useless for annotation purposes. You would really need a few >>> 100kb >>>>>> length or longer contigs to glean enough information for optimizing >>>>>> your >>>>> parameters. >>>>>> The general suggestions for any maker run are to use proteins from a >>>>> closely related organism or a couple of closely related organisms for >>>>> the >>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>> for >>>>> certain eukaryotes that have a bias for single exon transcripts (i.e. >>>>> some >>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>> initio >>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>> positives). >>>>>> Additional training would really depend on what your other contigs >>> look >>>>> like. Do you have any large contigs? I could look at one of those >>>>> and >>> give suggestions but the provided contig is just too short to glean >>> much. >>>>>> Thanks, >>>>>> Carson >>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>> Hello, >>>>>>> Please advice on the aforementioned query? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> ---------------------------- Original Message >>>>>>> ---------------------------- >>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>> From: "Parul Kudtarkar" >>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>> To: maker-devel at yandell-lab.org >>>>>>> >>>>>>>-------------------------------------------------------------------- >>>>>>>---- >>> -- >>>>> Hi, >>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>est,protein >>>>>>> and >>>>> contig file), agustus,genemarkE(we ran it outside maker and have gff3 >>>>>>> file >>>>>>> as input). The output that we get is combination of various >>>>>>> gene-predictors and evidences. I have attached sample result file. >>> What >>>>> would you recommend to get consensus result set? Bootstrapping the >>> resulting gff3 file (rerunning maker)? >>>>>>> Thanks, >>>>>>> Parul Kudtarkar >>>>>>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>> -- >>>>>>> Scientific Programmer >>>>>>> Center for Computational Regulatory Genomics >>>>>>> Beckman Institute, >>>>>>> California Institute of Technology >>>>>>> >>>>>>>http://www.spbase.org_______________________________________________ >>>>> maker-devel mailing list >>>>>>> maker-devel at box290.bluehost.com >>>>>>> >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>org >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 07:36:08 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:36:08 -0500 Subject: [maker-devel] Strange error at blastn step In-Reply-To: Message-ID: Sorry for the slow reply. I've been way for most of the last week. Could you do two more things before running another test. Update again to the latest development version, also set TMP to a non-NFS location like /tmp. Thanks, Carson From: Daniel Standage Date: Monday, 29 October, 2012 8:43 AM To: Carson Holt Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Strange error at blastn step I just ran svn update and tried again with the development version of Maker. Same long list of errors as in the last message. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Oct 29, 2012 at 9:39 AM, Daniel Standage wrote: > Carson, > > I was able to run the first svn update before the test job ran, but I didn't > get the message about this second update until after it has already executed > and failed. I got about 372 lines of such. > >> STATUS: Parsing control files... >> STATUS: Processing and indexing input FASTA files... >> STATUS: Setting up database for any GFF3 input... >> A data structure will be created for you at: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_datastore >> >> To access files for individual sequences use the datastore index: >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/DELETEME.maker.pdom.1.ma >> son.maker.output/DELETEME.maker.pdom.1.mason_master_datastore_index.log >> >> STATUS: Now running MAKER... >> WARNING: Cannot find >scaffold_0, trying to re-index the fasta. >> stop here: scaffold_0 >> ERROR: Fasta index error >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 239. >> Process::MpiChunk::_prepare('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 73 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c808b0)', 'HASH(0x3c8ec40)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 79 >> Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x3c71f30)') >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 56 >> Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x3c80640)', 0, >> 'Process::MpiChunk') called at >> /N/u/dstandag/Mason/local/src/maker-dev/bin/maker line 627 >> --> rank=NA, hostname=c4 >> ERROR: Failed in tier preparation >> WARNING: You must always set a rank before running MpiTiers >> FATAL: argument `seq_id` does not exist in MpiTier object >> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 86. >> >> Process::MpiChunk::_initialize_vars('Process::MpiChunk=HASH(0x3cc93d0)', >> 'HASH(0x3cc9400)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 47 >> Process::MpiChunk::new('Process::MpiChunk', 'HASH(0x3c80820)', 0, 0) >> called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 407 >> Process::MpiChunk::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f498)', 'HASH(0x3cc8f20)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 3811 >> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x3c8b300)', 'load', >> 'HASH(0x3c80820)', 0, 0) called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 310 >> Process::MpiChunk::_loader('Process::MpiChunk=HASH(0x3c8b300)', >> 'HASH(0x3c80820)', 0, 0, 'Process::MpiTiers=HASH(0x3c71f30)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 364 >> Process::MpiTiers::__ANON__() called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 415 >> eval {...} called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Error.pm line 407 >> Error::subs::try('CODE(0x3c8f9c0)', 'HASH(0x3c8fb28)') called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >> line 375 > > I'll try the next update and run the test again. I see a lot of references in > there to MPI, and just thought I would make it clear that although I am > running in a cluster environment, I am using the default serial version of > Maker, not the parallel MPI version. > > Also, after this failed, I tried changing the TMP directory so that it was > located on the same NFS mount as the scratch disk to which the output was > written. This did not seem to have any affect, and I saw the same issues with > the EST sequences unable to be found. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Fri, Oct 26, 2012 at 6:59 PM, Carson Holt wrote: >> >> >> From: Carson Holt >> Date: Friday, 26 October, 2012 6:10 PM >> To: Daniel Standage >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> I've been going over the indexing code using different scenarios and I may >> have isolated a candidate for what is causing this. Could you do one more >> 'svn update' inside the maker devel directory before running a test job? >> >> Thanks, >> Carson >> >> From: Daniel Standage >> Date: Friday, 26 October, 2012 2:29 PM >> To: Carson Holt >> Cc: "maker-devel at yandell-lab.org" >> >> Subject: Re: [maker-devel] Strange error at blastn step >> >> Got this from the compute node. Looks like native disk space to me. >> >> [dstandag at mason ~] df /tmp >> Filesystem 1K-blocks Used Available Use% Mounted on >> /dev/sda1 478573472 12319684 441943620 3% /tmp >> >> Installing a bundle of Perl prereqs for development version, will try that >> soon. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Fri, Oct 26, 2012 at 2:24 PM, Carson Holt wrote: >>> Ok. Try the developer release and see if it still happens. >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>> Date: Friday, 26 October, 2012 2:19 PM >>> >>> To: Carson Holt >>> Cc: "maker-devel at yandell-lab.org" >>> >>> Subject: Re: [maker-devel] Strange error at blastn step >>> >>> Unfortunately, the job is no longer running and as a result I cannot connect >>> to the compute nodes as I could while it was running. On the interactive >>> node, it looks like it's real disk, although it looks like there are some >>> tmpfs mounts. >>> >>> [dstandag at mason src] df /tmp >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> [dstandag at mason src] df >>> Filesystem 1K-blocks Used Available Use% Mounted on >>> login_x86_64 16497564 3077352 13420212 19% / >>> tmpfs 16497564 0 16497564 0% /dev/shm >>> tmpfs 10240 0 10240 0% /var/tmp >>> /dev/sdb2 462824304 180235660 259078476 42% /tmp >>> AFS 9000000 0 9000000 0% /afs >>> bl-nas1:/vol/hd00 3435973856 1775658144 1660315712 52% /N/hd00 >>> bl-nas1:/vol/hd01 3435973856 1684116928 1751856928 50% /N/hd01 >>> bl-nas2:/vol/hd02 3435973856 1856598656 1579375200 55% /N/hd02 >>> bl-nas2:/vol/hd03 3435973856 2747626240 688347616 80% /N/hd03 >>> bl-nas1:/vol/hdln 81920 3424 78496 5% /N/u >>> bl-nas2:/vol/soft 1258291200 837003424 421287776 67% /N/soft >>> bl-nas1:/vol/logs 419430400 67163328 352267072 17% /N/logs >>> ... >>> ... >>> >>> I'll see if I can launch another short job and verify this on the compute >>> nodes. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Fri, Oct 26, 2012 at 2:14 PM, Carson Holt wrote: >>>> The command 'df /tmp' will tell you whether /tmp is a tmpfs mount >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Friday, 26 October, 2012 2:12 PM >>>> To: Carson Holt >>>> Cc: "maker-devel at yandell-lab.org" >>>> >>>> Subject: Re: [maker-devel] Strange error at blastn step >>>> >>>> It looks like /tmp is indeed being used: the files I played with were under >>>> /tmp/maker_1YQF9o. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Fri, Oct 26, 2012 at 2:09 PM, Carson Holt wrote: >>>>> Check to see where /tmp is located? Some clusters have it set up as a >>>>> tmpfs directory and I have had problems with fasta indexes running from >>>>> tmpfs mounts in the past. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Friday, 26 October, 2012 2:05 PM >>>>> To: Carson Holt >>>>> >>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>> >>>>> The maker working directory is in a cluster environment with shared >>>>> scratch space (I'm guessing NFS-mounted). I didn't change the temp >>>>> directory setting, so it should be the local default (/tmp). >>>>> >>>>> I'll give the dev version a shot. Thanks. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Fri, Oct 26, 2012 at 1:57 PM, Carson Holt wrote: >>>>>> Could you try this development version and tell me if the error still >>>>>> happens? >>>>>> >>>>>> Use this command to download --> >>>>>> <> >>>>>> >>>>>> Username: <> >>>>>> Password: <> >>>>>> >>>>>> Are you running in an NFS mounted directory or are you resetting TMP to a >>>>>> different location? >>>>>> >>>>>> Thanks, >>>>>> Carson >>>>>> >>>>>> >>>>>> From: Daniel Standage >>>>>> Date: Friday, 26 October, 2012 1:52 PM >>>>>> To: Maker Mailing List >>>>>> Subject: Re: [maker-devel] Strange error at blastn step >>>>>> >>>>>> I have since installed Maker on a different machine and tried it out. The >>>>>> test run completed successfully, but as I commenced with the full genome >>>>>> annotation, I have noticed the following error popping up frequently. >>>>>> >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.8 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.8.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-10 hits >>>>>>> formating database... >>>>>>> #--------- command -------------# >>>>>>> Widget::formater: >>>>>>> /N/u/dstandag/Mason/local/bin/makeblastdb -dbtype prot -in >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 >>>>>>> #-------------------------------# >>>>>>> running blast search. >>>>>>> #--------- command -------------# >>>>>>> Widget::blastx: >>>>>>> /N/u/dstandag/Mason/local/bin/blastx -db >>>>>>> /tmp/maker_1YQF9o/Amel3%2E2_Dmel5%2E47%2Efaa.mpi.10.9 -query >>>>>>> /tmp/maker_1YQF9o/rank0/scaffold_0.0 -num_alignments 100000 >>>>>>> -num_descriptions 100000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 >>>>>>> -num_threads 16 -seg yes -soft_masking true -lcase_masking -show_gis >>>>>>> -out >>>>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.1.mason. >>>>>>> maker.output/maker.pdom.1.mason_datastore/scaffold_0/theVoid.scaffold_0/ >>>>>>> scaffold_0.0.Amel3%2E2_Dmel5%2E47%2Efaa.blastx.temp_dir/Amel3%2E2_Dmel5% >>>>>>> 2E47%2Efaa.mpi.10.9.blastx >>>>>>> #-------------------------------# >>>>>>> deleted:-6 hits >>>>>>> WARNING: Cannot find> comp59088_c1_seq7, trying to re-index the fasta. >>>>>>> stop here:comp59088_c1_seq7 >>>>>>> ERROR: Fasta index error >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while polishig ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 14 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_0 >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> --Next Contig-- >>>>>>> >>>>>>> #--------------------------------------------------------------------- >>>>>>> Now starting the contig!! >>>>>>> SeqID: scaffold_1 >>>>>>> Length: 5805686 >>>>>>> #--------------------------------------------------------------------- >>>>>> >>>>>> My first thought based on the message is that blastdbcmd could not find >>>>>> the sequence in the database. I verified this was the case--I could not >>>>>> extract sequence comp59088_c1_seq7 from the database Maker had created >>>>>> under /tmp. However, after removing the index files and re-running >>>>>> makeblastdb with the -parse_seqids option set, blastdbcmd successfully >>>>>> extracted the sequence. >>>>>> >>>>>> I was initially happy with this finding, but upon closer inspection it >>>>>> looks like Maker does not use blastdbcmd to extract sequences, but rather >>>>>> its own internal code. Therefore I'm still not sure where the problem is >>>>>> and how I might fix it. Any insights? >>>>>> >>>>>> Thanks! >>>>>> >>>>>> -- >>>>>> Daniel S. Standage >>>>>> Ph.D. Candidate >>>>>> Bioinformatics and Computational Biology Program >>>>>> Department of Genetics, Development, and Cell Biology >>>>>> Iowa State University >>>>>> >>>>>> >>>>>> >>>>>> On Thu, Oct 25, 2012 at 3:30 PM, Daniel Standage >>>>>> wrote: >>>>>>> Greetings! >>>>>>> >>>>>>> I am doing a test run of my Maker setup on a new machine, annotating a >>>>>>> pretty short contig (about 3kb). However, there seems to be a hiccup >>>>>>> during the blastn stage. This is the terminal message. >>>>>>> >>>>>>> #--------- command -------------# >>>>>>> Widget::blastn: >>>>>>> /share/home/01854/standage/local/bin/blastn -db >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/Pdom%2ETrinity%2ETrimmomatic%2Ef >>>>>>> asta.mpi.10.7 -query >>>>>>> /tmp/2881473.1.development/maker_i6ZSJi/rank0/scaffold_866.0 >>>>>>> -num_alignments 100000 -num_descriptions 100000 -evalue 1e-10 -gapextend >>>>>>> 3 -word_size 15 -reward 1 -penalty -3 -gapopen 3 -dbsize 1000 -searchsp >>>>>>> 500000000 -num_threads 16 -lcase_masking -dust yes -soft_masking true >>>>>>> -show_gis -out >>>>>>> /scratch/01854/standage/PdomGenomic/Annotation/scripts/maker.bogus.maker >>>>>>> .output/maker.bogus_datastore/scaffold_866/theVoid.scaffold_866/scaffold >>>>>>> _866.0.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn.temp_dir/Pdom%2ETrini >>>>>>> ty%2ETrimmomatic%2Efasta.mpi.10.7.blastn >>>>>>> #-------------------------------# >>>>>>> deleted:0 hits >>>>>>> ERROR: Could not obtain lock to format database >>>>>>> >>>>>>> >>>>>>> FATAL ERROR >>>>>>> ERROR: Failed while doing blastn of ESTs!! >>>>>>> >>>>>>> ERROR: Chunk failed at level 8 >>>>>>> !! >>>>>>> FAILED CONTIG:scaffold_866 >>>>>>> >>>>>>> Several blastn steps appeared to have completed successfully to this one >>>>>>> failing. Any ideas what could be causing this? >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> -- >>>>>>> Daniel S. Standage >>>>>>> Ph.D. Candidate >>>>>>> Bioinformatics and Computational Biology Program >>>>>>> Department of Genetics, Development, and Cell Biology >>>>>>> Iowa State University >>>>>>> >>>>>> >>>>>> _______________________________________________ maker-devel mailing list >>>>>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinf >>>>>> o/maker-devel_yandell-lab.org >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 5 07:41:57 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 09:41:57 -0500 Subject: [maker-devel] gff3_preds2models script In-Reply-To: <3207.131.215.15.234.1350942378.squirrel@webmail.caltech.edu> Message-ID: The gff3_preds2models doesn't support the shared ID method for model assembly. You will need to create a parent match feature and child match_part features (each with a unique ID and Parent= attribute). You can find examples in the GFF3 specification here --> http://www.sequenceontology.org/gff3.shtml Thanks, Carson On 12-10-22 5:46 PM, "Parul Kudtarkar" wrote: >Hello, > >I want to add gene structure(gene/mRNA/exon) to gff3 file. I am using >gff3_preds2models for this purpose. However I get following error >**WARNING: No top level feature found for ID WHL22.100252 >I have attached the sample input gff3 file and the list of ids > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 5 08:08:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 05 Nov 2012 10:08:36 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt , Maker Mailing List Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 08:14:18 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:14:18 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List < > maker-devel at yandell-lab.org> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: PdomMaker9.e44232.bz2 Type: application/x-bzip2 Size: 5881 bytes Desc: not available URL: From parulk at caltech.edu Mon Nov 5 14:40:46 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 5 Nov 2012 13:40:46 -0800 (PST) Subject: [maker-devel] Conensus gene model In-Reply-To: References: Message-ID: <4116.131.215.15.234.1352151646.squirrel@webmail.caltech.edu> Dear Carson, Thanks you very much, this is helpful. > The way models are generated, it really doesn't so much matter where the > protein alignments came from. Basically the protein alignment is just > creating a region of potential CDS. MAKER than gives that region as a > hint to the gene predictors, but the gene predictors really make the call > on how to finally structure the gene based on their training sets. You > can short circuit this by using the protein2genome option as a separate > run with only your primary proteins. MAKER will then try and turn those > protein alignments directly into genes. Results from that run can > sometimes be useful for generating training sets as well, or can be passed > back into MAKER as pred_gff so MAKEr has the option to turn those into > models as an alternative to the models produced by the ab initio > predictors. > > --Carson > > > On 12-10-31 8:04 PM, "Parul Kudtarkar" wrote: > >>Hi Jason, thanks for directions on generating training-set for augustus. >>Also as alignment evidence if we are providing protein sequences from the >>primary organism as well as other closely related species is there an >>option to give the primary protein file precedence over others? >>At the moment I have all the proteins(from primary organism as well as >>related species) into a single file as protein option in maker_opts.ctl >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Paul - >>> >>> I think I've posted on this before here if you are asking how to go >>> from >>> SNAP training to Augustus training. >>> http://sourceforge.net/mailarchive/message.php?msg_id=29361270 >>> >>> I do this type of training a lot - here some pointers. >>> >>> I often train by generating models using cegma on the genome and get >>>these >>> 400 or so good models as my training set. when I have EST or RNA-Seq I >>> use PASA to generate the best set of annotations. >>> >>> For CEGMA - then I run this script that comes with MAKER: >>> cegma2zff output.cegma.gff genome.fa >>> >>> Then I follow the SNAP directions >>> >>> fathom genome.ann genome.dna -categorize 1000 >>> fathom uni.ann uni.dna -export 1000 -plus >>> mkdir MYGENOME >>> cd MYGENOME >>> forge ../export.ann ../export.dna --OPTIONS >>> cd ../MYGENOME >>> hmm-assembler.pl MYGENOME MYGENOME > MYGENOME.snap.hmm >>> >>> I then also make the augustus training data like this running in the >>> directory that has the export.ann and export.dna files: >>> perl gene_prediction/zff2augustus_gbk.pl > train.gb >>> >>> using this script: >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/z >>>ff2augustus_gbk.pl >>> >>> I also make ZFF from GFF with this script if I got the RNA-Seq aligned >>>and >>> best models from PASA and incorporate all these data in to my SNAP >>> training set, and then export again back to gbk for the augustus >>>training. >>> >>>https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/p >>>asatraining2zff.pl >>> >>> Then you just need to run the Augustus training (autoAugTrain.pl) on >>> the >>> train.gb file. >>> >>> Jason >>> >>> On Oct 30, 2012, at 2:18 PM, Parul Kudtarkar >>> wrote: >>> >>>> Hello Carson and maker community, >>>> >>>> Thank you very much for your guidelines on using the maker-pipeline. >>>> Yes, >>>> green sea urchin genome that we are trying to annotate. >>>> We are running the on scaffolds and most of these scaffolds are small >>>>in >>>> size(very first genome assembly). We would typically expect 20,000 >>>>genes >>>> in this genome. So we are running maker using EST and proteins from >>>> the >>>> genome and out-groups to generate training dataset for SNAP and >>>> Augustus. >>>> Depending on the resulting predictions we may bootstrap the predicted >>>> genes once again using EST and proteins. >>>> >>>> Do you have any further suggestions? Also could you point how to >>>>convert >>>> training set generated for SNAP to be used as training set for >>>> Augustus >>>> as >>>> well? Would maker give equal weightage to SNAP and Augustus >>>> predictions >>>> for generating gene model? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> One thing you seem to be missing is protein evidence. >>>>> >>>>> Is this a sea urchin (I looked up some of the ESTs)? If so, I would >>>> recommend adding all proteins from the Strongylocentrotus purpuratus >>>> genome, then throw in another Deuterstome of your choice. Perhaps you >>>> should also add a couple of outgroup organisms like Nematostella >>>> vectensis >>>>> (cnidaria) and a protostome of your choice. Be careful if adding >>>>> adding >>>> to many protostome outgroups (i.e. C. elegans and Drosophila) because >>>> a >>>> big part of their evolution is gene loss (so distant cnidaria often >>>> match >>>>> deuterstomes better than most protostomes do). >>>>> >>>>> You could take the maker results when protein data is included and >>>>> use >>>> it >>>>> to retrain SNAP again. >>>>> >>>>> Even a 22 kb contig is still really short. Is this genome primarily >>>> constituted by short contigs like this? I would recommend running >>>>CEGMA >>>> once on this genome to get an appropriate estimate of how recoverable >>>> the >>>>> genes are going to be (http://korflab.ucdavis.edu/datasets/cegma/). >>>> Cegma >>>>> will give you an estimate for genome completeness as well as >>>>> estimates >>>> of >>>>> what percentage of genes will be found in their entirety and what >>>> percent >>>>> will be partial genes. This is important to do if your genome is >>>> fragmented as it will give you a reasonable expectation of what you >>>> can >>>> expected to recover (as short contigs don't annotate very well - you >>>> tend >>>>> to loose a lot). >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> On 12-10-15 3:45 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>> Hi Carson, >>>>>> Thanks. I have attached another contig which is 22 kb, with as many >>>>>>as >>>>>> 3 >>>> exons EST alignments. Could you please recommend additional training. >>>>We >>>> are currently running maker on the entire contig set and eventually >>>> merge >>>>>> all the gff3 contig predictions. The using suggested >>>>>>parameter/methods >>>> we >>>>>> would like to get a consensus gene-set with minimal false >>>>>> positives/negatives. >>>>>> Thanks, >>>>>> Parul >>>>>>> The contig in question is really too small to get much out of it >>>>>>> (only 5 >>>>>> kb). There was only one single exon EST alignments and a couple of >>>> predictions with no evidence support. Anything smaller than 10 kb is >>>> mostly useless for annotation purposes. You would really need a few >>>> 100kb >>>>>>> length or longer contigs to glean enough information for optimizing >>>>>>> your >>>>>> parameters. >>>>>>> The general suggestions for any maker run are to use proteins from >>>>>>> a >>>>>> closely related organism or a couple of closely related organisms >>>>>> for >>>>>> the >>>>>>> protein= option in maker. Also leave single_exon set to 0, except >>>>>>> for >>>>>> certain eukaryotes that have a bias for single exon transcripts >>>>>> (i.e. >>>>>> some >>>>>>> fungi and oomycetes). And leave keep_preds set to 0 because ab >>>>>>> initio >>>>>> predictors tend to over-predict by a wide margin (lots of false >>>>>>> positives). >>>>>>> Additional training would really depend on what your other contigs >>>> look >>>>>> like. Do you have any large contigs? I could look at one of those >>>>>> and >>>> give suggestions but the provided contig is just too short to glean >>>> much. >>>>>>> Thanks, >>>>>>> Carson >>>>>>> On 12-10-15 1:41 PM, "Parul Kudtarkar" wrote: >>>>>>>> Hello, >>>>>>>> Please advice on the aforementioned query? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> ---------------------------- Original Message >>>>>>>> ---------------------------- >>>>>>>> Subject: [maker-devel] Conensus gene model >>>>>>>> From: "Parul Kudtarkar" >>>>>>>> Date: Fri, October 12, 2012 2:46 pm >>>>>>>> To: maker-devel at yandell-lab.org >>>>>>>> >>>>>>>>-------------------------------------------------------------------- >>>>>>>>---- >>>> -- >>>>>> Hi, >>>>>>>> We are using snap(training set[hmm file] generated using >>>>>>>>est,protein >>>>>>>> and >>>>>> contig file), agustus,genemarkE(we ran it outside maker and have >>>>>> gff3 >>>>>>>> file >>>>>>>> as input). The output that we get is combination of various >>>>>>>> gene-predictors and evidences. I have attached sample result file. >>>> What >>>>>> would you recommend to get consensus result set? Bootstrapping the >>>> resulting gff3 file (rerunning maker)? >>>>>>>> Thanks, >>>>>>>> Parul Kudtarkar >>>>>>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>> -- >>>>>>>> Scientific Programmer >>>>>>>> Center for Computational Regulatory Genomics >>>>>>>> Beckman Institute, >>>>>>>> California Institute of Technology >>>>>>>> >>>>>>>>http://www.spbase.org_______________________________________________ >>>>>> maker-devel mailing list >>>>>>>> maker-devel at box290.bluehost.com >>>>>>>> >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab. >>>>>>>>org >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Wed Nov 7 07:00:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 09:00:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > Thanks. Could you also run with the --debug flag set on the command line for a > few minutes and send me that. > > --Carson > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt , Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on > native disk space, and relaunched. I have attached the output of the job that > failed in <5 minutes. It looks pretty similar to the errors I got the last > time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Mon Nov 5 08:05:45 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 5 Nov 2012 10:05:45 -0500 Subject: [maker-devel] Maker issues Message-ID: Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker.log Type: application/octet-stream Size: 48916 bytes Desc: not available URL: From daniel.standage at gmail.com Wed Nov 7 07:30:11 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 09:30:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: > >> Thanks. Could you also run with the --debug flag set on the command line >> for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt , Maker Mailing List < >> maker-devel at yandell-lab.org> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory >> is on native disk space, and relaunched. I have attached the output of the >> job that failed in <5 minutes. It looks pretty similar to the errors I got >> the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 08:29:34 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 10:29:34 -0500 Subject: [maker-devel] Chunk failed at level 6 error.. In-Reply-To: Message-ID: Sorry for the slow reply. I'm not on a long drive, but I am away this week. Could you send me the genemark hmm file and one of the contigs that fails. Thanks, Carson On 12-11-04 3:20 AM, "Gowthaman Ramasamy" wrote: >Hi Carson, >As it happens, I am sorry to bother you again on a weekend. Here is my >hoping that you are not on a long drive this time. > >I am running genemark prokaryote via maker on a genome with 36 >chromosomes. All but two finishes well. > >On those two, i am not able to find anything unusual. Following is the >error message i see. Could you please point to me what could be the >possible source of these errors. Thanks verymuch in advance... > >Widget::genemark: >/depot/perl-5.12.1/bin/perl >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/Widget/genemark/gm >hmm_wrap -m >./genemarkhmms/Enmo-1.0.2_susu_GenemarkS_prokaryotic.mod_hmm.mod -g >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/gmhmmp -p >/nethome/gramasamy/software/genemark_suite_linux_64/gmsuite/probuild -o >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/Enmo_susu%2E05.all.Enmo-1%2E0%2E2_susu_GenemarkS_prokar >yotic%2Emod_hmm%2Emod.genemark >/autoxfs/bifx/NGS/WUSTL/Enmo/Annotation/05_GMprok/01_gene_pred_Prok_05_11/ >05/Enmo_susu.05.maker.output/Enmo_susu.05_datastore/8F/8F/Enmo_susu.05//th >eVoid.Enmo_susu.05/query.fasta >#-------------------------------# >substr outside of string at >/nethome/gramasamy/software/maker-2.10/maker/bin/../lib/CGL/TranslationMac >hine.pm line 223. > >FATAL ERROR >ERROR: Failed while preparing masked sequence and ab-inits!! > >ERROR: Chunk failed at level 6 >!! >FAILED CONTIG:Enmo_susu.05 > > >Thanks once again, >Gowthaman From daniel.standage at gmail.com Wed Nov 7 09:43:17 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Wed, 7 Nov 2012 11:43:17 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed *loalize* to *localize* and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: > >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >> fasta indexer is broken. I have an open bug I am trying to resolve with >> the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >> >>> Thanks. Could you also run with the --debug flag set on the command line >>> for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List < >>> maker-devel at yandell-lab.org> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory >>> is on native disk space, and relaunched. I have attached the output of the >>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>> the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 7 09:46:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 07 Nov 2012 11:46:31 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Looked good for a while, but came across this error. > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > > > > --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is > repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> 1.006902 Bio::Root::Version >> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live >> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >> indexer is broken. I have an open bug I am trying to resolve with the >> Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> Thanks. Could you also run with the --debug flag set on the command line for >>> a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt , Maker Mailing List >>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP directory is >>> on native disk space, and relaunched. I have attached the output of the job >>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>> last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From daniel.standage at gmail.com Thu Nov 8 07:32:59 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 09:32:59 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > > It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to > *localize* and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >> and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >> >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>> fasta indexer is broken. I have an open bug I am trying to resolve with >>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>> >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List < >>>> maker-devel at yandell-lab.org> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>> errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Thu Nov 8 07:47:20 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Thu, 8 Nov 2012 14:47:20 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Hi Daniel, is it possible you have some proteins in your EST files? '------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw' Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [daniel.standage at gmail.com] Sent: Thursday, November 08, 2012 7:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From daniel.standage at gmail.com Thu Nov 8 08:48:52 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Thu, 8 Nov 2012 10:48:52 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> References: <7A60AB257EFF2B48B1F4C814817EA05331BB1D66@mxb2.hg.genetics.utah.edu> Message-ID: Based on Mark's suggestion, I took a look at the EST files. Luckily there is no protein sequence contamination. [dstandag at mason Transcriptome] grep -v '^>' Pdom.Trinity.Trimmomatic.fasta | grep -o . | sort | uniq -c 79400764 A 39834991 C 40702954 G 77980105 T [dstandag at mason Transcriptome] grep -v '^>' Pmet.Trinity.R.fasta | grep -o . | sort | uniq -c 18294708 A 9108213 C 9449127 G 17756470 T -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Thu, Nov 8, 2012 at 9:47 AM, Mark Yandell wrote: > Hi Daniel, > > is it possible you have some proteins in your EST files? > > '------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw' > > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [ > daniel.standage at gmail.com] > Sent: Thursday, November 08, 2012 7:32 AM > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and > is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > --Carson > > > From: Daniel Standage daniel.standage at gmail.com>> > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 08:02:21 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:02:21 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.make r.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold _7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffo ld_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58 983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 > --maxintron 10000 --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq37.for.716125-723330.0.fasta at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. ...as well as one occurrence of this error. > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869 > 077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sca > ffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar > --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7 > /theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm > :86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen > ome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p > m:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line > 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to > localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is >> repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> 1.006902 Bio::Root::Version >>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl live >>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta >>> indexer is broken. I have an open bug I am trying to resolve with the >>> Bioperl developers, but for now use the CPAN version of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt >>> Cc: Maker Mailing List >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> Thanks. Could you also run with the --debug flag set on the command line >>>> for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt , Maker Mailing List >>>> >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP directory is >>>> on native disk space, and relaunched. I have attached the output of the job >>>> that failed in <5 minutes. It looks pretty similar to the errors I got the >>>> last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Nov 12 08:13:38 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 12 Nov 2012 10:13:38 -0500 Subject: [maker-devel] Query on genemark results In-Reply-To: Message-ID: The previous bug was a complete lack of GeneMark results in the GFF3, not just a lack of consensus models from GeneMark. It is possible to get no consensus models from GeneMark if they score poorly. Send me the GFF3 results of your larger contigs and I can review it and tell you if any models are being improperly categorized. Thanks, Carson On 12-10-28 1:50 PM, "kokwei" wrote: >Hi, > >I have the same problems as posted by Andr? Gomes on 10/4/10. I still >have the same problems even though using the current available version >of maker (maker 2.1 and maker 2.26 beta version). > >I have tried to do the gene prediction on eukaryotic genome using 3 >ab-initio gene predictors (SNAP, Augustus and GeneMark-ES) using Maker. >From the fasta_merge output, I have 3 separate files of gene models >($prefix.all.maker.augustus_masked.proteins.fasta, >$prefix.all.maker.snap_masked.proteins.fasta and >$prefix.all.maker.genemark.proteins.fasta) and one >$prefix.all.maker.proteins.fasta (I presume this should be the consensus >gene models from 3 predictors' results, right?). > > From the consensus gene models file, I don't see even one result from >genemark but all from snap/augustus only. Is that normal? >Also from the file naming and gene model label in final gff file, it's >showing that genemark is not masked like those of augustus and snap? Is >that true? Why only augustus and snap masked but not genemark? Please >assist and thanks for your helps. > >Kok Wei > > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From mikael.durling at slu.se Tue Nov 13 06:57:36 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Tue, 13 Nov 2012 13:57:36 +0000 Subject: [maker-devel] NULs in master_datastore_index.log Message-ID: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Hello, In order to work around locking problems with SQLite, I tried running (latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason it seems maker does not detect the automounted volumes as being nfs mounted?). Running over NFSv4 makes SQLite happy, but then another problem popped up. It seems ds_utility.pm happens to write simultaneously to the datastore_index from several MPI ranks, which in my case results in stretches of NULs in the datastore file. This seems to result in maker trying to analyse the same contig simultaneously on two different MPI ranks. (I get rank failure notices on the output twice for the same rank, and maker complaining that the same GFF3 ID appears more than once). Any hints on how this can be handled? It appears as I should have installed and run maker on some other cluster without NFS mounted volumes to save myself a lot of hassles. Thanks in advance, Mikael From carsonhh at gmail.com Tue Nov 13 07:12:58 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 13 Nov 2012 09:12:58 -0500 Subject: [maker-devel] NULs in master_datastore_index.log In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C602B023E8@exchange2-2> Message-ID: Locks for not running contigs are a separate thing from the datastore index. They are handled by file locks in the directory for each contig. For the datastore index, it can be subject to race conditions if two processes happen to write an output string at the exact same time, but can be rebuilt in less than 2 min at the end of your job using the -dsindex flag. The failure notices you are getting might be because of the configuration of the NFS mount. MAKER will check the locks it creates several times while running a given contig to see if the lock was broken, and if it was then that contig will fail producing an error. This will happen before it does any activity that might conflict with the other active run of that contig by another process, so the process that broke the lock should continue without issue somewhere else, but you will get a trail of messages in the error log and maybe some ugliness in the datastore index. You can try altering the flags set for the NFS mount, or just set the retry count really high. You will have to run maker -dsindex once your MPI job finishes to get the datastore index log back in order on completion, but that only takes a couple of minutes to rebuild. --Carson On 12-11-13 8:57 AM, "Mikael Brandstr?m Durling" wrote: >Hello, > >In order to work around locking problems with SQLite, I tried running >(latest svn) maker off an NFSv4 export instead of NFSv3. (For some reason >it seems maker does not detect the automounted volumes as being nfs >mounted?). Running over NFSv4 makes SQLite happy, but then another >problem popped up. It seems ds_utility.pm happens to write simultaneously >to the datastore_index from several MPI ranks, which in my case results >in stretches of NULs in the datastore file. This seems to result in maker >trying to analyse the same contig simultaneously on two different MPI >ranks. (I get rank failure notices on the output twice for the same rank, >and maker complaining that the same GFF3 ID appears more than once). > >Any hints on how this can be handled? > >It appears as I should have installed and run maker on some other cluster >without NFS mounted volumes to save myself a lot of hassles. > >Thanks in advance, >Mikael > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From es9 at sanger.ac.uk Thu Nov 15 03:20:56 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 10:20:56 +0000 Subject: [maker-devel] Augustus training within Maker Message-ID: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Hi, Could you please confirm something for me: If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. To achieve this, do I need to change anything in maker_opts.ctl or do I leave augustus_species= #Augustus gene prediction species model as is, or should it be edited for the 2nd run? Many thanks Eleanor -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From dsth at ebi.ac.uk Thu Nov 15 04:14:31 2012 From: dsth at ebi.ac.uk (Daniel Hughes) Date: Thu, 15 Nov 2012 11:14:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: heya, Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus > species config folder of gene parameters, then Augustus runs using this > data alone. > I understand that with a second Maker run Augustus retrains using the > BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I > leave > augustus_species= #Augustus gene prediction species model > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. dan. -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Thu Nov 15 04:34:09 2012 From: es9 at sanger.ac.uk (Eleanor Stanley) Date: Thu, 15 Nov 2012 11:34:09 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> Message-ID: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this Ele On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > heya, > > Could you please confirm something for me: > > If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. > I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. > > To achieve this, do I need to change anything in maker_opts.ctl or do I leave > augustus_species= #Augustus gene prediction species model > > > AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. > > dan. > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Fri Nov 16 07:19:47 2012 From: carsonhh at gmail.com (Carson Holt) Date: Fri, 16 Nov 2012 09:19:47 -0500 Subject: [maker-devel] segmentation fault (core dumped) for maker running In-Reply-To: Message-ID: The correct file to update in Bioperl is /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm not Bioperl.pm, but technically you only have to fix whichever .pm file loads last. So if it's working then don't worry about it because one of the files fixed by the first command are loading after /usr/local/share/perl/5.14.2/Bio/DB/Fasta.pm. Thanks, Carson From: Hung Chih-Ming Date: Thursday, 15 November, 2012 2:02 AM To: Carson Holt Cc: Subject: segmentation fault (core dumped) for maker running Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From ymwur1 at gmail.com Thu Nov 15 00:02:55 2012 From: ymwur1 at gmail.com (Hung Chih-Ming) Date: Thu, 15 Nov 2012 15:02:55 +0800 Subject: [maker-devel] segmentation fault (core dumped) for maker running Message-ID: Hi Dr. Holt, I just installed maker-2.26-beta in a lunix-64 bite server with Ubuntu 12. But when I ran maker, I got an error message show segmentation fault (see below): STATUS: Parsing control files... STATUS: Processing and indexing input FASTA files... ????????? (core dumped) I updated the three modules, AnyDBM_File, BDB::SQLlite, or BerkeleyDB. And then I run the fix in maker/lib "sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)" Now maker seems to work! However, I could not follow the next step based on your response in the google discussion group, "You may also have to run the fix below on wherever Bioperl is installed as well, because it contains the same (DB_File GDBM_File NDBM_File SDBM_File) statement in the Bio::DB::Fasta module in one of the BEGIN statements." I tried to run this fix in the folder (/usr/local/share/perl/5.14.2/Bio/LiveSeq/IO/) containing Bioperl.pm. But it showed: sed: ?????? (it means no input files) I want to ask if this step is necessary? If so, what is the directory where I should run the fix? Thanks, Chih-Ming Chih-Ming Hung Postdoctoral researcher' Department of Life Science National Taiwan Normal University Taipei, Taiwan Email: ymwur1 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: From barry.moore at genetics.utah.edu Fri Nov 16 17:37:53 2012 From: barry.moore at genetics.utah.edu (Barry Moore) Date: Fri, 16 Nov 2012 17:37:53 -0700 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> Message-ID: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Dan is correct about the workings of the hint based communication between MAKER and the gene predictors - and just to clarify further. MAKER never 're-trains' Augustus or any of the other gene predictors. Many people will retrain the gene predictors between iterative MAKER runs, but this is a manual (and for Augustus non-trivial) step. B On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > Aha - that makes sense, so with every run Augustus is run with the BLAST hints available, thanks for clarifying this > > Ele > > > On 15 Nov 2012, at 11:14, Daniel Hughes wrote: > >> heya, >> >> Could you please confirm something for me: >> >> If with the first Maker run you provide the location of the Augustus species config folder of gene parameters, then Augustus runs using this data alone. >> I understand that with a second Maker run Augustus retrains using the BLAST evidence from the 1st run. >> >> To achieve this, do I need to change anything in maker_opts.ctl or do I leave >> augustus_species= #Augustus gene prediction species model >> >> >> AFAIK maker runs augustus, blast etc., as sort of raw compute stages in the earlier tier_types, the results of these stages e.g. protein alignments etc., are then 'synthesised' into 'hints' (early tier_type 3) that are provided to ab initio predicters capable of taking external 'hints' - such as augustus - that are used to generate the final models (after further adjustmnets wrt., utrs etc.). that is to say i think what you mean by first and second maker runs are actually internal usage of ab initios that occur at different stages of any single maker run and you should be shielded from this. >> >> dan. >> >> >> > > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From es9 at sanger.ac.uk Sat Nov 17 03:42:31 2012 From: es9 at sanger.ac.uk (es9) Date: Sat, 17 Nov 2012 10:42:31 +0000 Subject: [maker-devel] Augustus training within Maker In-Reply-To: <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> References: <6DA4D294-F4FA-4AF3-9B80-AAAE73839B91@sanger.ac.uk> <06889D83-071B-44A5-ADEC-D1A78FE0EFDF@sanger.ac.uk> <0490A065-4724-4221-83BC-4419BFBFC012@genetics.utah.edu> Message-ID: Thank you to you both for clarifying this ... I was get a smidge confused and reading previous posts I can see the answer had already been asked and replied to. Next time I will cruise the archives before posting! Regards, Eleanor > Dan is correct about the workings of the hint based communication > between MAKER and the gene predictors - and just to clarify further. > MAKER never 're-trains' Augustus or any of the other gene predictors. > Many people will retrain the gene predictors between iterative MAKER > runs, but this is a manual (and for Augustus non-trivial) step. > > B > > On Nov 15, 2012, at 4:34 AM, Eleanor Stanley wrote: > >> Aha - that makes sense, so with every run Augustus is run with the >> BLAST hints available, thanks for clarifying this >> >> Ele >> >> On 15 Nov 2012, at 11:14, Daniel Hughes wrote: >> >>> heya, >>> >>>> Could you please confirm something for me: >>>> >>>> If with the first Maker run you provide the location of the >>>> Augustus species config folder of gene parameters, then Augustus >>>> runs using this data alone. >>>> I understand that with a second Maker run Augustus retrains >>>> using the BLAST evidence from the 1st run. >>>> >>>> To achieve this, do I need to change anything in maker_opts.ctl >>>> or do I leave >>>> augustus_species= #Augustus gene prediction species model >>> >>> AFAIK maker runs augustus, blast etc., as sort of raw compute >>> stages in the earlier tier_types, the results of these stages e.g. >>> protein alignments etc., are then 'synthesised' into 'hints' >>> (early tier_type 3) that are provided to ab initio predicters >>> capable of taking external 'hints' - such as augustus - that are >>> used to generate the final models (after further adjustmnets wrt., >>> utrs etc.). that is to say i think what you mean by first and >>> second maker runs are actually internal usage of ab initios that >>> occur at different stages of any single maker run and you should >>> be shielded from this. >>> >>> dan. >> >> -- The Wellcome Trust Sanger Institute is operated by Genome >> Research Limited, a charity registered in England with number >> 1021457 and a company registered in England with number 2742969, >> whose registered office is 215 Euston Road, London, NW1 2BE. >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com [1] >> > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > Barry Moore > Research Scientist > Dept. of Human Genetics > University of Utah > Salt Lake City, UT 84112 > -------------------------------------------- > (801) 585-3543 > > > > Links: > ------ > [1] mailto:maker-devel at box290.bluehost.com -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. From parulk at caltech.edu Tue Nov 20 16:35:34 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:35:34 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction Message-ID: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Hello, I am running SNAP, Augustus and genemark(genemarkE results were calculated externally and gff3 file was provided to option pred_gff). However the resulting gff3 source field does not mention if the prediction were derived from SNAP, Augustus or genemark. I have attached the configuration file. Also is there any option where were could have priority for SNAP predictions? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4631 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 20 16:39:42 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 20 Nov 2012 15:39:42 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> References: <3062.131.215.15.234.1353454534.squirrel@webmail.caltech.edu> Message-ID: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Hello, Just found that for Scaffold of larger size it does explicitly specify the prediction source. Thanks, Parul > Hello, > > I am running SNAP, Augustus and genemark(genemarkE results were calculated > externally and gff3 file was provided to option pred_gff). However the > resulting gff3 source field does not mention if the prediction were > derived from SNAP, Augustus or genemark. I have attached the > configuration file. Also is there any option where were could have > priority for SNAP predictions? > > Thanks and regards, > Parul Kudtarkar > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From barry.utah at gmail.com Tue Nov 20 20:21:47 2012 From: barry.utah at gmail.com (Barry Moore) Date: Tue, 20 Nov 2012 20:21:47 -0700 Subject: [maker-devel] email about Maker In-Reply-To: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> References: <1353347288.90176.YahooMailNeo@web113208.mail.gq1.yahoo.com> Message-ID: Hi Jorge, These would be two different proteins identified on the same scaffold. The numbers don't have any meaning other than that the genes are numbered sequentially and so these two genes would be adjacent to each other. If you have access to the GFF3 file produced by Maker for this genome you should see those two IDs with adjacent but different coordinates as well. B On Nov 19, 2012, at 10:48 AM, Jorge Ibarra wrote: > Dear Dr Moore > > I have a quick question about Maker and I'd appreciate if you could answer that to me. I downloaded two protein sequences predicted by Maker with the following indentifiers: > > >maker_scaffold_7-snap-gene-1.23-mRNA-1 Glucosylceramidase > >maker_scaffold_7-snap-gene-1.24-mRNA-1 Glucosylceramidase > > The only thing that varies in the two sequences identifiers are the number 1.23 and 1.24, and I was wondering what this numbers mean. Their sequence are also really similar (96%). > > I wonder if these sequences represent two genes in the same scaffold (scaffold_7) or if they are two slightly different predictions of the same gene. > > So my question is what do those numbers (1.23 and 1.24) represent in Maker? > > Thank you. > > Jorge Ibarra > PhD student Barry Moore Research Scientist Dept. of Human Genetics University of Utah Salt Lake City, UT 84112 -------------------------------------------- (801) 585-3543 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 07:25:36 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 09:25:36 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <3100.131.215.15.234.1353454782.squirrel@webmail.caltech.edu> Message-ID: Is it possible that you just picked a contig that didn't have any pred_gff entries for snap and augustus the first time? The predictions you pass through should be of type match/match_part and will have the source as pred_gff:snap or pred_gff:augustus. Could you check and let me know or send me an example of entries from a contig you passed through and the results you are seeing? No. there is no priority given to one prediction over the other. They are choses based on evidence overlap similarity. Thanks, Carson On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >Hello, > >Just found that for Scaffold of larger size it does explicitly specify the >prediction source. > >Thanks, >Parul > >> Hello, >> >> I am running SNAP, Augustus and genemark(genemarkE results were >>calculated >> externally and gff3 file was provided to option pred_gff). However the >> resulting gff3 source field does not mention if the prediction were >> derived from SNAP, Augustus or genemark. I have attached the >> configuration file. Also is there any option where were could have >> priority for SNAP predictions? >> >> Thanks and regards, >> Parul Kudtarkar >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From benayoun at stanford.edu Wed Nov 21 11:45:55 2012 From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=) Date: Wed, 21 Nov 2012 10:45:55 -0800 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Message-ID: Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department *BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed Nov 21 13:58:05 2012 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 21 Nov 2012 15:58:05 -0500 Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? In-Reply-To: Message-ID: There are many ways of doing this. You can run everything separately and then copy all GFF3 files into a common folder and use the gff3_merge script that comes with maker to combine them. Alternatively you can run maker with the -g and -base options. This allows you to specify a new genome on the command line and the base name of the directory to write to. Using those flags you can swap in a different contig file while maintaining the same output directory for your job as a whole. Just run maker at the end of the run using the original fasta and the -dsindex flag, to sync the datastore index file so it is complete if you do this option. To split out contigs of interest you can also use the fasta_tool that comes with maker and use the -grep_header or ?select flags to indicate which contigs to retrieve. --Carson From: B?r?nice Benayoun Date: Wednesday, 21 November, 2012 1:45 PM To: Cc: Dario Riccardo Valenzano Subject: [maker-devel] Prioritizing specific scaffolds to be annotated? Hello, I am using the pipeline to try and annotate the assembly of a genome that we recently made in the lab (~70000 scaffolds). We have a specific interest in selected contigs for biological reasons (significant QTLs for a phenotype of interest that we'd like to link to potential genes), though of course we want to annotate most of the genome in the end.I was wondering if there was a way to bump some contigs up the list ? I have tried to just extract the specific contigs into a smaller fasta file and run maker separately just on them, but I don't know how to reintegrate them in the final complete output in the end and if it's even possible. Do you have any advice for this ? Thank you so much in advance for your most invaluable help ! Sincerely yours, B?r?nice -- B?r?nice A. BENAYOUN, Ph.D. Stanford University/Genetics Department BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases' M312 Alway Building 300, Pasteur Drive MC 5120 Stanford, CA 94305-5120 USA Email: benayoun at stanford.edu Web: www.stanford.edu/group/brunet/ _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 21 14:15:00 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 21 Nov 2012 13:15:00 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Dear Carson, That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb which is very small). I have attached a Scaffold of 1.5kb with no predictions and another Scaffold of 28kb. It is of course expected that we would not get any gene-prediction for small size Scaffolds. For next maker run would you recommend bootstrap to reduce false positives? Thanks and regards, Parul Kudtarkar > Is it possible that you just picked a contig that didn't have any pred_gff > entries for snap and augustus the first time? The predictions you pass > through should be of type match/match_part and will have the source as > pred_gff:snap or pred_gff:augustus. Could you check and let me know or > send me an example of entries from a contig you passed through and the > results you are seeing? > > No. there is no priority given to one prediction over the other. They are > choses based on evidence overlap similarity. > > Thanks, > Carson > > > > > On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: > >>Hello, >> >>Just found that for Scaffold of larger size it does explicitly specify >> the >>prediction source. >> >>Thanks, >>Parul >> >>> Hello, >>> >>> I am running SNAP, Augustus and genemark(genemarkE results were >>>calculated >>> externally and gff3 file was provided to option pred_gff). However the >>> resulting gff3 source field does not mention if the prediction were >>> derived from SNAP, Augustus or genemark. I have attached the >>> configuration file. Also is there any option where were could have >>> priority for SNAP predictions? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold118825.gff Type: application/octet-stream Size: 1719 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold20.gff Type: application/octet-stream Size: 377514 bytes Desc: not available URL: From carsonhh at gmail.com Sun Nov 25 15:55:32 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 17:55:32 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <1579.131.215.15.234.1353532500.squirrel@webmail.caltech.edu> Message-ID: I see both augustus and snap derived predictions (match/match_part) with augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that were derived from these predictions. There are no predictions from genemark. Is that what you were expecting? If not could you specify how it varies. With respect to bootstrapping, it really depends how well trained your gene predictors are. In general only one round of bootstrapping may be necessary after newly training a gene predictor. Thanks, Carson On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >Dear Carson, > >That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >which is very small). I have attached a Scaffold of 1.5kb with no >predictions and another Scaffold of 28kb. It is of course expected that we >would not get any gene-prediction for small size Scaffolds. > >For next maker run would you recommend bootstrap to reduce false >positives? > >Thanks and regards, >Parul Kudtarkar > >> Is it possible that you just picked a contig that didn't have any >>pred_gff >> entries for snap and augustus the first time? The predictions you pass >> through should be of type match/match_part and will have the source as >> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >> send me an example of entries from a contig you passed through and the >> results you are seeing? >> >> No. there is no priority given to one prediction over the other. They >>are >> choses based on evidence overlap similarity. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >> >>>Hello, >>> >>>Just found that for Scaffold of larger size it does explicitly specify >>> the >>>prediction source. >>> >>>Thanks, >>>Parul >>> >>>> Hello, >>>> >>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>calculated >>>> externally and gff3 file was provided to option pred_gff). However the >>>> resulting gff3 source field does not mention if the prediction were >>>> derived from SNAP, Augustus or genemark. I have attached the >>>> configuration file. Also is there any option where were could have >>>> priority for SNAP predictions? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Sun Nov 25 21:10:11 2012 From: carsonhh at gmail.com (Carson Holt) Date: Sun, 25 Nov 2012 23:10:11 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt Cc: Maker Mailing List Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more detail > to the errors in the development version if you do an 'svn update'. Then you > will know the system specific reason why close or opened failed. For the > other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker. > output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1 > 869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_2 > 3.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker. > output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_ > c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, > there are some intermittent issues. I've seen a couple occurrences of the > following error... > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq101.for.716125-721460.0.fasta -t >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 >> --maxintron 10000 --showcigar --percent 20 > >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold >> _23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker >> .output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp5898 >> 3_c0_seq37.for.716125-723330.0.fasta at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > > ...as well as one occurrence of this error. > >> #-------------------------------# >> Calling out to FastaSeq::convert at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker >> .output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.186 >> 9077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >> affold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >> --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_ >> 7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.p >> m:86 >> STACK: Widget::exonerate::est2genome::assemble >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge >> nome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:82 >> STACK: polisher::exonerate::est::polish >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est. >> pm:44 >> STACK: GI::to_polisher >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:166>> 3 >> STACK: Process::MpiChunk::run >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling uri_escape at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> Calling File::Path::mkpath at >>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>> line 433. >>> >>> >>> >>> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to >> localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps and >>> is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl live >>>> (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command line >>>>> for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List >>>>> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP directory >>>>> is on native disk space, and relaunched. I have attached the output of the >>>>> job that failed in <5 minutes. It looks pretty similar to the errors I got >>>>> the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Sun Nov 25 21:56:31 2012 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 26 Nov 2012 04:56:31 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: , Message-ID: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> good detective work there Carson! Mark Yandell Professor of Human Genetics H.A. & Edna Benning Presidential Endowed Chair Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ph:801-587-7707 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] Sent: Sunday, November 25, 2012 9:10 PM To: Daniel Standage Cc: Maker Mailing List Subject: Re: [maker-devel] Maker issues I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. That is why you get --> ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. Thanks, Carson From: Daniel Standage > Date: Friday, 23 November, 2012 3:06 PM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta thanks, Carson From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_23 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_23 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. ...as well as one occurrence of this error. #-------------------------------# Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. running est2genome search. #--------- command -------------# Widget::exonerate::est2genome: /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se q93.est_exonerate.0 #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Sequence is a protein. Cannot revcom STACK: Error::throw STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 ----------------------------------------------------------- --> rank=NA, hostname=c4 ERROR: Failed while polishig ESTs ERROR: Chunk failed at level:2, tier_type:2 FAILED CONTIG:scaffold_7 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_7 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. I'll let you know if I see anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: Thanks. Typo now fixed on my end too ;-) Thanks, Carson From: Daniel Standage > Date: Wednesday, 7 November, 2012 11:43 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Looked good for a while, but came across this error. total clusters:20 now processing 0 flattening EST clusters doing tblastx of alt-ESTs Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. --> rank=NA, hostname=c4 ERROR: Failed while doing tblastx of alt-ESTs ERROR: Chunk failed at level:4, tier_type:2 FAILED CONTIG:scaffold_58 ERROR: Chunk failed at level:5, tier_type:0 FAILED CONTIG:scaffold_58 examining contents of the fasta file and run log Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. --Next Contig-- It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: Done. Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. Thanks, Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:14 AM To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues Debug output attached (bzip2 compressed). -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. --Carson From: Daniel Standage > Date: Monday, 5 November, 2012 10:05 AM To: Carson Holt >, Maker Mailing List > Subject: Maker issues Carson, I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University From cjfields at illinois.edu Sun Nov 25 22:33:52 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 05:33:52 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { if ( $str =~ m/U/i ) { $alphabet = 'rna'; } else { $alphabet = 'dna'; } } else { $alphabet = 'protein'; } Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. chris On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > good detective work there Carson! > > > Mark Yandell > Professor of Human Genetics > H.A. & Edna Benning Presidential Endowed Chair > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ph:801-587-7707 > > ________________________________________ > From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] > Sent: Sunday, November 25, 2012 9:10 PM > To: Daniel Standage > Cc: Maker Mailing List > Subject: Re: [maker-devel] Maker issues > > I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. > That is why you get --> > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > > You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. > > Thanks, > Carson > > > > From: Daniel Standage > > Date: Friday, 23 November, 2012 3:06 PM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Thanks for your reply, and sorry for my delayed response. > > I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 > STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 > STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: > Thanks. Typo now fixed on my end too ;-) > > Thanks, > Carson > > > From: Daniel Standage > > Date: Wednesday, 7 November, 2012 11:43 AM > > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Looked good for a while, but came across this error. > > total clusters:20 now processing 0 > flattening EST clusters > doing tblastx of alt-ESTs > Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > --> rank=NA, hostname=c4 > ERROR: Failed while doing tblastx of alt-ESTs > ERROR: Chunk failed at level:4, tier_type:2 > FAILED CONTIG:scaffold_58 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_58 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. > > > > --Next Contig-- > > It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: > Done. > > Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: > 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. > > Thanks, > Carson > > > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:14 AM > To: Carson Holt > > Cc: Maker Mailing List > > Subject: Re: Maker issues > > Debug output attached (bzip2 compressed). > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: > Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. > > --Carson > > > From: Daniel Standage > > Date: Monday, 5 November, 2012 10:05 AM > To: Carson Holt >, Maker Mailing List > > Subject: Maker issues > > Carson, > > I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From daniel.standage at gmail.com Mon Nov 26 04:08:56 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Mon, 26 Nov 2012 06:08:56 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thanks for the responses from everybody! The genomic sequence I am annotating is coming directly from AllPaths-LG, which I've noticed retains as much ambiguity as possible--thus the seldom seen ambiguity nucleotides which in this case seem to outnumber the resolved nucleotides. On one hand, I would hate to lose all the information these ambiguity characters provide by replacing them with Ns, but on the other hand if most tools treat them as such, then it might not make much of a difference. Another option I guess would be to replace ambiguity nucleotides by the most likely explicit nucleotide based solely on sequence composition. This would retain more information than an N, and would at least partially correct. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 26, 2012 at 12:33 AM, Fields, Christopher J < cjfields at illinois.edu> wrote: > This is coming from BioPerl trying to guess the alphabet if one is not > provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just > committed, in fact). It's probably best to explicitly set this when > possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell > wrote: > > > good detective work there Carson! > > > > > > Mark Yandell > > Professor of Human Genetics > > H.A. & Edna Benning Presidential Endowed Chair > > Eccles Institute of Human Genetics > > University of Utah > > 15 North 2030 East, Room 2100 > > Salt Lake City, UT 84112-5330 > > ph:801-587-7707 > > > > ________________________________________ > > From: maker-devel-bounces at yandell-lab.org [ > maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [ > carsonhh at gmail.com] > > Sent: Sunday, November 25, 2012 9:10 PM > > To: Daniel Standage > > Cc: Maker Mailing List > > Subject: Re: [maker-devel] Maker issues > > > > I think the problem is in the sequence of your scaffold. I pulled this > out of the exonerate alignment --> > > WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC > > > > Notice the letters W, K, R, M, etc. While these are technically legal > nucleotides, many external programs, and in this case BioPerl doesn't > handle them well. > > That is why you get --> > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > > > You might want to replace them in your input fasta with the letter 'N' > so they are treated as masked. You will have to delete the mpi_blastdb > directory to let maker rebuild the fasta indexes and you will probably have > to set clean_try=1 in the control files so that MAKER deletes old result > files that contain those characters on the retry. The other error may be > just a snowball effect from the first error, so you should see of it still > happens after fixing the input fasta file. > > > > Thanks, > > Carson > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Friday, 23 November, 2012 3:06 PM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Thanks for your reply, and sorry for my delayed response. > > > > I have attached the first file you requested, but the other two do not > exist. I have attached a listing of the files in that directory. Let me > know if you need anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: > > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 > > > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > > > thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Thursday, 8 November, 2012 9:32 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_23 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_23 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > ...as well as one occurrence of this error. > > > > #-------------------------------# > > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > > running est2genome search. > > #--------- command -------------# > > Widget::exonerate::est2genome: > > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > > > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > > q93.est_exonerate.0 > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Sequence is a protein. Cannot revcom > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > > ----------------------------------------------------------- > > --> rank=NA, hostname=c4 > > ERROR: Failed while polishig ESTs > > ERROR: Chunk failed at level:2, tier_type:2 > > FAILED CONTIG:scaffold_7 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_7 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > I'll let you know if I see anything else. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Typo now fixed on my end too ;-) > > > > Thanks, > > Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Wednesday, 7 November, 2012 11:43 AM > > > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Looked good for a while, but came across this error. > > > > total clusters:20 now processing 0 > > flattening EST clusters > > doing tblastx of alt-ESTs > > Undefined subroutine &GI::loalize_file called at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. > > --> rank=NA, hostname=c4 > > ERROR: Failed while doing tblastx of alt-ESTs > > ERROR: Chunk failed at level:4, tier_type:2 > > FAILED CONTIG:scaffold_58 > > > > ERROR: Chunk failed at level:5, tier_type:0 > > FAILED CONTIG:scaffold_58 > > > > examining contents of the fasta file and run log > > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > > > > > --Next Contig-- > > > > It seems pretty clear that there is a typo in GI.pm. I changed loalize > to localize and relaunched. > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < > daniel.standage at gmail.com> wrote: > > Done. > > > > Test job has successfully cleared the preliminary Fasta indexing steps > and is repeat masking. I'll let you know if there are any problems. Thanks! > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt carsonhh at gmail.com>> wrote: > > 1.006902 Bio::Root::Version > /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm > > > > One thing I noticed, in the debug output is that you are using Bioperl > live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's > fasta indexer is broken. I have an open bug I am trying to resolve with > the Bioperl developers, but for now use the CPAN version of Bioperl. > > > > Thanks, > > Carson > > > > > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:14 AM > > To: Carson Holt > > > Cc: Maker Mailing List maker-devel at yandell-lab.org>> > > Subject: Re: Maker issues > > > > Debug output attached (bzip2 compressed). > > > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt carsonhh at gmail.com>> wrote: > > Thanks. Could you also run with the --debug flag set on the command line > for a few minutes and send me that. > > > > --Carson > > > > > > From: Daniel Standage daniel.standage at gmail.com>> > > Date: Monday, 5 November, 2012 10:05 AM > > To: Carson Holt >, Maker > Mailing List maker-devel at yandell-lab.org>> > > Subject: Maker issues > > > > Carson, > > > > I updated to the latest development version, made sure the TMP directory > is on native disk space, and relaunched. I have attached the output of the > job that failed in <5 minutes. It looks pretty similar to the errors I got > the last time I used the dev version. > > > > -- > > Daniel S. Standage > > Ph.D. Candidate > > Bioinformatics and Computational Biology Program > > Department of Genetics, Development, and Cell Biology > > Iowa State University > > > > > > > > > > > > > > > > _______________________________________________ > > maker-devel mailing list > > maker-devel at box290.bluehost.com > > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Carson.Holt at oicr.on.ca Mon Nov 26 09:53:59 2012 From: Carson.Holt at oicr.on.ca (Carson Holt) Date: Mon, 26 Nov 2012 16:53:59 +0000 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: Thank you for the commit to Bioperl. I'll can also manipulate the alphabet value in the object hash right before calling the revcomp method, it's not the most elegant solution but the seq object creation is insulated from my control so I can't set it there --> Bio::Search::HSP::HSPI.pm line 578 I would still recommend losing the ambiguous bases though as they will very likely still cause problems in some downstream application. Thanks, Carson On 12-11-26 12:33 AM, "Fields, Christopher J" wrote: >This is coming from BioPerl trying to guess the alphabet if one is not >provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > >Easy enough to fix to allow for additional ambiguous nucleotides (just >committed, in fact). It's probably best to explicitly set this when >possible, though; it is a guess, after all. > >chris > >On Nov 25, 2012, at 10:56 PM, Mark Yandell >wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>[carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this >>out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal >>nucleotides, many external programs, and in this case BioPerl doesn't >>handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' >>so they are treated as masked. You will have to delete the mpi_blastdb >>directory to let maker rebuild the fasta indexes and you will probably >>have to set clean_try=1 in the control files so that MAKER deletes old >>result files that contain those characters on the retry. The other >>error may be just a snowball effect from the first error, so you should >>see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage >>> >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not >>exist. I have attached a listing of the files in that directory. Let me >>know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>> wrote: >> The first error is an IO error with your system. I've added some more >>detail to the errors in the development version if you do an 'svn >>update'. Then you will know the system specific reason why close or >>opened failed. For the other error, could you send me this file --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/sc >>affold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta >> >> And this one --> >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. >>However, there are some intermittent issues. I've seen a couple >>occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq101.for.716125-721460.0.fasta -t >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.m >>aker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/ >>comp58983_c0_seq37.for.716125-723330.0.fasta at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.m >>aker.output/maker.pd >> >>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for >>.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> >>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastor >>e/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>--showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> >>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaff >>old_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom >>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_in >>fo.pm:86 >> STACK: Widget::exonerate::est2genome::assemble >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/es >>t2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:82 >> STACK: polisher::exonerate::est::polish >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ >>est.pm:44 >> STACK: GI::to_polisher >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:1663 >> STACK: Process::MpiChunk::run >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:335 >> STACK: Process::MpiChunk::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >>:351 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: Process::MpiTiers::run_all >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm >>:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>> wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >>> >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>> wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps >>and is repeat masking. I'll let you know if there are any problems. >>Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>> wrote: >> 1.006902 Bio::Root::Version >>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl >>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>It's fasta indexer is broken. I have an open bug I am trying to resolve >>with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List >>> >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>> wrote: >> Thanks. Could you also run with the --debug flag set on the command >>line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage >>> >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker >>Mailing List >>> >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP >>directory is on native disk space, and relaunched. I have attached the >>output of the job that failed in <5 minutes. It looks pretty similar to >>the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > From parulk at caltech.edu Mon Nov 26 12:21:23 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 11:21:23 -0800 (PST) Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: References: Message-ID: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Hello Carson, Thanks for the feedback.Genemark was run outside maker and the resulting gff3 file was provided as option to pred_gff. What would the source in the gff3 of maker result state of the predictions where made from pred_gff? Thanks and regards, Parul Kudtarkar > I see both augustus and snap derived predictions (match/match_part) with > augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that > were derived from these predictions. There are no predictions from > genemark. Is that what you were expecting? If not could you specify how > it varies. > > With respect to bootstrapping, it really depends how well trained your > gene predictors are. In general only one round of bootstrapping may be > necessary after newly training a gene predictor. > > Thanks, > Carson > > > > On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: > >>Dear Carson, >> >>That is correct. There were no pred_gff for smaller size Scaffolds(~1.5kb >>which is very small). I have attached a Scaffold of 1.5kb with no >>predictions and another Scaffold of 28kb. It is of course expected that >> we >>would not get any gene-prediction for small size Scaffolds. >> >>For next maker run would you recommend bootstrap to reduce false >>positives? >> >>Thanks and regards, >>Parul Kudtarkar >> >>> Is it possible that you just picked a contig that didn't have any >>>pred_gff >>> entries for snap and augustus the first time? The predictions you pass >>> through should be of type match/match_part and will have the source as >>> pred_gff:snap or pred_gff:augustus. Could you check and let me know or >>> send me an example of entries from a contig you passed through and the >>> results you are seeing? >>> >>> No. there is no priority given to one prediction over the other. They >>>are >>> choses based on evidence overlap similarity. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>> >>>>Hello, >>>> >>>>Just found that for Scaffold of larger size it does explicitly specify >>>> the >>>>prediction source. >>>> >>>>Thanks, >>>>Parul >>>> >>>>> Hello, >>>>> >>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>calculated >>>>> externally and gff3 file was provided to option pred_gff). However >>>>> the >>>>> resulting gff3 source field does not mention if the prediction were >>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>> configuration file. Also is there any option where were could have >>>>> priority for SNAP predictions? >>>>> >>>>> Thanks and regards, >>>>> Parul Kudtarkar >>>>> >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>> >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From jason.stajich at gmail.com Mon Nov 26 14:32:42 2012 From: jason.stajich at gmail.com (Jason Stajich) Date: Mon, 26 Nov 2012 13:32:42 -0800 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> References: , <7A60AB257EFF2B48B1F4C814817EA0533CF5A196@mxb2.hg.genetics.utah.edu> <118F034CF4C3EF48A96F86CE585B94BF4CF2A0D4@CITESMBX5.ad.uillinois.edu> Message-ID: right - you can explicitly set the alphabet to 'dna' when building a sequence object but I don't know if this down in MAKER code that is tripping up? Jason On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" wrote: > This is coming from BioPerl trying to guess the alphabet if one is not provided. The specific spot: > > if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { > if ( $str =~ m/U/i ) { > $alphabet = 'rna'; > } else { > $alphabet = 'dna'; > } > } else { > $alphabet = 'protein'; > } > > Easy enough to fix to allow for additional ambiguous nucleotides (just committed, in fact). It's probably best to explicitly set this when possible, though; it is a guess, after all. > > chris > > On Nov 25, 2012, at 10:56 PM, Mark Yandell wrote: > >> good detective work there Carson! >> >> >> Mark Yandell >> Professor of Human Genetics >> H.A. & Edna Benning Presidential Endowed Chair >> Eccles Institute of Human Genetics >> University of Utah >> 15 North 2030 East, Room 2100 >> Salt Lake City, UT 84112-5330 >> ph:801-587-7707 >> >> ________________________________________ >> From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt [carsonhh at gmail.com] >> Sent: Sunday, November 25, 2012 9:10 PM >> To: Daniel Standage >> Cc: Maker Mailing List >> Subject: Re: [maker-devel] Maker issues >> >> I think the problem is in the sequence of your scaffold. I pulled this out of the exonerate alignment --> >> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >> >> Notice the letters W, K, R, M, etc. While these are technically legal nucleotides, many external programs, and in this case BioPerl doesn't handle them well. >> That is why you get --> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> >> You might want to replace them in your input fasta with the letter 'N' so they are treated as masked. You will have to delete the mpi_blastdb directory to let maker rebuild the fasta indexes and you will probably have to set clean_try=1 in the control files so that MAKER deletes old result files that contain those characters on the retry. The other error may be just a snowball effect from the first error, so you should see of it still happens after fixing the input fasta file. >> >> Thanks, >> Carson >> >> >> >> From: Daniel Standage > >> Date: Friday, 23 November, 2012 3:06 PM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Thanks for your reply, and sorry for my delayed response. >> >> I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt > wrote: >> The first error is an IO error with your system. I've added some more detail to the errors in the development version if you do an 'svn update'. Then you will know the system specific reason why close or opened failed. For the other error, could you send me this file --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >> >> This one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta >> >> And this one --> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta >> >> thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Thursday, 8 November, 2012 9:32 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error... >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60. >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_23 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_23 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> ...as well as one occurrence of this error. >> >> #-------------------------------# >> Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >> running est2genome search. >> #--------- command -------------# >> Widget::exonerate::est2genome: >> /N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd >> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >> q93.est_exonerate.0 >> #-------------------------------# >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Sequence is a protein. Cannot revcom >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >> STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >> STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >> STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_info.pm:86 >> STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:686 >> STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2genome.pm:961 >> STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:82 >> STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.pm:44 >> STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >> STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >> STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 >> STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 >> STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 >> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >> ----------------------------------------------------------- >> --> rank=NA, hostname=c4 >> ERROR: Failed while polishig ESTs >> ERROR: Chunk failed at level:2, tier_type:2 >> FAILED CONTIG:scaffold_7 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_7 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> I'll let you know if I see anything else. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt > wrote: >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage > >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433. >> >> >> >> --Next Contig-- >> >> It seems pretty clear that there is a typo in GI.pm. I changed loalize to localize and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage > wrote: >> Done. >> >> Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks! >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt > wrote: >> 1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >> >> One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl. >> >> Thanks, >> Carson >> >> >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:14 AM >> To: Carson Holt > >> Cc: Maker Mailing List > >> Subject: Re: Maker issues >> >> Debug output attached (bzip2 compressed). >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt > wrote: >> Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that. >> >> --Carson >> >> >> From: Daniel Standage > >> Date: Monday, 5 November, 2012 10:05 AM >> To: Carson Holt >, Maker Mailing List > >> Subject: Maker issues >> >> Carson, >> >> I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version. >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Jason Stajich jason.stajich at gmail.com jason at bioperl.org From parulk at caltech.edu Mon Nov 26 14:35:48 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 13:35:48 -0800 (PST) Subject: [maker-devel] AED score Message-ID: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Dear Maker community, For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K genes however I am getting 8 times the expected gene count indicating too many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes how to go about this? Thanks and regards, Parul Kudtarkar -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Mon Nov 26 14:37:43 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:37:43 -0500 Subject: [maker-devel] Maker issues In-Reply-To: Message-ID: The sequence object is being created well down into BioPerl (outside of my control), but I think I can explicitly set the alphabet to 'dna' by modifying the existing object just before calling the revcomp method to get around that. Thanks, Carson On 12-11-26 4:32 PM, "Jason Stajich" wrote: >right - you can explicitly set the alphabet to 'dna' when building a >sequence object but I don't know if this down in MAKER code that is >tripping up? > >Jason >On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" > wrote: > >> This is coming from BioPerl trying to guess the alphabet if one is not >>provided. The specific spot: >> >> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >> if ( $str =~ m/U/i ) { >> $alphabet = 'rna'; >> } else { >> $alphabet = 'dna'; >> } >> } else { >> $alphabet = 'protein'; >> } >> >> Easy enough to fix to allow for additional ambiguous nucleotides (just >>committed, in fact). It's probably best to explicitly set this when >>possible, though; it is a guess, after all. >> >> chris >> >> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>wrote: >> >>> good detective work there Carson! >>> >>> >>> Mark Yandell >>> Professor of Human Genetics >>> H.A. & Edna Benning Presidential Endowed Chair >>> Eccles Institute of Human Genetics >>> University of Utah >>> 15 North 2030 East, Room 2100 >>> Salt Lake City, UT 84112-5330 >>> ph:801-587-7707 >>> >>> ________________________________________ >>> From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>[carsonhh at gmail.com] >>> Sent: Sunday, November 25, 2012 9:10 PM >>> To: Daniel Standage >>> Cc: Maker Mailing List >>> Subject: Re: [maker-devel] Maker issues >>> >>> I think the problem is in the sequence of your scaffold. I pulled >>>this out of the exonerate alignment --> >>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>> >>> Notice the letters W, K, R, M, etc. While these are technically legal >>>nucleotides, many external programs, and in this case BioPerl doesn't >>>handle them well. >>> That is why you get --> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> >>> You might want to replace them in your input fasta with the letter 'N' >>>so they are treated as masked. You will have to delete the mpi_blastdb >>>directory to let maker rebuild the fasta indexes and you will probably >>>have to set clean_try=1 in the control files so that MAKER deletes old >>>result files that contain those characters on the retry. The other >>>error may be just a snowball effect from the first error, so you should >>>see of it still happens after fixing the input fasta file. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Friday, 23 November, 2012 3:06 PM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Thanks for your reply, and sorry for my delayed response. >>> >>> I have attached the first file you requested, but the other two do not >>>exist. I have attached a listing of the files in that directory. Let me >>>know if you need anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> wrote: >>> The first error is an IO error with your system. I've added some more >>>detail to the errors in the development version if you do an 'svn >>>update'. Then you will know the system specific reason why close or >>>opened failed. For the other error, could you send me this file --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>> >>> This one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta >>> >>> And this one --> >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta >>> >>> thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Thursday, 8 November, 2012 9:32 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Scaling up to whole-genome annotation, things seem to be going well. >>>However, there are some intermittent issues. I've seen a couple >>>occurrences of the following error... >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>--minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> couldn't close >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>60. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_23 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_23 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> ...as well as one occurrence of this error. >>> >>> #-------------------------------# >>> Calling out to FastaSeq::convert at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>> running est2genome search. >>> #--------- command -------------# >>> Widget::exonerate::est2genome: >>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>maker.output/maker.pd >>> >>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>> >>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>--showcigar --percent 20 > >>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>> >>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>> q93.est_exonerate.0 >>> #-------------------------------# >>> >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Sequence is a protein. Cannot revcom >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>> STACK: Bio::PrimarySeqI::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>> STACK: Bio::LocatableSeq::revcom >>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>nfo.pm:86 >>> STACK: Widget::exonerate::est2genome::assemble >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:686 >>> STACK: Widget::exonerate::est2genome::parse >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>st2genome.pm:961 >>> STACK: polisher::exonerate::est::e_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:82 >>> STACK: polisher::exonerate::est::polish >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>/est.pm:44 >>> STACK: GI::to_polisher >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>> STACK: GI::polish_exonerate >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>> STACK: Process::MpiChunk::_go >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:1663 >>> STACK: Process::MpiChunk::run >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:335 >>> STACK: Process::MpiChunk::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m:351 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: Process::MpiTiers::run_all >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>m:286 >>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while polishig ESTs >>> ERROR: Chunk failed at level:2, tier_type:2 >>> FAILED CONTIG:scaffold_7 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_7 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> I'll let you know if I see anything else. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> wrote: >>> Thanks. Typo now fixed on my end too ;-) >>> >>> Thanks, >>> Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Wednesday, 7 November, 2012 11:43 AM >>> >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Looked good for a while, but came across this error. >>> >>> total clusters:20 now processing 0 >>> flattening EST clusters >>> doing tblastx of alt-ESTs >>> Undefined subroutine &GI::loalize_file called at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>> --> rank=NA, hostname=c4 >>> ERROR: Failed while doing tblastx of alt-ESTs >>> ERROR: Chunk failed at level:4, tier_type:2 >>> FAILED CONTIG:scaffold_58 >>> >>> ERROR: Chunk failed at level:5, tier_type:0 >>> FAILED CONTIG:scaffold_58 >>> >>> examining contents of the fasta file and run log >>> Calling Datastore::MD5::mkdir at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling uri_escape at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> Calling File::Path::mkpath at >>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>m line 433. >>> >>> >>> >>> --Next Contig-- >>> >>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>to localize and relaunched. >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> wrote: >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>>and is repeat masking. I'll let you know if there are any problems. >>>Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> wrote: >>> 1.006902 Bio::Root::Version >>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>> >>> One thing I noticed, in the debug output is that you are using Bioperl >>>live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>It's fasta indexer is broken. I have an open bug I am trying to >>>resolve with the Bioperl developers, but for now use the CPAN version >>>of Bioperl. >>> >>> Thanks, >>> Carson >>> >>> >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:14 AM >>> To: Carson Holt > >>> Cc: Maker Mailing List >>>> >>> Subject: Re: Maker issues >>> >>> Debug output attached (bzip2 compressed). >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> wrote: >>> Thanks. Could you also run with the --debug flag set on the command >>>line for a few minutes and send me that. >>> >>> --Carson >>> >>> >>> From: Daniel Standage >>>> >>> Date: Monday, 5 November, 2012 10:05 AM >>> To: Carson Holt >, Maker >>>Mailing List >>>> >>> Subject: Maker issues >>> >>> Carson, >>> >>> I updated to the latest development version, made sure the TMP >>>directory is on native disk space, and relaunched. I have attached the >>>output of the job that failed in <5 minutes. It looks pretty similar to >>>the errors I got the last time I used the dev version. >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >Jason Stajich >jason.stajich at gmail.com >jason at bioperl.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 14:46:48 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:46:48 -0500 Subject: [maker-devel] AED score In-Reply-To: <2000.131.215.15.234.1353965748.squirrel@webmail.caltech.edu> Message-ID: AED score with 1 are the ones you don't want. 0 is best and 1 is worst as it is a distance metric. You can use the AED_threshold parameter to require better matching to the evidence by setting it closer to 0. You can also try to increase protein homology evidence as some of your calls may be split genes due to lack of evidence linking them. --Carson On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >Dear Maker community, > >For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect 20-30K >genes however I am getting 8 times the expected gene count indicating too >many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if yes how >to go about this? > >Thanks and regards, >Parul Kudtarkar > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From carsonhh at gmail.com Mon Nov 26 14:48:18 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 16:48:18 -0500 Subject: [maker-devel] ab-initio gene-prediction In-Reply-To: <4307.131.215.15.234.1353957683.squirrel@webmail.caltech.edu> Message-ID: They should show up as genemark or pred_gff:genemark. Could you verify that the input file from genemark indeed contained predictions that should have been on this contig as not all contigs may have calls from genemark? --Carson On 12-11-26 2:21 PM, "Parul Kudtarkar" wrote: >Hello Carson, > >Thanks for the feedback.Genemark was run outside maker and the resulting >gff3 file was provided as option to pred_gff. What would the source in the >gff3 of maker result state of the predictions where made from pred_gff? > >Thanks and regards, >Parul Kudtarkar > >> I see both augustus and snap derived predictions (match/match_part) with >> augustus/snap in the source column, and maker genes (mRNA/exon/CDS) that >> were derived from these predictions. There are no predictions from >> genemark. Is that what you were expecting? If not could you specify how >> it varies. >> >> With respect to bootstrapping, it really depends how well trained your >> gene predictors are. In general only one round of bootstrapping may be >> necessary after newly training a gene predictor. >> >> Thanks, >> Carson >> >> >> >> On 12-11-21 4:15 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson, >>> >>>That is correct. There were no pred_gff for smaller size >>>Scaffolds(~1.5kb >>>which is very small). I have attached a Scaffold of 1.5kb with no >>>predictions and another Scaffold of 28kb. It is of course expected that >>> we >>>would not get any gene-prediction for small size Scaffolds. >>> >>>For next maker run would you recommend bootstrap to reduce false >>>positives? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>> Is it possible that you just picked a contig that didn't have any >>>>pred_gff >>>> entries for snap and augustus the first time? The predictions you >>>>pass >>>> through should be of type match/match_part and will have the source as >>>> pred_gff:snap or pred_gff:augustus. Could you check and let me know >>>>or >>>> send me an example of entries from a contig you passed through and the >>>> results you are seeing? >>>> >>>> No. there is no priority given to one prediction over the other. They >>>>are >>>> choses based on evidence overlap similarity. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> On 12-11-20 6:39 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Hello, >>>>> >>>>>Just found that for Scaffold of larger size it does explicitly specify >>>>> the >>>>>prediction source. >>>>> >>>>>Thanks, >>>>>Parul >>>>> >>>>>> Hello, >>>>>> >>>>>> I am running SNAP, Augustus and genemark(genemarkE results were >>>>>>calculated >>>>>> externally and gff3 file was provided to option pred_gff). However >>>>>> the >>>>>> resulting gff3 source field does not mention if the prediction were >>>>>> derived from SNAP, Augustus or genemark. I have attached the >>>>>> configuration file. Also is there any option where were could have >>>>>> priority for SNAP predictions? >>>>>> >>>>>> Thanks and regards, >>>>>> Parul Kudtarkar >>>>>> >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>> >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > From cjfields at illinois.edu Mon Nov 26 14:55:04 2012 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 26 Nov 2012 21:55:04 +0000 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> That makes sense. The change I made should also allow these sequences to 'just work', but this would of course require a BioPerl update. We could also make that change within BioPerl if needed if we know where it might be; it seems in this case a returned sequence should be 'dna' if the application is exonerate. chris On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > The sequence object is being created well down into BioPerl (outside of my > control), but I think I can explicitly set the alphabet to 'dna' by > modifying the existing object just before calling the revcomp method to > get around that. > > Thanks, > Carson > > > On 12-11-26 4:32 PM, "Jason Stajich" wrote: > >> right - you can explicitly set the alphabet to 'dna' when building a >> sequence object but I don't know if this down in MAKER code that is >> tripping up? >> >> Jason >> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >> wrote: >> >>> This is coming from BioPerl trying to guess the alphabet if one is not >>> provided. The specific spot: >>> >>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>> if ( $str =~ m/U/i ) { >>> $alphabet = 'rna'; >>> } else { >>> $alphabet = 'dna'; >>> } >>> } else { >>> $alphabet = 'protein'; >>> } >>> >>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>> committed, in fact). It's probably best to explicitly set this when >>> possible, though; it is a guess, after all. >>> >>> chris >>> >>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>> wrote: >>> >>>> good detective work there Carson! >>>> >>>> >>>> Mark Yandell >>>> Professor of Human Genetics >>>> H.A. & Edna Benning Presidential Endowed Chair >>>> Eccles Institute of Human Genetics >>>> University of Utah >>>> 15 North 2030 East, Room 2100 >>>> Salt Lake City, UT 84112-5330 >>>> ph:801-587-7707 >>>> >>>> ________________________________________ >>>> From: maker-devel-bounces at yandell-lab.org >>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>> [carsonhh at gmail.com] >>>> Sent: Sunday, November 25, 2012 9:10 PM >>>> To: Daniel Standage >>>> Cc: Maker Mailing List >>>> Subject: Re: [maker-devel] Maker issues >>>> >>>> I think the problem is in the sequence of your scaffold. I pulled >>>> this out of the exonerate alignment --> >>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>> >>>> Notice the letters W, K, R, M, etc. While these are technically legal >>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>> handle them well. >>>> That is why you get --> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> >>>> You might want to replace them in your input fasta with the letter 'N' >>>> so they are treated as masked. You will have to delete the mpi_blastdb >>>> directory to let maker rebuild the fasta indexes and you will probably >>>> have to set clean_try=1 in the control files so that MAKER deletes old >>>> result files that contain those characters on the retry. The other >>>> error may be just a snowball effect from the first error, so you should >>>> see of it still happens after fixing the input fasta file. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Friday, 23 November, 2012 3:06 PM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Thanks for your reply, and sorry for my delayed response. >>>> >>>> I have attached the first file you requested, but the other two do not >>>> exist. I have attached a listing of the files in that directory. Let me >>>> know if you need anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>> > wrote: >>>> The first error is an IO error with your system. I've added some more >>>> detail to the errors in the development version if you do an 'svn >>>> update'. Then you will know the system specific reason why close or >>>> opened failed. For the other error, could you send me this file --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/ >>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>> >>>> This one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta >>>> >>>> And this one --> >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>> >>>> thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Thursday, 8 November, 2012 9:32 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Scaling up to whole-genome annotation, things seem to be going well. >>>> However, there are some intermittent issues. I've seen a couple >>>> occurrences of the following error... >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> couldn't close >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason. >>>> maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2 >>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line >>>> 60. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_23 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> ...as well as one occurrence of this error. >>>> >>>> #-------------------------------# >>>> Calling out to FastaSeq::convert at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. >>>> running est2genome search. >>>> #--------- command -------------# >>>> Widget::exonerate::est2genome: >>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason. >>>> maker.output/maker.pd >>>> >>>> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.fo >>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>> >>>> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto >>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>> --showcigar --percent 20 > >>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>> >>>> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaf >>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>> q93.est_exonerate.0 >>>> #-------------------------------# >>>> >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Sequence is a protein. Cannot revcom >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>> STACK: Bio::PrimarySeqI::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 >>>> STACK: Bio::LocatableSeq::revcom >>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 >>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice_i >>>> nfo.pm:86 >>>> STACK: Widget::exonerate::est2genome::assemble >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:686 >>>> STACK: Widget::exonerate::est2genome::parse >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e >>>> st2genome.pm:961 >>>> STACK: polisher::exonerate::est::e_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:82 >>>> STACK: polisher::exonerate::est::polish >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate >>>> /est.pm:44 >>>> STACK: GI::to_polisher >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>> STACK: GI::polish_exonerate >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>> STACK: Process::MpiChunk::_go >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:1663 >>>> STACK: Process::MpiChunk::run >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:335 >>>> STACK: Process::MpiChunk::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m:351 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: Process::MpiTiers::run_all >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p >>>> m:286 >>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while polishig ESTs >>>> ERROR: Chunk failed at level:2, tier_type:2 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_7 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> I'll let you know if I see anything else. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>> > wrote: >>>> Thanks. Typo now fixed on my end too ;-) >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>> >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Looked good for a while, but came across this error. >>>> >>>> total clusters:20 now processing 0 >>>> flattening EST clusters >>>> doing tblastx of alt-ESTs >>>> Undefined subroutine &GI::loalize_file called at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >>>> --> rank=NA, hostname=c4 >>>> ERROR: Failed while doing tblastx of alt-ESTs >>>> ERROR: Chunk failed at level:4, tier_type:2 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> ERROR: Chunk failed at level:5, tier_type:0 >>>> FAILED CONTIG:scaffold_58 >>>> >>>> examining contents of the fasta file and run log >>>> Calling Datastore::MD5::mkdir at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling uri_escape at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> Calling File::Path::mkpath at >>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p >>>> m line 433. >>>> >>>> >>>> >>>> --Next Contig-- >>>> >>>> It seems pretty clear that there is a typo in GI.pm. I changed loalize >>>> to localize and relaunched. >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>> > wrote: >>>> Done. >>>> >>>> Test job has successfully cleared the preliminary Fasta indexing steps >>>> and is repeat masking. I'll let you know if there are any problems. >>>> Thanks! >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>> > wrote: >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>> It's fasta indexer is broken. I have an open bug I am trying to >>>> resolve with the Bioperl developers, but for now use the CPAN version >>>> of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt > >>>> Cc: Maker Mailing List >>>> > >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>> > wrote: >>>> Thanks. Could you also run with the --debug flag set on the command >>>> line for a few minutes and send me that. >>>> >>>> --Carson >>>> >>>> >>>> From: Daniel Standage >>>> > >>>> Date: Monday, 5 November, 2012 10:05 AM >>>> To: Carson Holt >, Maker >>>> Mailing List >>>> > >>>> Subject: Maker issues >>>> >>>> Carson, >>>> >>>> I updated to the latest development version, made sure the TMP >>>> directory is on native disk space, and relaunched. I have attached the >>>> output of the job that failed in <5 minutes. It looks pretty similar to >>>> the errors I got the last time I used the dev version. >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> Jason Stajich >> jason.stajich at gmail.com >> jason at bioperl.org >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > From carsonhh at gmail.com Mon Nov 26 15:07:46 2012 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 26 Nov 2012 17:07:46 -0500 Subject: [maker-devel] Maker issues In-Reply-To: <118F034CF4C3EF48A96F86CE585B94BF4CF2AFF2@CITESMBX5.ad.uillinois.edu> Message-ID: The seq object is being create in Bio::Search::HSP::HSPI.pm line 578 which itself is several layers deep into BioPerl after creation of a Bio::Search::Hit object. I think explicitly setting the alphabet would require modifications to a number of modules that create hits from Bio::SearchIO so that the alphabet gets stored early on, but that seems like a lot of work and could break any number of things along the way. The current change should allow BioPerl to guess right. After all the upstream code did explicitly call revcomp, so it obviously thinks that the sequence can be reverse complimented, so BioPerl is now just verifying that the alphabet matches legal characters, even if it is an unlikely match. --Carson On 12-11-26 4:55 PM, "Fields, Christopher J" wrote: >That makes sense. The change I made should also allow these sequences to >'just work', but this would of course require a BioPerl update. > >We could also make that change within BioPerl if needed if we know where >it might be; it seems in this case a returned sequence should be 'dna' if >the application is exonerate. > >chris > >On Nov 26, 2012, at 3:37 PM, Carson Holt wrote: > >> The sequence object is being created well down into BioPerl (outside of >>my >> control), but I think I can explicitly set the alphabet to 'dna' by >> modifying the existing object just before calling the revcomp method to >> get around that. >> >> Thanks, >> Carson >> >> >> On 12-11-26 4:32 PM, "Jason Stajich" wrote: >> >>> right - you can explicitly set the alphabet to 'dna' when building a >>> sequence object but I don't know if this down in MAKER code that is >>> tripping up? >>> >>> Jason >>> On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J" >>> wrote: >>> >>>> This is coming from BioPerl trying to guess the alphabet if one is not >>>> provided. The specific spot: >>>> >>>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) { >>>> if ( $str =~ m/U/i ) { >>>> $alphabet = 'rna'; >>>> } else { >>>> $alphabet = 'dna'; >>>> } >>>> } else { >>>> $alphabet = 'protein'; >>>> } >>>> >>>> Easy enough to fix to allow for additional ambiguous nucleotides (just >>>> committed, in fact). It's probably best to explicitly set this when >>>> possible, though; it is a guess, after all. >>>> >>>> chris >>>> >>>> On Nov 25, 2012, at 10:56 PM, Mark Yandell >>>> >>>> wrote: >>>> >>>>> good detective work there Carson! >>>>> >>>>> >>>>> Mark Yandell >>>>> Professor of Human Genetics >>>>> H.A. & Edna Benning Presidential Endowed Chair >>>>> Eccles Institute of Human Genetics >>>>> University of Utah >>>>> 15 North 2030 East, Room 2100 >>>>> Salt Lake City, UT 84112-5330 >>>>> ph:801-587-7707 >>>>> >>>>> ________________________________________ >>>>> From: maker-devel-bounces at yandell-lab.org >>>>> [maker-devel-bounces at yandell-lab.org] on behalf of Carson Holt >>>>> [carsonhh at gmail.com] >>>>> Sent: Sunday, November 25, 2012 9:10 PM >>>>> To: Daniel Standage >>>>> Cc: Maker Mailing List >>>>> Subject: Re: [maker-devel] Maker issues >>>>> >>>>> I think the problem is in the sequence of your scaffold. I pulled >>>>> this out of the exonerate alignment --> >>>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC >>>>> >>>>> Notice the letters W, K, R, M, etc. While these are technically >>>>>legal >>>>> nucleotides, many external programs, and in this case BioPerl doesn't >>>>> handle them well. >>>>> That is why you get --> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> >>>>> You might want to replace them in your input fasta with the letter >>>>>'N' >>>>> so they are treated as masked. You will have to delete the >>>>>mpi_blastdb >>>>> directory to let maker rebuild the fasta indexes and you will >>>>>probably >>>>> have to set clean_try=1 in the control files so that MAKER deletes >>>>>old >>>>> result files that contain those characters on the retry. The other >>>>> error may be just a snowball effect from the first error, so you >>>>>should >>>>> see of it still happens after fixing the input fasta file. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Friday, 23 November, 2012 3:06 PM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Thanks for your reply, and sorry for my delayed response. >>>>> >>>>> I have attached the first file you requested, but the other two do >>>>>not >>>>> exist. I have attached a listing of the files in that directory. Let >>>>>me >>>>> know if you need anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt >>>>> > wrote: >>>>> The first error is an IO error with your system. I've added some >>>>>more >>>>> detail to the errors in the development version if you do an 'svn >>>>> update'. Then you will know the system specific reason why close or >>>>> opened failed. For the other error, could you send me this file --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_ >>>>>7/ >>>>> scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 >>>>> >>>>> This one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta >>>>> >>>>> And this one --> >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta >>>>> >>>>> thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Thursday, 8 November, 2012 9:32 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Scaling up to whole-genome annotation, things seem to be going well. >>>>> However, there are some intermittent issues. I've seen a couple >>>>> occurrences of the following error... >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq101.for.716125-721460.0.fasta -t >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome >>>>> --minintron 20 --maxintron 10000 --showcigar --percent 20 > >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> couldn't close >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.maso >>>>>n. >>>>> >>>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold >>>>>_2 >>>>> 3/comp58983_c0_seq37.for.716125-723330.0.fasta at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm >>>>>line >>>>> 60. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_23 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> ...as well as one occurrence of this error. >>>>> >>>>> #-------------------------------# >>>>> Calling out to FastaSeq::convert at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>1480. >>>>> running est2genome search. >>>>> #--------- command -------------# >>>>> Widget::exonerate::est2genome: >>>>> /N/hd01/dstandag/Mason/local/bin/exonerate -q >>>>> >>>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.maso >>>>>n. >>>>> maker.output/maker.pd >>>>> >>>>> >>>>>om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93. >>>>>fo >>>>> r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno >>>>> >>>>> >>>>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datas >>>>>to >>>>> re/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta >>>>> -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 >>>>> --showcigar --percent 20 > >>>>> /N/dc/scratch/dstandag/PdomGenomic/Annotation/ >>>>> >>>>> >>>>>output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc >>>>>af >>>>> fold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se >>>>> q93.est_exonerate.0 >>>>> #-------------------------------# >>>>> >>>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>>> MSG: Sequence is a protein. Cannot revcom >>>>> STACK: Error::throw >>>>> STACK: Bio::Root::Root::throw >>>>> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 >>>>> STACK: Bio::PrimarySeqI::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:38 >>>>>1 >>>>> STACK: Bio::LocatableSeq::revcom >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:5 >>>>>77 >>>>> STACK: exonerate::splice_info::needs_to_be_revcomped >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/splice >>>>>_i >>>>> nfo.pm:86 >>>>> STACK: Widget::exonerate::est2genome::assemble >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:686 >>>>> STACK: Widget::exonerate::est2genome::parse >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate >>>>>/e >>>>> st2genome.pm:961 >>>>> STACK: polisher::exonerate::est::e_exonerate >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:82 >>>>> STACK: polisher::exonerate::est::polish >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonera >>>>>te >>>>> /est.pm:44 >>>>> STACK: GI::to_polisher >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 >>>>> STACK: GI::polish_exonerate >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 >>>>> STACK: Process::MpiChunk::_go >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:1663 >>>>> STACK: Process::MpiChunk::run >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:335 >>>>> STACK: Process::MpiChunk::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m:351 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: Process::MpiTiers::run_all >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers >>>>>.p >>>>> m:286 >>>>> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 >>>>> ----------------------------------------------------------- >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while polishig ESTs >>>>> ERROR: Chunk failed at level:2, tier_type:2 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_7 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> I'll let you know if I see anything else. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Typo now fixed on my end too ;-) >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Wednesday, 7 November, 2012 11:43 AM >>>>> >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Looked good for a while, but came across this error. >>>>> >>>>> total clusters:20 now processing 0 >>>>> flattening EST clusters >>>>> doing tblastx of alt-ESTs >>>>> Undefined subroutine &GI::loalize_file called at >>>>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line >>>>>2648. >>>>> --> rank=NA, hostname=c4 >>>>> ERROR: Failed while doing tblastx of alt-ESTs >>>>> ERROR: Chunk failed at level:4, tier_type:2 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> ERROR: Chunk failed at level:5, tier_type:0 >>>>> FAILED CONTIG:scaffold_58 >>>>> >>>>> examining contents of the fasta file and run log >>>>> Calling Datastore::MD5::mkdir at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling uri_escape at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> Calling File::Path::mkpath at >>>>> >>>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk >>>>>.p >>>>> m line 433. >>>>> >>>>> >>>>> >>>>> --Next Contig-- >>>>> >>>>> It seems pretty clear that there is a typo in GI.pm. I changed >>>>>loalize >>>>> to localize and relaunched. >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage >>>>> > wrote: >>>>> Done. >>>>> >>>>> Test job has successfully cleared the preliminary Fasta indexing >>>>>steps >>>>> and is repeat masking. I'll let you know if there are any problems. >>>>> Thanks! >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt >>>>> > wrote: >>>>> 1.006902 Bio::Root::Version >>>>> >>>>>/N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.p >>>>>m >>>>> >>>>> One thing I noticed, in the debug output is that you are using >>>>>Bioperl >>>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). >>>>> It's fasta indexer is broken. I have an open bug I am trying to >>>>> resolve with the Bioperl developers, but for now use the CPAN version >>>>> of Bioperl. >>>>> >>>>> Thanks, >>>>> Carson >>>>> >>>>> >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:14 AM >>>>> To: Carson Holt > >>>>> Cc: Maker Mailing List >>>>> > >>>>> Subject: Re: Maker issues >>>>> >>>>> Debug output attached (bzip2 compressed). >>>>> >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt >>>>> > wrote: >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> > >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt >, >>>>>Maker >>>>> Mailing List >>>>> > >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached >>>>>the >>>>> output of the job that failed in <5 minutes. It looks pretty similar >>>>>to >>>>> the errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> maker-devel mailing list >>>>> maker-devel at box290.bluehost.com >>>>> >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> >>>> >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> Jason Stajich >>> jason.stajich at gmail.com >>> jason at bioperl.org >>> >>> >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> > From parulk at caltech.edu Mon Nov 26 15:15:58 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Mon, 26 Nov 2012 14:15:58 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <2223.131.215.15.234.1353968158.squirrel@webmail.caltech.edu> Dear Carson, Thanks, I retrain/rerun using better AED score to filter false negatives. > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From daniel.standage at gmail.com Fri Nov 23 13:06:34 2012 From: daniel.standage at gmail.com (Daniel Standage) Date: Fri, 23 Nov 2012 15:06:34 -0500 Subject: [maker-devel] Maker issues In-Reply-To: References: Message-ID: Thanks for your reply, and sorry for my delayed response. I have attached the first file you requested, but the other two do not exist. I have attached a listing of the files in that directory. Let me know if you need anything else. -- Daniel S. Standage Ph.D. Candidate Bioinformatics and Computational Biology Program Department of Genetics, Development, and Cell Biology Iowa State University On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt wrote: > The first error is an IO error with your system. I've added some more > detail to the errors in the development version if you do an 'svn update'. > Then you will know the system specific reason why close or opened failed. > For the other error, could you send me this file --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > > This one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > > And this one --> > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > > thanks, > Carson > > > > > From: Daniel Standage > Date: Thursday, 8 November, 2012 9:32 AM > > To: Carson Holt > Cc: Maker Mailing List > Subject: Re: Maker issues > > Scaling up to whole-genome annotation, things seem to be going well. > However, there are some intermittent issues. I've seen a couple occurrences > of the following error... > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta > -t > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0 > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > couldn't close > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta > at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line > 60. > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_23 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_23 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > > ...as well as one occurrence of this error. > > #-------------------------------# > Calling out to FastaSeq::convert at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480. > running est2genome search. > #--------- command -------------# > Widget::exonerate::est2genome: > /N/hd01/dstandag/Mason/local/bin/exonerate -q > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd > om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta > -t /N/dc/scratch/dstandag/PdomGenomic/Anno > > tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta > -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 > --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/ > > output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se > q93.est_exonerate.0 > #-------------------------------# > > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Sequence is a protein. Cannot revcom > STACK: Error::throw > STACK: Bio::Root::Root::throw > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368 > STACK: Bio::PrimarySeqI::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381 > STACK: Bio::LocatableSeq::revcom > /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577 > STACK: exonerate::splice_info::needs_to_be_revcomped > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/ > splice_info.pm:86 > STACK: Widget::exonerate::est2genome::assemble > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:686 > STACK: Widget::exonerate::est2genome::parse > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/ > est2genome.pm:961 > STACK: polisher::exonerate::est::e_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:82 > STACK: polisher::exonerate::est::polish > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/ > est.pm:44 > STACK: GI::to_polisher > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670 > STACK: GI::polish_exonerate > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517 > STACK: Process::MpiChunk::_go > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663 > STACK: Process::MpiChunk::run > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335 > STACK: Process::MpiChunk::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: Process::MpiTiers::run_all > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286 > STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644 > ----------------------------------------------------------- > --> rank=NA, hostname=c4 > ERROR: Failed while polishig ESTs > ERROR: Chunk failed at level:2, tier_type:2 > FAILED CONTIG:scaffold_7 > > ERROR: Chunk failed at level:5, tier_type:0 > FAILED CONTIG:scaffold_7 > > examining contents of the fasta file and run log > Calling Datastore::MD5::mkdir at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling uri_escape at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > Calling File::Path::mkpath at > /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm > line 433. > > > I'll let you know if I see anything else. > > > -- > Daniel S. Standage > Ph.D. Candidate > Bioinformatics and Computational Biology Program > Department of Genetics, Development, and Cell Biology > Iowa State University > > > > On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt wrote: > >> Thanks. Typo now fixed on my end too ;-) >> >> Thanks, >> Carson >> >> >> From: Daniel Standage >> Date: Wednesday, 7 November, 2012 11:43 AM >> >> To: Carson Holt >> Cc: Maker Mailing List >> Subject: Re: Maker issues >> >> Looked good for a while, but came across this error. >> >> total clusters:20 now processing 0 >> flattening EST clusters >> doing tblastx of alt-ESTs >> Undefined subroutine &GI::loalize_file called at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648. >> --> rank=NA, hostname=c4 >> ERROR: Failed while doing tblastx of alt-ESTs >> ERROR: Chunk failed at level:4, tier_type:2 >> FAILED CONTIG:scaffold_58 >> >> ERROR: Chunk failed at level:5, tier_type:0 >> FAILED CONTIG:scaffold_58 >> >> examining contents of the fasta file and run log >> Calling Datastore::MD5::mkdir at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling uri_escape at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> Calling File::Path::mkpath at >> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm >> line 433. >> >> >> >> --Next Contig-- >> >> >> It seems pretty clear that there is a typo in GI.pm. I changed *loalize*to >> *localize* and relaunched. >> >> >> -- >> Daniel S. Standage >> Ph.D. Candidate >> Bioinformatics and Computational Biology Program >> Department of Genetics, Development, and Cell Biology >> Iowa State University >> >> >> >> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage < >> daniel.standage at gmail.com> wrote: >> >>> Done. >>> >>> Test job has successfully cleared the preliminary Fasta indexing steps >>> and is repeat masking. I'll let you know if there are any problems. Thanks! >>> >>> >>> -- >>> Daniel S. Standage >>> Ph.D. Candidate >>> Bioinformatics and Computational Biology Program >>> Department of Genetics, Development, and Cell Biology >>> Iowa State University >>> >>> >>> >>> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt wrote: >>> >>>> 1.006902 Bio::Root::Version >>>> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm >>>> >>>> One thing I noticed, in the debug output is that you are using Bioperl >>>> live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's >>>> fasta indexer is broken. I have an open bug I am trying to resolve with >>>> the Bioperl developers, but for now use the CPAN version of Bioperl. >>>> >>>> Thanks, >>>> Carson >>>> >>>> >>>> >>>> >>>> From: Daniel Standage >>>> Date: Monday, 5 November, 2012 10:14 AM >>>> To: Carson Holt >>>> Cc: Maker Mailing List >>>> Subject: Re: Maker issues >>>> >>>> Debug output attached (bzip2 compressed). >>>> >>>> >>>> -- >>>> Daniel S. Standage >>>> Ph.D. Candidate >>>> Bioinformatics and Computational Biology Program >>>> Department of Genetics, Development, and Cell Biology >>>> Iowa State University >>>> >>>> >>>> >>>> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt wrote: >>>> >>>>> Thanks. Could you also run with the --debug flag set on the command >>>>> line for a few minutes and send me that. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> From: Daniel Standage >>>>> Date: Monday, 5 November, 2012 10:05 AM >>>>> To: Carson Holt , Maker Mailing List < >>>>> maker-devel at yandell-lab.org> >>>>> Subject: Maker issues >>>>> >>>>> Carson, >>>>> >>>>> I updated to the latest development version, made sure the TMP >>>>> directory is on native disk space, and relaunched. I have attached the >>>>> output of the job that failed in <5 minutes. It looks pretty similar to the >>>>> errors I got the last time I used the dev version. >>>>> >>>>> -- >>>>> Daniel S. Standage >>>>> Ph.D. Candidate >>>>> Bioinformatics and Computational Biology Program >>>>> Department of Genetics, Development, and Cell Biology >>>>> Iowa State University >>>>> >>>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... 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-rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303233.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303234.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:19 scaffold_23.1037324-1038206.gnl%7CDmel_r5%2E47%7CFBpp0303235.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038212.gnl%7CAmel_4%2E5%7CGB40495-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB40142-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038218.gnl%7CAmel_4%2E5%7CGB53378-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 scaffold_23.1037324-1038224.gnl%7CAmel_4%2E5%7CGB43258-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:19 scaffold_23.1037324-1038248.gnl%7CAmel_4%2E5%7CGB48486-PA.p_exonerate -rw-r--r-- 1 dstandag biol 576 Nov 8 11:19 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Nov 8 06:55 scaffold_23.11767-15264.gnl%7CDmel_r5%2E47%7CFBpp0079114.p_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:20 scaffold_23.1177210-1187515.comp55832_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 06:57 scaffold_23.118600-121630.comp56223_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:05 scaffold_23.119493-121535.gnl%7CAmel_4%2E5%7CGB42515-PA.p_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0080719.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:05 scaffold_23.119689-121538.gnl%7CDmel_r5%2E47%7CFBpp0085457.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:24 scaffold_23.11.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 33K Nov 8 06:28 scaffold_23.11.drosophila.rb.out -rw-r--r-- 1 dstandag biol 469K Nov 8 12:05 scaffold_23.11.final.section -rw-r--r-- 1 dstandag biol 198K Nov 8 11:19 scaffold_23.11.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 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-rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:25 scaffold_23.1239438-1240065.comp58697_c2_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:25 scaffold_23.1240020-1240577.comp51041_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:25 scaffold_23.1253831-1255409.comp58531_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:58 scaffold_23.125651-126606.comp51692_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:57 scaffold_23.126190-129712.comp51692_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:58 scaffold_23.126190-129712.comp51692_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:05 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dstandag biol 5.4K Nov 8 07:05 scaffold_23.129450-131047.gnl%7CAmel_4%2E5%7CGB47192-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 11:35 scaffold_23.1296927-1297434.gnl%7CAmel_4%2E5%7CGB43383-PA.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:29 scaffold_23.12.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 24K Nov 8 06:29 scaffold_23.12.drosophila.rb.out -rw-r--r-- 1 dstandag biol 343K Nov 8 12:05 scaffold_23.12.final.section -rw-r--r-- 1 dstandag biol 119K Nov 8 11:24 scaffold_23.12.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 104K Nov 8 11:28 scaffold_23.12.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 41K Nov 8 07:09 scaffold_23.1-2.raw.section -rw-r--r-- 1 dstandag biol 344K Nov 8 11:29 scaffold_23.12.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:29 scaffold_23.12.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1307615-1308418.comp1419599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 26K Nov 8 11:35 scaffold_23.1308043-1330696.gnl%7CAmel_4%2E5%7CGB48919-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1308162-1309528.comp44341_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302629.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302630.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1327971.gnl%7CDmel_r5%2E47%7CFBpp0302631.p_exonerate -rw-r--r-- 1 dstandag biol 579 Nov 8 11:35 scaffold_23.1308337-1330258.gnl%7CDmel_r5%2E47%7CFBpp0302633.p_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:30 scaffold_23.1309128-1310251.comp26811_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 11:30 scaffold_23.1309844-1319042.comp55832_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:58 scaffold_23.131077-131586.comp59045_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1314850-1319042.comp55832_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 132K Nov 8 11:40 scaffold_23.13-14.raw.section -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1316714-1317272.comp1218705_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:59 scaffold_23.131685-132925.comp58909_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:59 scaffold_23.131685-134704.comp58909_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 8.3K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:59 scaffold_23.131685-134801.comp58909_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:58 scaffold_23.131685-136702.comp58909_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 06:59 scaffold_23.131685-136702.comp58909_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 11:30 scaffold_23.1318842-1326844.comp55832_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 11:30 scaffold_23.1318842-1329152.comp55832_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 11:30 scaffold_23.1318842-1331426.comp55832_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 06:58 scaffold_23.132429-133368.comp59433_c2_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1325517-1326265.comp1845494_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:59 scaffold_23.132575-133077.comp59433_c2_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 06:59 scaffold_23.132639-133189.comp59433_c2_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:59 scaffold_23.132947-134681.comp58909_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 06:59 scaffold_23.132947-134704.comp58909_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 06:58 scaffold_23.132947-134704.comp58909_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:59 scaffold_23.132947-134801.comp58909_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 06:58 scaffold_23.132947-134801.comp58909_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 11:30 scaffold_23.1331331-1332259.comp40535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:59 scaffold_23.133194-134178.comp58909_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 06:59 scaffold_23.133194-134681.comp58909_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 11:30 scaffold_23.1331948-1333303.comp32761_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1333133-1334007.comp56864_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1333600-1334315.comp56864_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 11:30 scaffold_23.1333918-1335419.comp56864_c3_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1335705.comp56864_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1333918-1337728.comp56864_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:35 scaffold_23.1334768-1337724.gnl%7CAmel_4%2E5%7CGB48917-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:05 scaffold_23.133512-135390.gnl%7CAmel_4%2E5%7CGB45366-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1335366-1335970.comp1729875_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:30 scaffold_23.1336887-1337499.comp1746631_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:00 scaffold_23.133757-134452.comp58909_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1340213-1340817.comp3166415_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1341145-1341745.comp2137934_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1341790-1342546.comp2308491_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 06:58 scaffold_23.134716-136043.comp58909_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:30 scaffold_23.1351224-1351773.comp56864_c3_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1351855-1352444.comp49157_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:30 scaffold_23.1352403-1353237.comp50400_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 11:30 scaffold_23.1352824-1354274.comp50400_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:30 scaffold_23.1353863-1354457.comp32051_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:30 scaffold_23.1354103-1354916.comp32051_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 11:30 scaffold_23.1354495-1355883.comp28788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 11:30 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scaffold_23.1361370-1362023.comp63024_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:30 scaffold_23.1361962-1362628.comp56945_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 11:30 scaffold_23.1362208-1364017.comp56945_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1363621-1364241.comp56945_c15_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:30 scaffold_23.1363824-1364656.comp56945_c3_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:30 scaffold_23.1364241-1365534.comp56945_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 11:30 scaffold_23.1365475-1366354.comp58627_c6_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:30 scaffold_23.1365475-1367018.comp58627_c6_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 11:30 scaffold_23.1366668-1368555.comp58344_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 11:30 scaffold_23.1369001-1370345.comp57731_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 11:30 scaffold_23.1369932-1370651.comp57731_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.137055-137860.comp53917_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 11:30 scaffold_23.1370982-1372429.comp58968_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 scaffold_23.1372006-1372825.comp56955_c2_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 11:30 scaffold_23.1372006-1373472.comp56955_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 11:30 scaffold_23.1373883-1375967.comp53188_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:00 scaffold_23.137439-138464.comp53917_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:30 scaffold_23.1376023-1376568.comp58089_c12_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 11:30 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-rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:35 scaffold_23.1389507.1410090.0.comp58089_c6_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 scaffold_23.1389801-1390543.comp47217_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 07:00 scaffold_23.138981-140060.comp58679_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1389854-1390711.comp47217_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 11:36 scaffold_23.1390291-1390966.comp47217_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 11:36 scaffold_23.1390743-1392000.comp58289_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1391585-1392360.comp58289_c8_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1391945-1392597.comp58289_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 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-rw-r--r-- 1 dstandag biol 5.4K Nov 8 11:36 scaffold_23.1397553-1399112.comp58089_c14_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:00 scaffold_23.139809-140616.comp39902_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1398718-1399314.comp58089_c8_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1398899-1399721.comp58089_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:36 scaffold_23.1399307-1400290.comp58089_c6_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 11:36 scaffold_23.1399900-1400941.comp58089_c17_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 58K Nov 8 11:35 scaffold_23.13.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 34K Nov 8 06:30 scaffold_23.13.drosophila.rb.out -rw-r--r-- 1 dstandag biol 1.5M Nov 8 12:05 scaffold_23.13.final.section -rw-r--r-- 1 dstandag biol 364K Nov 8 11:29 scaffold_23.13.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 430K Nov 8 11:33 scaffold_23.13.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 1.4M Nov 8 11:35 scaffold_23.13.raw.section -rw-r--r-- 1 dstandag biol 9.4K Nov 8 06:30 scaffold_23.13.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1400609-1401459.comp55139_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:36 scaffold_23.1401269-1402022.comp55139_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1401609-1402216.comp55139_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1401986-1402776.comp55139_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.3K Nov 8 11:36 scaffold_23.1402425-1403729.comp53666_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:00 scaffold_23.140332-144653.comp32064_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1403482-1404578.comp48783_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1404302-1405136.comp56313_c10_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:36 scaffold_23.1404714-1405577.comp56313_c9_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 11:36 scaffold_23.1404752-1405577.comp56313_c9_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 11:36 scaffold_23.1405378-1406432.comp58905_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406035-1406617.comp58905_c6_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 11:36 scaffold_23.1406210-1406799.comp57287_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 11:36 scaffold_23.1406210-1408214.comp57287_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409289.comp57287_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 11:36 scaffold_23.1407792-1409306.comp57287_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 11:36 scaffold_23.1408987-1409890.comp55527_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:36 scaffold_23.1409724-1410684.comp53099_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410284-1410885.comp53099_c3_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1410463-1411098.comp53099_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 11:36 scaffold_23.1410682-1411329.comp53099_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411082-1411787.comp53099_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 11:40 scaffold_23.1411196-1420373.gnl%7CAmel_4%2E5%7CGB48913-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:36 scaffold_23.1411769-1412299.comp53730_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 11:36 scaffold_23.1411806-1412343.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:36 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2.1K Nov 8 11:46 scaffold_23.1628188-1628869.comp53690_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1628995-1629629.comp1757695_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 11:46 scaffold_23.1629447-1630245.comp2225268_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 11:51 scaffold_23.1630078-1640599.gnl%7CAmel_4%2E5%7CGB48912-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1631027-1631710.comp54929_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 11:46 scaffold_23.1633935-1634941.comp469996_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 11:46 scaffold_23.1634612-1635227.comp1032535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 11:46 scaffold_23.1634842-1635615.comp9891_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 11:46 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06:46 scaffold_23.47976-52664.comp57565_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 06:46 scaffold_23.47976-52664.comp57565_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:15 scaffold_23.480590-481471.comp28980_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481059-481744.comp5788_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:15 scaffold_23.481631-482286.comp31314_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:15 scaffold_23.481869-482552.comp1406842_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K 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-rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:22 scaffold_23.4.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503515-504045.comp57130_c2_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503604-504201.comp59180_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:20 scaffold_23.503604-504204.comp59180_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.503604-504276.comp59180_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:20 scaffold_23.503604-504336.comp59180_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:20 scaffold_23.503654-504201.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:20 scaffold_23.503654-504350.comp59180_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:20 scaffold_23.503699-504221.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 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2.2K Nov 8 07:20 scaffold_23.570506-571138.comp58475_c5_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:48 scaffold_23.57128-61415.comp57935_c3_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.57128-61415.comp57935_c3_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:47 scaffold_23.57128-61415.comp57935_c3_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 07:20 scaffold_23.577559-578709.comp58715_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 07:20 scaffold_23.577559-578885.comp58715_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:20 scaffold_23.578520-579331.comp17262_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:20 scaffold_23.579634-580662.comp19872_c0_seq1.est_exonerate -rw-r--r-- 1 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dstandag biol 4.5K Nov 8 07:20 scaffold_23.588308-588965.comp58681_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:20 scaffold_23.588513-589494.comp58681_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:21 scaffold_23.588513-589516.comp58681_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:26 scaffold_23.589528-590438.comp56568_c1_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 07:26 scaffold_23.590043-590860.comp56568_c1_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-591973.comp56568_c1_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 6.0K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-592195.comp56568_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:26 scaffold_23.590043-597449.comp56568_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 07:26 scaffold_23.590182-590860.comp56568_c1_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:26 scaffold_23.590437-591973.comp56568_c1_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 07:26 scaffold_23.590437-592195.comp56568_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:26 scaffold_23.590437-597449.comp56568_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.5K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CAmel_4%2E5%7CGB42672-PA.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0291239.p_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 08:01 scaffold_23.590687-592150.gnl%7CDmel_r5%2E47%7CFBpp0293789.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 08:01 scaffold_23.590687-592189.gnl%7CDmel_r5%2E47%7CFBpp0071071.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0081035.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303794.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303795.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590885-591687.gnl%7CDmel_r5%2E47%7CFBpp0303796.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590885-592138.gnl%7CAmel_4%2E5%7CGB44981-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.590894-591937.gnl%7CAmel_4%2E5%7CGB44980-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.590909-591693.gnl%7CDmel_r5%2E47%7CFBpp0083755.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:26 scaffold_23.591776-592368.comp42067_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.592659-593271.comp59308_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.592659-593380.comp59308_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:26 scaffold_23.592965-593648.comp48548_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:26 scaffold_23.593120-593648.comp48548_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:26 scaffold_23.593237-593841.comp59308_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.594070-594730.comp1421803_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:26 scaffold_23.598316-598868.comp54258_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:26 scaffold_23.599941-600713.comp58738_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 47K Nov 8 07:25 scaffold_23.5.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 49K Nov 8 06:22 scaffold_23.5.drosophila.rb.out -rw-r--r-- 1 dstandag biol 917K Nov 8 12:05 scaffold_23.5.final.section -rw-r--r-- 1 dstandag biol 730K Nov 8 07:19 scaffold_23.5.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 416K Nov 8 07:23 scaffold_23.5.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 976K Nov 8 07:25 scaffold_23.5.raw.section -rw-r--r-- 1 dstandag biol 9.3K Nov 8 06:23 scaffold_23.5.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:26 scaffold_23.600393-600917.comp59155_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:26 scaffold_23.600937-601763.comp1225959_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:26 scaffold_23.604794-607215.comp51953_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 08:01 scaffold_23.604967-608877.gnl%7CAmel_4%2E5%7CGB43104-PA.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 07:26 scaffold_23.606823-608989.comp51953_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:26 scaffold_23.608733-612437.comp56721_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:27 scaffold_23.608733-612437.comp56721_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:26 scaffold_23.608733-614550.comp56721_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 07:27 scaffold_23.608733-614550.comp56721_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609085-612369.gnl%7CAmel_4%2E5%7CGB54556-PA.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0070184.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303734.p_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:01 scaffold_23.609109-612366.gnl%7CDmel_r5%2E47%7CFBpp0303735.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0071164.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.609263-610821.gnl%7CDmel_r5%2E47%7CFBpp0304872.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.61000-61642.comp57935_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 8.2K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.5K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 06:49 scaffold_23.61260-63533.comp57576_c4_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 8.1K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 8.0K Nov 8 06:49 scaffold_23.61260-63600.comp57576_c4_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:01 scaffold_23.612645-614365.gnl%7CAmel_4%2E5%7CGB43132-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.612828-614317.gnl%7CDmel_r5%2E47%7CFBpp0074633.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.613400-614111.gnl%7CDmel_r5%2E47%7CFBpp0075906.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:26 scaffold_23.614151-614876.comp1433111_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 6.8K Nov 8 07:27 scaffold_23.614490-616677.comp62542_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615220-616300.gnl%7CDmel_r5%2E47%7CFBpp0080690.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.615229-616300.gnl%7CAmel_4%2E5%7CGB48404-PA.p_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 07:30 scaffold_23.616573-622123.comp53298_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.1K Nov 8 06:55 scaffold_23.61662-63231.gnl%7CAmel_4%2E5%7CGB47823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:01 scaffold_23.617032-621897.gnl%7CAmel_4%2E5%7CGB43186-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.617361-621707.gnl%7CDmel_r5%2E47%7CFBpp0078372.p_exonerate -rw-r--r-- 1 dstandag biol 5.3K Nov 8 06:49 scaffold_23.62025-63600.comp57576_c4_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 scaffold_23.62037-63192.gnl%7CDmel_r5%2E47%7CFBpp0070204.p_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 06:55 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-rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:27 scaffold_23.622010-624802.comp57205_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:28 scaffold_23.622010-624802.comp57205_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 scaffold_23.622010-624802.comp57205_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:29 scaffold_23.622010-624802.comp57205_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:30 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dstandag biol 9.8K Nov 8 07:27 scaffold_23.622010-625026.comp57205_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:30 scaffold_23.622010-625026.comp57205_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:28 scaffold_23.622010-625026.comp57205_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:30 scaffold_23.622010-625178.comp57205_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:27 scaffold_23.622010-625178.comp57205_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:29 scaffold_23.622010-625178.comp57205_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 scaffold_23.622010-625178.comp57205_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:28 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-rw-r--r-- 1 dstandag biol 6.9K Nov 8 08:01 scaffold_23.635723-637373.gnl%7CDmel_r5%2E47%7CFBpp0082101.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:30 scaffold_23.637770-638562.comp42460_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:30 scaffold_23.638373-640543.comp40473_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649502.gnl%7CAmel_4%2E5%7CGB43214-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638434-649511.gnl%7CDmel_r5%2E47%7CFBpp0292225.p_exonerate -rw-r--r-- 1 dstandag biol 27K Nov 8 08:01 scaffold_23.638434-649538.gnl%7CAmel_4%2E5%7CGB45049-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.638434-649601.gnl%7CDmel_r5%2E47%7CFBpp0288420.p_exonerate -rw-r--r-- 1 dstandag biol 55K Nov 8 08:01 scaffold_23.638434-650174.gnl%7CAmel_4%2E5%7CGB49952-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638437-649103.gnl%7CAmel_4%2E5%7CGB42359-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.638440-647567.gnl%7CAmel_4%2E5%7CGB55144-PA.p_exonerate -rw-r--r-- 1 dstandag biol 28K Nov 8 08:01 scaffold_23.638440-649430.gnl%7CDmel_r5%2E47%7CFBpp0293284.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 08:01 scaffold_23.638443-649532.gnl%7CAmel_4%2E5%7CGB42373-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.63987-64717.comp59376_c14_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 07:30 scaffold_23.640205-641458.comp934535_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.641067-641742.comp17454_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.9K Nov 8 08:01 scaffold_23.641259-642288.gnl%7CAmel_4%2E5%7CGB41007-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K Nov 8 07:30 scaffold_23.641345-642764.comp17454_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:30 scaffold_23.642369-643170.comp1226599_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.642760-643453.comp3200316_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 06:49 scaffold_23.64294-84968.comp42086_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:01 scaffold_23.645509-646340.gnl%7CAmel_4%2E5%7CGB49823-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:30 scaffold_23.647483-648154.comp3284778_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:55 scaffold_23.649-1243.gnl%7CDmel_r5%2E47%7CFBpp0290776.p_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:01 scaffold_23.649971-651261.gnl%7CAmel_4%2E5%7CGB49951-PA.p_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:30 scaffold_23.651850-655866.comp56215_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 scaffold_23.651850-655866.comp56215_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:31 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Nov 8 08:02 scaffold_23.659787-662130.gnl%7CDmel_r5%2E47%7CFBpp0293463.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075012.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659799-662091.gnl%7CDmel_r5%2E47%7CFBpp0075013.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0073292.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:02 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0290751.p_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:01 scaffold_23.659802-662079.gnl%7CDmel_r5%2E47%7CFBpp0304481.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659802-662082.gnl%7CDmel_r5%2E47%7CFBpp0075772.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659802-662088.gnl%7CDmel_r5%2E47%7CFBpp0293948.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662097.gnl%7CAmel_4%2E5%7CGB47477-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659802-662121.gnl%7CAmel_4%2E5%7CGB41363-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662139.gnl%7CAmel_4%2E5%7CGB43707-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.0K Nov 8 08:01 scaffold_23.659802-662290.gnl%7CAmel_4%2E5%7CGB51586-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659802-662299.gnl%7CAmel_4%2E5%7CGB49425-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0089153.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0290826.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304233.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0304234.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659805-662299.gnl%7CDmel_r5%2E47%7CFBpp0305596.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:01 scaffold_23.659808-662094.gnl%7CAmel_4%2E5%7CGB52193-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CAmel_4%2E5%7CGB47284-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:02 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0076890.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 08:01 scaffold_23.659808-662097.gnl%7CDmel_r5%2E47%7CFBpp0085042.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB44431-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659808-662130.gnl%7CAmel_4%2E5%7CGB49047-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083843.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:01 scaffold_23.659808-662130.gnl%7CDmel_r5%2E47%7CFBpp0083906.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.659817-662079.gnl%7CAmel_4%2E5%7CGB46102-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0073585.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0082346.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 08:02 scaffold_23.659880-662097.gnl%7CDmel_r5%2E47%7CFBpp0305521.p_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 07:31 scaffold_23.664598-665339.comp57441_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.664951-665488.comp59321_c5_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 06:55 scaffold_23.66506-67079.gnl%7CAmel_4%2E5%7CGB47837-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088318.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088319.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0088320.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089257.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0089258.p_exonerate -rw-r--r-- 1 dstandag biol 4.1K Nov 8 06:55 scaffold_23.66506-74678.gnl%7CDmel_r5%2E47%7CFBpp0288398.p_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 07:31 scaffold_23.665135-665802.comp285497_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 5.0K Nov 8 07:31 scaffold_23.665399-666883.comp53689_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.666469-667197.comp53689_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.4K Nov 8 07:31 scaffold_23.667162-667951.comp52180_c1_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 2.8K Nov 8 07:31 scaffold_23.667162-671428.comp52180_c1_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 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dstandag biol 3.3K Nov 8 07:31 scaffold_23.667978-669042.comp59180_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 07:31 scaffold_23.668017-669001.comp59180_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 4.4K Nov 8 07:31 scaffold_23.668059-668959.comp59180_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.668936-669683.comp382769_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.66912-67979.comp5946_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:31 scaffold_23.669726-671764.comp52180_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 06:49 scaffold_23.67030-67979.comp5946_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 9.3K Nov 8 07:31 scaffold_23.671029-677447.comp52180_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.671054-671764.comp52180_c2_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.671886-672575.comp57527_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671901-672561.comp57527_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672538.comp57527_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 07:31 scaffold_23.671939-672575.comp57527_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41577-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB41578-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB46989-PA.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 08:02 scaffold_23.672017-672599.gnl%7CAmel_4%2E5%7CGB50263-PA.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.672098-672598.comp59502_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 07:31 scaffold_23.672970-673610.comp59089_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 3.7K Nov 8 07:31 scaffold_23.673324-674422.comp53293_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:31 scaffold_23.673999-677447.comp52180_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076415.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0076416.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302862.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302863.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:02 scaffold_23.674205-676007.gnl%7CDmel_r5%2E47%7CFBpp0302864.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0081016.p_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 08:02 scaffold_23.674205-676010.gnl%7CDmel_r5%2E47%7CFBpp0304068.p_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 07:31 scaffold_23.675963-676551.comp408860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 07:31 scaffold_23.677207-677898.comp772804_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.5K Nov 8 06:49 scaffold_23.67721-68472.comp350940_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:31 scaffold_23.677525-678233.comp53322_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.2K Nov 8 07:31 scaffold_23.677908-678920.comp53322_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.8K Nov 8 07:31 scaffold_23.677908-679249.comp53322_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.9K Nov 8 07:31 scaffold_23.678839-682919.comp32442_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 07:31 scaffold_23.679979-680866.comp36035_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 07:31 scaffold_23.679979-681267.comp36035_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.1M Nov 8 11:03 scaffold_23.6-7.raw.section -rw-r--r-- 1 dstandag biol 1.8K Nov 8 07:31 scaffold_23.680259-680866.comp36035_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 07:31 scaffold_23.680259-681267.comp36035_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 4.9K Nov 8 08:02 scaffold_23.680843-682232.gnl%7CAmel_4%2E5%7CGB50275-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 08:02 scaffold_23.680846-682172.gnl%7CDmel_r5%2E47%7CFBpp0070979.p_exonerate -rw-r--r-- 1 dstandag biol 4.6K Nov 8 07:50 scaffold_23.682524-683916.comp33074_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 07:44 scaffold_23.683503-684184.comp59066_c0_seq140.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:46 scaffold_23.683503-688813.comp59066_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:35 scaffold_23.683503-688813.comp59066_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:53 scaffold_23.683503-688813.comp59066_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:50 scaffold_23.683503-688813.comp59066_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:33 scaffold_23.683503-688813.comp59066_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:55 scaffold_23.683503-688813.comp59066_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:37 scaffold_23.683503-688813.comp59066_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:40 scaffold_23.683503-688813.comp59066_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:36 scaffold_23.683503-688813.comp59066_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 07:44 scaffold_23.683503-688813.comp59066_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683763-688813.comp59066_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:43 scaffold_23.683882-688813.comp59066_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:36 scaffold_23.683882-688813.comp59066_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:48 scaffold_23.683882-688813.comp59066_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:51 scaffold_23.683882-688813.comp59066_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:56 scaffold_23.683882-688813.comp59066_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:47 scaffold_23.683882-688813.comp59066_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:32 scaffold_23.683882-688813.comp59066_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:42 scaffold_23.683882-688813.comp59066_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:49 scaffold_23.683882-688813.comp59066_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:50 scaffold_23.683882-688813.comp59066_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 07:35 scaffold_23.683988-688813.comp59066_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:32 scaffold_23.684333-688813.comp59066_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:49 scaffold_23.684333-688813.comp59066_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:47 scaffold_23.684333-688813.comp59066_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:51 scaffold_23.684333-688813.comp59066_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:52 scaffold_23.684333-688813.comp59066_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:54 scaffold_23.684333-688813.comp59066_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:33 scaffold_23.684333-688813.comp59066_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:44 scaffold_23.684333-688813.comp59066_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:41 scaffold_23.684333-688813.comp59066_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:38 scaffold_23.684333-688813.comp59066_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:39 scaffold_23.684333-688813.comp59066_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:34 scaffold_23.684333-688813.comp59066_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:43 scaffold_23.684333-688975.comp59066_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:53 scaffold_23.684333-688975.comp59066_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:48 scaffold_23.684333-688975.comp59066_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:45 scaffold_23.684333-688975.comp59066_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 07:55 scaffold_23.684333-688975.comp59066_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721817.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 128K Nov 8 11:01 scaffold_23.684758.721839.0.gnl%7CPmet_v0%2E01%7CTrans008419%2Efor_tblastx%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 12K Nov 8 07:56 scaffold_23.684971-688813.comp59066_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.684971-688813.comp59066_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.684971-688813.comp59066_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:42 scaffold_23.684971-688813.comp59066_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:37 scaffold_23.684971-688975.comp59066_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:41 scaffold_23.684971-688975.comp59066_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.684975-688813.comp59066_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:39 scaffold_23.684975-688813.comp59066_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.684975-688813.comp59066_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.684975-688813.comp59066_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:45 scaffold_23.684975-688975.comp59066_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 07:53 scaffold_23.684975-688975.comp59066_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq1%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 33K Nov 8 08:02 scaffold_23.685011.718537.0.comp58143_c0_seq2%2Efor_blastn%2Efasta.blastn -rw-r--r-- 1 dstandag biol 12K Nov 8 07:38 scaffold_23.685264-688813.comp59066_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:41 scaffold_23.685264-688813.comp59066_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:34 scaffold_23.685264-688813.comp59066_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685264-688813.comp59066_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685264-688813.comp59066_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:52 scaffold_23.685264-688813.comp59066_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:32 scaffold_23.685264-688813.comp59066_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685264-688813.comp59066_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:37 scaffold_23.685264-688975.comp59066_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:49 scaffold_23.685264-688975.comp59066_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685264-688975.comp59066_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685334-688813.comp59066_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:35 scaffold_23.685334-688813.comp59066_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:46 scaffold_23.685334-688813.comp59066_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:48 scaffold_23.685334-688813.comp59066_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685334-688813.comp59066_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:49 scaffold_23.685334-688813.comp59066_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:54 scaffold_23.685334-688975.comp59066_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:52 scaffold_23.685334-688975.comp59066_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:46 scaffold_23.685334-688975.comp59066_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 07:45 scaffold_23.685334-688975.comp59066_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.68540-69483.comp433_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 11:02 scaffold_23.685479.720745.0.gnl%7CAmel_4%2E5%7CGB49172-PA%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072421%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0072422%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0290562%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304412%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304413%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 13K Nov 8 11:02 scaffold_23.685497.720745.0.gnl%7CDmel_r5%2E47%7CFBpp0304414%2Efor_blastx%2Efasta.blastx -rw-r--r-- 1 dstandag biol 11K Nov 8 07:44 scaffold_23.685588-688813.comp59066_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:55 scaffold_23.685588-688813.comp59066_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:33 scaffold_23.685588-688813.comp59066_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:51 scaffold_23.685588-688813.comp59066_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:36 scaffold_23.685588-688813.comp59066_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:32 scaffold_23.685588-688813.comp59066_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 10K Nov 8 07:49 scaffold_23.685588-688813.comp59066_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:39 scaffold_23.685588-688813.comp59066_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:52 scaffold_23.685801-688813.comp59066_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:41 scaffold_23.685801-688813.comp59066_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 9.9K Nov 8 07:44 scaffold_23.685801-688813.comp59066_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:42 scaffold_23.685801-688813.comp59066_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 9.8K Nov 8 07:46 scaffold_23.685801-688813.comp59066_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:54 scaffold_23.685801-688813.comp59066_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:51 scaffold_23.685801-688813.comp59066_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:45 scaffold_23.685801-688975.comp59066_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 9.6K Nov 8 07:42 scaffold_23.685801-688975.comp59066_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:32 scaffold_23.685801-688975.comp59066_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 9.7K Nov 8 07:37 scaffold_23.685801-688975.comp59066_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 9.1K Nov 8 07:38 scaffold_23.686019-688813.comp59066_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:37 scaffold_23.686019-688813.comp59066_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 07:53 scaffold_23.686019-688813.comp59066_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 07:52 scaffold_23.686019-688813.comp59066_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 9.2K Nov 8 07:42 scaffold_23.686019-688813.comp59066_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 9.4K Nov 8 07:45 scaffold_23.686019-688975.comp59066_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:56 scaffold_23.686019-688975.comp59066_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:32 scaffold_23.686019-688975.comp59066_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 9.0K Nov 8 07:55 scaffold_23.686019-688975.comp59066_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 9.5K Nov 8 07:52 scaffold_23.686019-688975.comp59066_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:43 scaffold_23.686506-688813.comp59066_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686506-688813.comp59066_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:48 scaffold_23.686506-688813.comp59066_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:38 scaffold_23.686506-688813.comp59066_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:54 scaffold_23.686506-688813.comp59066_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 7.1K Nov 8 07:34 scaffold_23.686506-688813.comp59066_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 6.9K Nov 8 07:44 scaffold_23.686506-688813.comp59066_c0_seq135.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:35 scaffold_23.686506-688975.comp59066_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:51 scaffold_23.686506-688975.comp59066_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:43 scaffold_23.686506-688975.comp59066_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:38 scaffold_23.686506-688975.comp59066_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 7.6K Nov 8 07:51 scaffold_23.686591-688813.comp59066_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 7.5K Nov 8 07:37 scaffold_23.686591-688813.comp59066_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 07:44 scaffold_23.686591-688813.comp59066_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:32 scaffold_23.686591-688813.comp59066_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 7.0K Nov 8 07:41 scaffold_23.686591-688813.comp59066_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 7.9K Nov 8 07:54 scaffold_23.686591-688975.comp59066_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 7.8K Nov 8 07:39 scaffold_23.686591-688975.comp59066_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:56 scaffold_23.686591-688975.comp59066_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 7.7K Nov 8 07:40 scaffold_23.686591-688975.comp59066_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 7.3K Nov 8 07:46 scaffold_23.686591-688975.comp59066_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 7.2K Nov 8 07:45 scaffold_23.686591-688975.comp59066_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 6.3K Nov 8 07:49 scaffold_23.686979-688813.comp59066_c0_seq136.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 07:51 scaffold_23.686979-688813.comp59066_c0_seq139.est_exonerate -rw-r--r-- 1 dstandag biol 6.7K Nov 8 07:39 scaffold_23.686979-688975.comp59066_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 6.5K Nov 8 07:51 scaffold_23.686979-688975.comp59066_c0_seq137.est_exonerate -rw-r--r-- 1 dstandag biol 6.6K Nov 8 07:54 scaffold_23.686979-688975.comp59066_c0_seq138.est_exonerate -rw-r--r-- 1 dstandag biol 1.5K Nov 8 07:56 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scaffold_23.690234-691062.comp58228_c7_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 2.0K Nov 8 06:49 scaffold_23.69062-69744.comp433_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.7K Nov 8 08:03 scaffold_23.692420-694948.comp51249_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 08:03 scaffold_23.694556-695181.comp839860_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:03 scaffold_23.694811-708737.comp58143_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 scaffold_23.695279-710945.gnl%7CAmel_4%2E5%7CGB49172-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072421.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0072422.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0290562.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304412.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304413.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.695297-710945.gnl%7CDmel_r5%2E47%7CFBpp0304414.p_exonerate -rw-r--r-- 1 dstandag biol 6.4K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 5.5K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 3.1K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 6.2K Nov 8 08:03 scaffold_23.695822-699690.comp59447_c1_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 6.1K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 5.4K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 5.6K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 3.5K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 5.7K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 5.9K Nov 8 08:03 scaffold_23.695863-699690.comp59447_c1_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 2.3K Nov 8 08:03 scaffold_23.696083-696661.comp59447_c1_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 2.7K Nov 8 08:03 scaffold_23.696083-696714.comp59447_c1_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 2.6K Nov 8 08:03 scaffold_23.696083-696748.comp59447_c1_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 08:03 scaffold_23.696083-696759.comp59447_c1_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 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dstandag biol 957K Nov 8 08:01 scaffold_23.6.Amel3%2E2_Dmel5%2E47%2Efaa.blastx -rw-r--r-- 1 dstandag biol 30K Nov 8 06:23 scaffold_23.6.drosophila.rb.out -rw-r--r-- 1 dstandag biol 4.8M Nov 8 12:05 scaffold_23.6.final.section -rw-r--r-- 1 dstandag biol 2.7M Nov 8 07:25 scaffold_23.6.Pdom%2ETrinity%2ETrimmomatic%2Efasta.blastn -rw-r--r-- 1 dstandag biol 1.2M Nov 8 07:59 scaffold_23.6.Pmet%2ETrinity%2ER%2Efasta.tblastx -rw-r--r-- 1 dstandag biol 5.5M Nov 8 08:02 scaffold_23.6.raw.section -rw-r--r-- 1 dstandag biol 562K Nov 8 06:24 scaffold_23.6.te_proteins%2Efasta.repeatrunner -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.70076-70676.comp16610_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0089425.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0290563.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:02 scaffold_23.701849-710945.gnl%7CDmel_r5%2E47%7CFBpp0304411.p_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 06:49 scaffold_23.70266-70881.comp1005591_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.8K Nov 8 08:03 scaffold_23.708515-711952.comp58143_c1_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 3.3K Nov 8 06:49 scaffold_23.71180-72221.comp36225_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 8.4K Nov 8 08:03 scaffold_23.712095-715429.comp54313_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 5.8K Nov 8 11:03 scaffold_23.712367-714691.gnl%7CAmel_4%2E5%7CGB49161-PA.p_exonerate -rw-r--r-- 1 dstandag biol 3.4K Nov 8 08:03 scaffold_23.712520-713560.comp54814_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 4.2K Nov 8 08:03 scaffold_23.712520-713766.comp54814_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.0K Nov 8 08:03 scaffold_23.712609-713560.comp54814_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 3.8K Nov 8 08:03 scaffold_23.712609-713766.comp54814_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:50 scaffold_23.716125-720215.comp58983_c0_seq107.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:04 scaffold_23.716125-720215.comp58983_c0_seq108.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq109.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:47 scaffold_23.716125-720215.comp58983_c0_seq110.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq126.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:46 scaffold_23.716125-720215.comp58983_c0_seq127.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720215.comp58983_c0_seq128.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720215.comp58983_c0_seq129.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:45 scaffold_23.716125-720215.comp58983_c0_seq130.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 10:51 scaffold_23.716125-720215.comp58983_c0_seq131.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720215.comp58983_c0_seq132.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:03 scaffold_23.716125-720215.comp58983_c0_seq133.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 08:06 scaffold_23.716125-720215.comp58983_c0_seq134.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:53 scaffold_23.716125-720628.comp58983_c0_seq100.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:03 scaffold_23.716125-720628.comp58983_c0_seq102.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-720628.comp58983_c0_seq103.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:48 scaffold_23.716125-720628.comp58983_c0_seq118.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 10:51 scaffold_23.716125-720628.comp58983_c0_seq119.est_exonerate -rw-r--r-- 1 dstandag biol 14K Nov 8 08:06 scaffold_23.716125-720628.comp58983_c0_seq120.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:07 scaffold_23.716125-720628.comp58983_c0_seq121.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:49 scaffold_23.716125-720628.comp58983_c0_seq122.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:52 scaffold_23.716125-720628.comp58983_c0_seq123.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:50 scaffold_23.716125-720628.comp58983_c0_seq124.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 08:05 scaffold_23.716125-720628.comp58983_c0_seq125.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721166.comp58983_c0_seq111.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq112.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:07 scaffold_23.716125-721166.comp58983_c0_seq113.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq114.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 10:45 scaffold_23.716125-721166.comp58983_c0_seq115.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:03 scaffold_23.716125-721166.comp58983_c0_seq116.est_exonerate -rw-r--r-- 1 dstandag biol 15K Nov 8 08:05 scaffold_23.716125-721166.comp58983_c0_seq117.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq83.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-721166.comp58983_c0_seq84.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:51 scaffold_23.716125-721166.comp58983_c0_seq85.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-721166.comp58983_c0_seq92.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 08:08 scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:46 scaffold_23.716125-721460.comp58983_c0_seq104.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:47 scaffold_23.716125-721460.comp58983_c0_seq105.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq106.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:45 scaffold_23.716125-721460.comp58983_c0_seq72.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:53 scaffold_23.716125-721460.comp58983_c0_seq73.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-721460.comp58983_c0_seq74.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:48 scaffold_23.716125-721460.comp58983_c0_seq75.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:49 scaffold_23.716125-721460.comp58983_c0_seq79.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:44 scaffold_23.716125-721460.comp58983_c0_seq82.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:52 scaffold_23.716125-721460.comp58983_c0_seq86.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq66.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-721720.comp58983_c0_seq68.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:46 scaffold_23.716125-721720.comp58983_c0_seq69.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 08:03 scaffold_23.716125-721720.comp58983_c0_seq70.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:45 scaffold_23.716125-721720.comp58983_c0_seq93.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 08:06 scaffold_23.716125-721720.comp58983_c0_seq94.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:48 scaffold_23.716125-721720.comp58983_c0_seq95.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:47 scaffold_23.716125-721720.comp58983_c0_seq96.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:53 scaffold_23.716125-721720.comp58983_c0_seq97.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq98.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:51 scaffold_23.716125-721720.comp58983_c0_seq99.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq58.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:45 scaffold_23.716125-722098.comp58983_c0_seq59.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:48 scaffold_23.716125-722098.comp58983_c0_seq60.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:53 scaffold_23.716125-722098.comp58983_c0_seq61.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:50 scaffold_23.716125-722098.comp58983_c0_seq62.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq63.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:04 scaffold_23.716125-722098.comp58983_c0_seq87.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:05 scaffold_23.716125-722098.comp58983_c0_seq88.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 08:06 scaffold_23.716125-722098.comp58983_c0_seq89.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:47 scaffold_23.716125-722098.comp58983_c0_seq90.est_exonerate -rw-r--r-- 1 dstandag biol 18K Nov 8 10:49 scaffold_23.716125-722098.comp58983_c0_seq91.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:46 scaffold_23.716125-722428.comp58983_c0_seq45.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:08 scaffold_23.716125-722428.comp58983_c0_seq46.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:49 scaffold_23.716125-722428.comp58983_c0_seq47.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:53 scaffold_23.716125-722428.comp58983_c0_seq48.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:06 scaffold_23.716125-722428.comp58983_c0_seq49.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:05 scaffold_23.716125-722428.comp58983_c0_seq50.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:47 scaffold_23.716125-722428.comp58983_c0_seq76.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:52 scaffold_23.716125-722428.comp58983_c0_seq77.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq78.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722428.comp58983_c0_seq80.est_exonerate -rw-r--r-- 1 dstandag biol 19K Nov 8 08:04 scaffold_23.716125-722428.comp58983_c0_seq81.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq38.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:50 scaffold_23.716125-722757.comp58983_c0_seq39.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:05 scaffold_23.716125-722757.comp58983_c0_seq40.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:52 scaffold_23.716125-722757.comp58983_c0_seq41.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq42.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq43.est_exonerate -rw-r--r-- 1 dstandag biol 23K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq44.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:06 scaffold_23.716125-722757.comp58983_c0_seq64.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 08:04 scaffold_23.716125-722757.comp58983_c0_seq65.est_exonerate -rw-r--r-- 1 dstandag biol 20K Nov 8 10:51 scaffold_23.716125-722757.comp58983_c0_seq67.est_exonerate -rw-r--r-- 1 dstandag biol 21K Nov 8 10:46 scaffold_23.716125-722757.comp58983_c0_seq71.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:47 scaffold_23.716125-723330.comp58983_c0_seq34.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:05 scaffold_23.716125-723330.comp58983_c0_seq35.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 08:04 scaffold_23.716125-723330.comp58983_c0_seq36.est_exonerate -rw-r--r-- 1 dstandag biol 25K Nov 8 10:44 scaffold_23.716125-723330.comp58983_c0_seq37.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq51.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:51 scaffold_23.716125-723330.comp58983_c0_seq52.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:48 scaffold_23.716125-723330.comp58983_c0_seq53.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq54.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:50 scaffold_23.716125-723330.comp58983_c0_seq55.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 08:07 scaffold_23.716125-723330.comp58983_c0_seq56.est_exonerate -rw-r--r-- 1 dstandag biol 22K Nov 8 10:45 scaffold_23.716125-723330.comp58983_c0_seq57.est_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 10:47 scaffold_23.716125-725421.comp58983_c0_seq23.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq24.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq25.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 10:48 scaffold_23.716125-725421.comp58983_c0_seq26.est_exonerate -rw-r--r-- 1 dstandag biol 31K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq27.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:46 scaffold_23.716125-725421.comp58983_c0_seq28.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:05 scaffold_23.716125-725421.comp58983_c0_seq29.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:04 scaffold_23.716125-725421.comp58983_c0_seq30.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:45 scaffold_23.716125-725421.comp58983_c0_seq31.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 08:07 scaffold_23.716125-725421.comp58983_c0_seq32.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 10:49 scaffold_23.716125-725421.comp58983_c0_seq33.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq10.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:49 scaffold_23.716125-728040.comp58983_c0_seq11.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq12.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq13.est_exonerate -rw-r--r-- 1 dstandag biol 37K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq14.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq15.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:46 scaffold_23.716125-728040.comp58983_c0_seq16.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq17.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:50 scaffold_23.716125-728040.comp58983_c0_seq18.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq19.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 08:05 scaffold_23.716125-728040.comp58983_c0_seq20.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:51 scaffold_23.716125-728040.comp58983_c0_seq21.est_exonerate -rw-r--r-- 1 dstandag biol 35K Nov 8 10:52 scaffold_23.716125-728040.comp58983_c0_seq22.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:48 scaffold_23.716125-728040.comp58983_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:53 scaffold_23.716125-728040.comp58983_c0_seq4.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:47 scaffold_23.716125-728040.comp58983_c0_seq5.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 10:45 scaffold_23.716125-728040.comp58983_c0_seq6.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:07 scaffold_23.716125-728040.comp58983_c0_seq7.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:06 scaffold_23.716125-728040.comp58983_c0_seq8.est_exonerate -rw-r--r-- 1 dstandag biol 38K Nov 8 08:04 scaffold_23.716125-728040.comp58983_c0_seq9.est_exonerate -rw-r--r-- 1 dstandag biol 29K Nov 8 06:55 scaffold_23.7171-17933.gnl%7CAmel_4%2E5%7CGB46618-PA.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070125.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070126.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070127.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0070128.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291468.p_exonerate -rw-r--r-- 1 dstandag biol 32K Nov 8 11:03 scaffold_23.717214-728034.gnl%7CDmel_r5%2E47%7CFBpp0291469.p_exonerate -rw-r--r-- 1 dstandag biol 40K Nov 8 11:03 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dstandag biol 3.2K Nov 8 10:53 scaffold_23.728443-729727.comp45774_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.729783-730395.comp2904457_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 10:53 scaffold_23.730057-730704.comp1503238_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.9K Nov 8 06:49 scaffold_23.73016-73676.comp16138_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 scaffold_23.731277-731906.comp1893859_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 10:53 scaffold_23.733065-733673.comp3350191_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.7K Nov 8 06:49 scaffold_23.73345-73945.comp16138_c1_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 3.6K Nov 8 10:53 scaffold_23.734599-735763.comp1287295_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.9K Nov 8 06:49 scaffold_23.73525-74446.comp9823_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 1.8K Nov 8 10:53 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-rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0290962.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303730.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.748242-767804.gnl%7CDmel_r5%2E47%7CFBpp0303731.p_exonerate -rw-r--r-- 1 dstandag biol 11K Nov 8 11:03 scaffold_23.748248-752313.gnl%7CAmel_4%2E5%7CGB49163-PA.p_exonerate -rw-r--r-- 1 dstandag biol 2.2K Nov 8 06:49 scaffold_23.75148-75896.comp276986_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 17K Nov 8 10:56 scaffold_23.751890-761021.comp49210_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 16K Nov 8 10:55 scaffold_23.751890-761021.comp49210_c0_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 13K Nov 8 10:54 scaffold_23.751890-761021.comp49210_c0_seq3.est_exonerate -rw-r--r-- 1 dstandag biol 12K Nov 8 11:03 scaffold_23.752357-755378.gnl%7CAmel_4%2E5%7CGB49169-PA.p_exonerate -rw-r--r-- 1 dstandag biol 4.7K 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11:03 scaffold_23.772644-773319.gnl%7CDmel_r5%2E47%7CFBpp0075479.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773322.gnl%7CAmel_4%2E5%7CGB48430-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773325.gnl%7CDmel_r5%2E47%7CFBpp0077688.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772644-773328.gnl%7CDmel_r5%2E47%7CFBpp0071844.p_exonerate -rw-r--r-- 1 dstandag biol 572 Nov 8 11:03 scaffold_23.772644-773349.gnl%7CAmel_4%2E5%7CGB40139-PA.p_exonerate -rw-r--r-- 1 dstandag biol 575 Nov 8 11:03 scaffold_23.772647-773280.gnl%7CDmel_r5%2E47%7CFBpp0072463.p_exonerate -rw-r--r-- 1 dstandag biol 8.6K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 7.4K Nov 8 10:57 scaffold_23.774192-776945.comp56485_c2_seq2.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 06:49 scaffold_23.77438-78155.comp13284_c0_seq1.est_exonerate -rw-r--r-- 1 dstandag biol 2.1K Nov 8 10:57 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Name: scaffold_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0 Type: application/octet-stream Size: 4812 bytes Desc: not available URL: From parulk at caltech.edu Tue Nov 27 15:39:18 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:39:18 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Hello Carson, Just to confirm, Is there a script that would filter gene models at specific AED score. Alternatively if I were to do this within maker with regards to parameters in maker_opts.ctl file I would have to provide my predicted genes gff3 file to model_gff and set AED_threshold at desired threshold? Thanks and regards, Parul Kudtarkar > AED score with 1 are the ones you don't want. 0 is best and 1 is worst as > it is a distance metric. You can use the AED_threshold parameter to > require better matching to the evidence by setting it closer to 0. You can > also try to increase protein homology evidence as some of your calls may > be split genes due to lack of evidence linking them. > > --Carson > > > On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: > >>Dear Maker community, >> >>For gene-prediction I get training data-set from evidence based >>prediction, I use this data-set to train SNAP as well as Augustus >>predictions, followed by boot-strapping. I would typically expect 20-30K >>genes however I am getting 8 times the expected gene count indicating too >>many false positives. Is there a way to further refine these >>predication/script to retain predictions with AED score 1 and if yes how >>to go about this? >> >>Thanks and regards, >>Parul Kudtarkar >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From parulk at caltech.edu Tue Nov 27 15:41:12 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:41:12 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu> Message-ID: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From dence at genetics.utah.edu Tue Nov 27 15:55:49 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Tue, 27 Nov 2012 22:55:49 +0000 Subject: [maker-devel] AED score In-Reply-To: <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: Hi Parul, I think the way you described (with the maker_opts.ctl file) is how you want to proceed. You still need to give the genome too. Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] Sent: Tuesday, November 27, 2012 3:41 PM To: Parul Kudtarkar Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] AED score Also, are there any other parameters that are required when filtering based on AED score? > Hello Carson, > > Just to confirm, Is there a script that would filter gene models at > specific AED score. > Alternatively if I were to do this within maker with regards to parameters > in maker_opts.ctl file I would have to provide my predicted genes gff3 > file to model_gff and set AED_threshold at desired threshold? > > Thanks and regards, > Parul Kudtarkar > >> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >> as >> it is a distance metric. You can use the AED_threshold parameter to >> require better matching to the evidence by setting it closer to 0. You >> can >> also try to increase protein homology evidence as some of your calls may >> be split genes due to lack of evidence linking them. >> >> --Carson >> >> >> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >> >>>Dear Maker community, >>> >>>For gene-prediction I get training data-set from evidence based >>>prediction, I use this data-set to train SNAP as well as Augustus >>>predictions, followed by boot-strapping. I would typically expect 20-30K >>>genes however I am getting 8 times the expected gene count indicating >>> too >>>many false positives. Is there a way to further refine these >>>predication/script to retain predictions with AED score 1 and if yes how >>>to go about this? >>> >>>Thanks and regards, >>>Parul Kudtarkar >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Tue Nov 27 15:59:22 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Tue, 27 Nov 2012 14:59:22 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: <3578.131.215.15.234.1354055958.squirrel@webmail.caltech.edu>, <3595.131.215.15.234.1354056072.squirrel@webmail.caltech.edu> Message-ID: <3841.131.215.15.234.1354057162.squirrel@webmail.caltech.edu> Thanks for quick response Daniel, I'll do it through maker. > Hi Parul, > > I think the way you described (with the maker_opts.ctl file) is how you > want to proceed. You still need to give the genome too. > > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar > [parulk at caltech.edu] > Sent: Tuesday, November 27, 2012 3:41 PM > To: Parul Kudtarkar > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] AED score > > Also, are there any other parameters that are required when filtering > based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >> parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>> may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>> 20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>> how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > > -- > Scientific Programmer > Center for Computational Regulatory Genomics > Beckman Institute, > California Institute of Technology > http://www.spbase.org > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From kapeelc at gmail.com Tue Nov 27 18:23:12 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Tue, 27 Nov 2012 18:23:12 -0700 Subject: [maker-devel] Maker error message Message-ID: Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: From dence at genetics.utah.edu Tue Nov 27 18:38:33 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 01:38:33 +0000 Subject: [maker-devel] Maker error message In-Reply-To: References: Message-ID: Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Nov 27 20:39:56 2012 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 27 Nov 2012 22:39:56 -0500 Subject: [maker-devel] AED score In-Reply-To: Message-ID: Use the AED_threshold option in the maker_opts.ctl file if you just want to restrict final gene models to close matches directly within maker. On the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset for SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. Thanks, Carson On 12-11-27 5:55 PM, "Daniel Ence" wrote: >Hi Parul, > >I think the way you described (with the maker_opts.ctl file) is how you >want to proceed. You still need to give the genome too. > >Daniel > > >Daniel Ence >Graduate Student >Eccles Institute of Human Genetics >University of Utah >15 North 2030 East, Room 2100 >Salt Lake City, UT 84112-5330 >________________________________________ >From: maker-devel-bounces at yandell-lab.org >[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >Sent: Tuesday, November 27, 2012 3:41 PM >To: Parul Kudtarkar >Cc: maker-devel at yandell-lab.org >Subject: Re: [maker-devel] AED score > >Also, are there any other parameters that are required when filtering >based on AED score? > >> Hello Carson, >> >> Just to confirm, Is there a script that would filter gene models at >> specific AED score. >> Alternatively if I were to do this within maker with regards to >>parameters >> in maker_opts.ctl file I would have to provide my predicted genes gff3 >> file to model_gff and set AED_threshold at desired threshold? >> >> Thanks and regards, >> Parul Kudtarkar >> >>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>> as >>> it is a distance metric. You can use the AED_threshold parameter to >>> require better matching to the evidence by setting it closer to 0. You >>> can >>> also try to increase protein homology evidence as some of your calls >>>may >>> be split genes due to lack of evidence linking them. >>> >>> --Carson >>> >>> >>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>> >>>>Dear Maker community, >>>> >>>>For gene-prediction I get training data-set from evidence based >>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>predictions, followed by boot-strapping. I would typically expect >>>>20-30K >>>>genes however I am getting 8 times the expected gene count indicating >>>> too >>>>many false positives. Is there a way to further refine these >>>>predication/script to retain predictions with AED score 1 and if yes >>>>how >>>>to go about this? >>>> >>>>Thanks and regards, >>>>Parul Kudtarkar >>>> >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>> >>>> >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>> >>> >> >> >> -- >> Scientific Programmer >> Center for Computational Regulatory Genomics >> Beckman Institute, >> California Institute of Technology >> http://www.spbase.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From dence at genetics.utah.edu Wed Nov 28 12:25:22 2012 From: dence at genetics.utah.edu (Daniel Ence) Date: Wed, 28 Nov 2012 19:25:22 +0000 Subject: [maker-devel] Maker error message In-Reply-To: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Hi Kapeel,? Please keep this discussion on the maker-devel group, so we can get everyone's input to help resolve this issue with maker.? Can you sen me the maker_opts file that you were using? The options that might be relevant include the libraries you were giving repeatrunner and repeatmasker. Thanks, Daniel? Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________________ From: kapeelc at gmail.com [kapeelc at gmail.com] Sent: Wednesday, November 28, 2012 11:39 AM To: Daniel Ence Subject: Re: Maker error message Hi Daniel, Here is the output around the error: j_size:94 current j:76 j_size:94 current j:77 j_size:94 current j:78 j_size:94 current j:79 j_size:94 current j:80 j_size:94 current j:81 j_size:94 current j:82 j_size:94 current j:83 j_size:94 current j:84 j_size:94 current j:85 j_size:94 current j:86 j_size:94 current j:87 j_size:94 current j:88 j_size:94 current j:89 j_size:94 current j:90 j_size:94 current j:91 j_size:94 current j:92 j_size:94 current j:93 ...finished clustering. re reading repeat masker report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out re reading blast report. /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner deleted:1 hits in cluster::shadow_cluster... DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 --Next Contig-- Processing run.log file... Maker is now finished!!! For RepeatMasker I am using wublast as the search engine. The run log had this: LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 LOGCHILD /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 DIED RANK 0 DIED COUNT 2 Is there way to skip the the failed chunk and move forward?? Thanks Kapeel Hi Kapeel, I think we need some more information about the settings that you're running maker with. Can you give more of the output around the error? Also, since maker is dying during the repeatmasking stage, can you tell us more about the settings you have for RepeatMasker? Thanks, Daniel Daniel Ence Graduate Student Eccles Institute of Human Genetics University of Utah 15 North 2030 East, Room 2100 Salt Lake City, UT 84112-5330 ________________________________ From: maker-devel-bounces at yandell-lab.org [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule [kapeelc at gmail.com] Sent: Tuesday, November 27, 2012 6:23 PM To: maker-devel at yandell-lab.org Subject: [maker-devel] Maker error message Hi, I recently ran into this error for chr5. I am using maker 2.26 . DiedERROR: Failed while processing all repeats ERROR: Chunk failed at level:3, tier_type:1 FAILED CONTIG:Chr5 ERROR: Chunk failed at level:2, tier_type:0 FAILED CONTIG:Chr5 Could someone help me understand this error and why its happening? Thanks, -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org Quoted from: http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html From kapeelc at gmail.com Wed Nov 28 13:15:13 2012 From: kapeelc at gmail.com (Kapeel Chougule) Date: Wed, 28 Nov 2012 13:15:13 -0700 Subject: [maker-devel] Maker error message In-Reply-To: References: <22771585.26421.1354127950084.JavaMail.nabble@ben.nabble.com> Message-ID: Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get > everyone's input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that > might be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific.out > re reading blast report. > > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're > running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html > -- * Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu * -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4831 bytes Desc: not available URL: From carsonhh at gmail.com Thu Nov 29 07:22:42 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:22:42 -0500 Subject: [maker-devel] AED score In-Reply-To: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Message-ID: There are certain characteristics that are apparent in this contig. First it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many of them to align spuriously which produces very short gene models that are more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial bias to get back very short and incomplete models. How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as well as get an estimate of fragmentation as one of the statistics produced is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), and if they are distantly related to other annotated species few proteins may align to the contigs because the introns in the alignments tend to be so long and exons so short that it pushes down the significance scores too much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. Thanks, Carson On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >Dear Carson and Daniel, > >Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 >genes with AED score less than 0.75. However there were no genes predicted >in the output file(see attached file Scaffold1_out). I have also attached >the maker_opts.ctl. Could you please advice on this. > >Thanks and regards, >Parul Kudtarkar > >> Use the AED_threshold option in the maker_opts.ctl file if you just want >> to restrict final gene models to close matches directly within maker. >>On >> the other hand, if you are trying to build a dataset for training gene >> predictors, use the maker2zff script for generating a filtered dataset >>for >> SNAP training. There are a number of filters available. Just call the >> script once without parameters to see the options. >> >> Thanks, >> Carson >> >> >> >> >> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >> >>>Hi Parul, >>> >>>I think the way you described (with the maker_opts.ctl file) is how you >>>want to proceed. You still need to give the genome too. >>> >>>Daniel >>> >>> >>>Daniel Ence >>>Graduate Student >>>Eccles Institute of Human Genetics >>>University of Utah >>>15 North 2030 East, Room 2100 >>>Salt Lake City, UT 84112-5330 >>>________________________________________ >>>From: maker-devel-bounces at yandell-lab.org >>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>>[parulk at caltech.edu] >>>Sent: Tuesday, November 27, 2012 3:41 PM >>>To: Parul Kudtarkar >>>Cc: maker-devel at yandell-lab.org >>>Subject: Re: [maker-devel] AED score >>> >>>Also, are there any other parameters that are required when filtering >>>based on AED score? >>> >>>> Hello Carson, >>>> >>>> Just to confirm, Is there a script that would filter gene models at >>>> specific AED score. >>>> Alternatively if I were to do this within maker with regards to >>>>parameters >>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>> file to model_gff and set AED_threshold at desired threshold? >>>> >>>> Thanks and regards, >>>> Parul Kudtarkar >>>> >>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>>> worst >>>>> as >>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>> require better matching to the evidence by setting it closer to 0. >>>>>You >>>>> can >>>>> also try to increase protein homology evidence as some of your calls >>>>>may >>>>> be split genes due to lack of evidence linking them. >>>>> >>>>> --Carson >>>>> >>>>> >>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>> >>>>>>Dear Maker community, >>>>>> >>>>>>For gene-prediction I get training data-set from evidence based >>>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>>predictions, followed by boot-strapping. I would typically expect >>>>>>20-30K >>>>>>genes however I am getting 8 times the expected gene count indicating >>>>>> too >>>>>>many false positives. Is there a way to further refine these >>>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>>how >>>>>>to go about this? >>>>>> >>>>>>Thanks and regards, >>>>>>Parul Kudtarkar >>>>>> >>>>>>-- >>>>>>Scientific Programmer >>>>>>Center for Computational Regulatory Genomics >>>>>>Beckman Institute, >>>>>>California Institute of Technology >>>>>>http://www.spbase.org >>>>>> >>>>>> >>>>>>_______________________________________________ >>>>>>maker-devel mailing list >>>>>>maker-devel at box290.bluehost.com >>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o >>>>>>rg >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scientific Programmer >>>> Center for Computational Regulatory Genomics >>>> Beckman Institute, >>>> California Institute of Technology >>>> http://www.spbase.org >>>> >>> >>> >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >>> >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> >>>_______________________________________________ >>>maker-devel mailing list >>>maker-devel at box290.bluehost.com >>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >> >> >> _______________________________________________ >> maker-devel mailing list >> maker-devel at box290.bluehost.com >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 07:52:25 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 09:52:25 -0500 Subject: [maker-devel] Maker error message In-Reply-To: Message-ID: There should normally be more error message than that. The module used to capture the error returns the string "Died" without an end line character when there is a problem capturing the STDERR of the failure (and I see that phrase here), so could you run this again and see if it produces a different message the second time. Also I'm going to send you instructions on download the development version of MAKER in a separate message (off list). It is easier for me to make changes and have you test them immediately that way. Also there are already some bug fixes in the devel version so it's good to rule those out. Thanks, Carson From: Kapeel Chougule Date: Wednesday, 28 November, 2012 3:15 PM To: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Maker error message Attached is the maker_opts file. I am using my own customized repeat library and repeat_protein files. The length of the identifiers was shortened to < 50 characters as in my previous run it complained for identifiers having > 50 characters. Thank you, Kapeel On Wed, Nov 28, 2012 at 12:25 PM, Daniel Ence wrote: > Hi Kapeel, > > Please keep this discussion on the maker-devel group, so we can get everyone's > input to help resolve this issue with maker. > > Can you sen me the maker_opts file that you were using? The options that might > be relevant include the libraries you were giving repeatrunner and > repeatmasker. > > Thanks, > Daniel > > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________________ > From: kapeelc at gmail.com [kapeelc at gmail.com] > Sent: Wednesday, November 28, 2012 11:39 AM > To: Daniel Ence > Subject: Re: Maker error message > > Hi Daniel, > > Here is the output around the error: > > j_size:94 current j:76 > j_size:94 current j:77 > j_size:94 current j:78 > j_size:94 current j:79 > j_size:94 current j:80 > j_size:94 current j:81 > j_size:94 current j:82 > j_size:94 current j:83 > j_size:94 current j:84 > j_size:94 current j:85 > j_size:94 current j:86 > j_size:94 current j:87 > j_size:94 current j:88 > j_size:94 current j:89 > j_size:94 current j:90 > j_size:94 current j:91 > j_size:94 current j:92 > j_size:94 current j:93 > ...finished clustering. > re reading repeat masker report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.PReDa_121015_short%2Efasta.specific > .out > re reading blast report. > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/Chr5.64.TE_protein_db_121015_short_header%2 > Efasta.repeatrunner > deleted:1 hits > in cluster::shadow_cluster... > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > > > > --Next Contig-- > > Processing run.log file... > > Maker is now finished!!! > > > For RepeatMasker I am using wublast as the search engine. > > The run log had this: > > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.62 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.63 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > LOGCHILD > /opt/Sma_Processing/Kapeel/japonica_maker_run/jap_chr5/Chr5.maker.output/Chr5_ > datastore/8A/9B/Chr5//theVoid.Chr5/run.log.child.64 > DIED RANK 0 > DIED COUNT 2 > > Is there way to skip the the failed chunk and move forward?? > > Thanks > > Kapeel > > > Hi Kapeel, > > I think we need some more information about the settings that you're running > maker with. Can you give more of the output around the error? Also, since > maker is dying during the repeatmasking stage, can you tell us more about > the settings you have for RepeatMasker? > > > > Thanks, > Daniel > > Daniel Ence > Graduate Student > Eccles Institute of Human Genetics > University of Utah > 15 North 2030 East, Room 2100 > Salt Lake City, UT 84112-5330 > ________________________________ > From: maker-devel-bounces at yandell-lab.org > [maker-devel-bounces at yandell-lab.org] on behalf of Kapeel Chougule > [kapeelc at gmail.com] > Sent: Tuesday, November 27, 2012 6:23 PM > To: maker-devel at yandell-lab.org > Subject: [maker-devel] Maker error message > > Hi, > > I recently ran into this error for chr5. I am using maker 2.26 . > > DiedERROR: Failed while processing all repeats > ERROR: Chunk failed at level:3, tier_type:1 > FAILED CONTIG:Chr5 > > ERROR: Chunk failed at level:2, tier_type:0 > FAILED CONTIG:Chr5 > > Could someone help me understand this error and why its happening? > > Thanks, > > -- > > Kapeel Chougule > Systems Programmer > Arizona Genomics Institute (AGI) > Thomas W. Keating Bioresearch Building > University of Arizona > 1657 E. Helen Street > Tucson, AZ 85719 > www.genome.arizona.edu > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > Quoted from: > http://gmod.827538.n3.nabble.com/Maker-error-message-tp4027051p4027052.html -- Kapeel Chougule Systems Programmer Arizona Genomics Institute (AGI) Thomas W. Keating Bioresearch Building University of Arizona 1657 E. Helen Street Tucson, AZ 85719 www.genome.arizona.edu _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From parulk at caltech.edu Wed Nov 28 14:40:51 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Wed, 28 Nov 2012 13:40:51 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1233.131.215.15.234.1354138851.squirrel@webmail.caltech.edu> Dear Carson and Daniel, Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least 5 genes with AED score less than 0.75. However there were no genes predicted in the output file(see attached file Scaffold1_out). I have also attached the maker_opts.ctl. Could you please advice on this. Thanks and regards, Parul Kudtarkar > Use the AED_threshold option in the maker_opts.ctl file if you just want > to restrict final gene models to close matches directly within maker. On > the other hand, if you are trying to build a dataset for training gene > predictors, use the maker2zff script for generating a filtered dataset for > SNAP training. There are a number of filters available. Just call the > script once without parameters to see the options. > > Thanks, > Carson > > > > > On 12-11-27 5:55 PM, "Daniel Ence" wrote: > >>Hi Parul, >> >>I think the way you described (with the maker_opts.ctl file) is how you >>want to proceed. You still need to give the genome too. >> >>Daniel >> >> >>Daniel Ence >>Graduate Student >>Eccles Institute of Human Genetics >>University of Utah >>15 North 2030 East, Room 2100 >>Salt Lake City, UT 84112-5330 >>________________________________________ >>From: maker-devel-bounces at yandell-lab.org >>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >>[parulk at caltech.edu] >>Sent: Tuesday, November 27, 2012 3:41 PM >>To: Parul Kudtarkar >>Cc: maker-devel at yandell-lab.org >>Subject: Re: [maker-devel] AED score >> >>Also, are there any other parameters that are required when filtering >>based on AED score? >> >>> Hello Carson, >>> >>> Just to confirm, Is there a script that would filter gene models at >>> specific AED score. >>> Alternatively if I were to do this within maker with regards to >>>parameters >>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>> file to model_gff and set AED_threshold at desired threshold? >>> >>> Thanks and regards, >>> Parul Kudtarkar >>> >>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >>>> worst >>>> as >>>> it is a distance metric. You can use the AED_threshold parameter to >>>> require better matching to the evidence by setting it closer to 0. You >>>> can >>>> also try to increase protein homology evidence as some of your calls >>>>may >>>> be split genes due to lack of evidence linking them. >>>> >>>> --Carson >>>> >>>> >>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>> >>>>>Dear Maker community, >>>>> >>>>>For gene-prediction I get training data-set from evidence based >>>>>prediction, I use this data-set to train SNAP as well as Augustus >>>>>predictions, followed by boot-strapping. I would typically expect >>>>>20-30K >>>>>genes however I am getting 8 times the expected gene count indicating >>>>> too >>>>>many false positives. Is there a way to further refine these >>>>>predication/script to retain predictions with AED score 1 and if yes >>>>>how >>>>>to go about this? >>>>> >>>>>Thanks and regards, >>>>>Parul Kudtarkar >>>>> >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>> >>>>> >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>> >>>> >>>> >>> >>> >>> -- >>> Scientific Programmer >>> Center for Computational Regulatory Genomics >>> Beckman Institute, >>> California Institute of Technology >>> http://www.spbase.org >>> >> >> >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org >> >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >> >>_______________________________________________ >>maker-devel mailing list >>maker-devel at box290.bluehost.com >>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1.gff Type: application/octet-stream Size: 594162 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Scaffold1_out.gff Type: application/octet-stream Size: 371508 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: maker_opts.ctl Type: application/octet-stream Size: 4561 bytes Desc: not available URL: From mikael.durling at slu.se Thu Nov 29 09:20:10 2012 From: mikael.durling at slu.se (=?iso-8859-1?Q?Mikael_Brandstr=F6m_Durling?=) Date: Thu, 29 Nov 2012 16:20:10 +0000 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids Message-ID: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Hello all, I'm running Maker (2.26 / r956 from svn) with a previous run in the input as maker_gff. However, the maker mpi ranks quit stop one after another with the following error messages. prepare section files Gathering GFF3 input into hits - chunk:3 ERROR: Non-unique top level ID for While this is technically legal in GFF3, it usually indicates a poorly fomatted GFF3 file (perhaps you tried to merge two GFF3 files without accounting for unique IDs). MAKER will not handle these correctly. --> rank=4, hostname=my-mgrid2 ERROR: Failed while prepare section files ERROR: Chunk failed at level:12, tier_type:2 FAILED CONTIG:scf_89936 In the end no ranks are running, but maker doesn't quit. Checking the maker_gff input, I do find duplicated ids, as this sample: scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.082870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.082870 but not for the scaffold found in the error message above. Are those two errors unrelated? If I run maker without providing a maker_gff the run works fine. Any input on this issue would be appreciated as I would like the reannotation to work in order to carry forward human readable names. cheers, Mikael ------------------------------------- Mikael Brandstr?m Durling, PhD Assistant Professor Sveriges lantbruksuniversitet Swedish University of Agricultural Sciences Uppsala BioCenter Dept of Forest Mycology and Plant Pathology Box 7026, 75007 Uppsala Visiting address: Almas All? 5 Telefon: 018-671503 mikael.durling at slu.se, www.slu.se/mykopat From carsonhh at gmail.com Thu Nov 29 09:23:39 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 11:23:39 -0500 Subject: [maker-devel] Maker failing on reannotation due to duplicate toplevel ids In-Reply-To: <35FD181EEB48324AB043FDB803E7D1C6048060B3@exchange2-1> Message-ID: You can get the fixed version by doing svn update inside the maker directory. I will be changing the download version to 2.27 on yandell0lab.org, probably this weekend. Thanks, Carson On 12-11-29 11:20 AM, "Mikael Brandstr?m Durling" wrote: >Hello all, > >I'm running Maker (2.26 / r956 from svn) with a previous run in the input >as maker_gff. However, the maker mpi ranks quit stop one after another >with the following error messages. > >prepare section files >Gathering GFF3 input into hits - chunk:3 >ERROR: Non-unique top level ID for >While this is technically legal in GFF3, it usually >indicates a poorly fomatted GFF3 file (perhaps you >tried to merge two GFF3 files without accounting for >unique IDs). MAKER will not handle these correctly. > >--> rank=4, hostname=my-mgrid2 >ERROR: Failed while prepare section files >ERROR: Chunk failed at level:12, tier_type:2 >FAILED CONTIG:scf_89936 > >In the end no ranks are running, but maker doesn't quit. > >Checking the maker_gff input, I do find duplicated ids, as this sample: > >scf_89779 snap_masked match 3327927 3330228 82.61 + . ID=scf_89779:hit:158 >:33_0;Name=snap_masked-scf_89779-abinit-gene-33.92-mRNA-1 >scf_89779 est_gff:cufflinks expressed_sequence_match 3381415 3383015 113.0 >82870 + . ID=scf_89779:hit:158:33_0;Name=1:CR_CR_17.8567.1;score=113.08287 >0 > >but not for the scaffold found in the error message above. Are those two >errors unrelated? > >If I run maker without providing a maker_gff the run works fine. > >Any input on this issue would be appreciated as I would like the >reannotation to work in order to carry forward human readable names. > >cheers, >Mikael > > > > >------------------------------------- >Mikael Brandstr?m Durling, PhD >Assistant Professor > >Sveriges lantbruksuniversitet >Swedish University of Agricultural Sciences > >Uppsala BioCenter >Dept of Forest Mycology and Plant Pathology >Box 7026, 75007 Uppsala >Visiting address: Almas All? 5 >Telefon: 018-671503 >mikael.durling at slu.se, www.slu.se/mykopat > > > >_______________________________________________ >maker-devel mailing list >maker-devel at box290.bluehost.com >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From parulk at caltech.edu Thu Nov 29 17:31:40 2012 From: parulk at caltech.edu (Parul Kudtarkar) Date: Thu, 29 Nov 2012 16:31:40 -0800 (PST) Subject: [maker-devel] AED score In-Reply-To: References: Message-ID: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Thanks for the guidance Carson, total contig size is 330,611 with N50 of 39.17kb. I agree we have short ESTs. So this is the possible reason when filtering based on AED score 0.75 there are no gene models predicted despite the model_gff file has few genes with scores less than 0.75? Thanks and regards, Parul Kudtarkar > There are certain characteristics that are apparent in this contig. First > it seems to be repeat rich with a very low gene density. You also have very short ESTs, and because of the lengths you are probably getting many > of them to align spuriously which produces very short gene models that are > more than likely false positives or at the very least just a piece of a gene. I would turn off est2genome as a predictor for this reason unless you can get longer EST assemblies (i.e. From mRNAseq). Your protein alignments also seem to be few and far between. You probably need to add > more proteins from a couple of related species, and you might consider using protein2genome rather than est2genome as a predictor if you are still working to generate a training set. Also est2genome produced models > almost always have an AED score near 0 so mixing est2genome with the AED_threshold with such limited protein support does create an artificial > bias to get back very short and incomplete models. > > How many contigs do you have in total and what is the N50 value for the assembly? If you have a large number of very short contigs, you will get very inflated gene counts because you get genes split across contigs and many contigs tend t be subtle rearrangements of other contigs just assembled in a slightly different way (so you can get bits and pieces of the same genes just rearranged). This scenario is another confounding factor if using the est2genome predictor with short ESTs. I would recommend running CEGMA to get an estimate for the genome completeness as > well as get an estimate of fragmentation as one of the statistics produced > is a percent of genes that are found complete (end to end) vs those that are partial. CEGMA identifies house keeping genes that tend to be shorter > and less intron rich than other genes in the genome, so if CEGMA gives a high partial percentage and a low complete percentage, then this pattern can be expected to be even more exaggerated for other genes in the genome. > > If your genome is highly fragmented or proteins do not align well then there are other strategies. For example, some vertebrate genomes end up having extremely fragmented assemblies (on the order of 100,000 contigs), > and if they are distantly related to other annotated species few proteins > may align to the contigs because the introns in the alignments tend to be > so long and exons so short that it pushes down the significance scores too > much. In those cases heavy mRNAseq seems to be the best if not only way to get enough evidence to stitch gene models together. > > Thanks, > Carson > > > > On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: > >>Dear Carson and Daniel, >>Thanks. I ran sample file for filtering genes based on AED score. The input gff3 file was provided to option model_pred(see attached file Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >> 5 >>genes with AED score less than 0.75. However there were no genes >> predicted >>in the output file(see attached file Scaffold1_out). I have also attached >>the maker_opts.ctl. Could you please advice on this. >>Thanks and regards, >>Parul Kudtarkar >>> Use the AED_threshold option in the maker_opts.ctl file if you just want >>> to restrict final gene models to close matches directly within maker. >>>On >>> the other hand, if you are trying to build a dataset for training gene predictors, use the maker2zff script for generating a filtered dataset >>>for >>> SNAP training. There are a number of filters available. Just call the script once without parameters to see the options. >>> Thanks, >>> Carson >>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>Hi Parul, >>>>I think the way you described (with the maker_opts.ctl file) is how you >>>>want to proceed. You still need to give the genome too. >>>>Daniel >>>>Daniel Ence >>>>Graduate Student >>>>Eccles Institute of Human Genetics >>>>University of Utah >>>>15 North 2030 East, Room 2100 >>>>Salt Lake City, UT 84112-5330 >>>>________________________________________ >>>>From: maker-devel-bounces at yandell-lab.org >>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar [parulk at caltech.edu] >>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>To: Parul Kudtarkar >>>>Cc: maker-devel at yandell-lab.org >>>>Subject: Re: [maker-devel] AED score >>>>Also, are there any other parameters that are required when filtering based on AED score? >>>>> Hello Carson, >>>>> Just to confirm, Is there a script that would filter gene models at specific AED score. >>>>> Alternatively if I were to do this within maker with regards to >>>>>parameters >>>>> in maker_opts.ctl file I would have to provide my predicted genes gff3 >>>>> file to model_gff and set AED_threshold at desired threshold? Thanks and regards, >>>>> Parul Kudtarkar >>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is worst >>>>>> as >>>>>> it is a distance metric. You can use the AED_threshold parameter to >>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>You >>>>>> can >>>>>> also try to increase protein homology evidence as some of your calls >>>>>>may >>>>>> be split genes due to lack of evidence linking them. >>>>>> --Carson >>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>Dear Maker community, >>>>>>>For gene-prediction I get training data-set from evidence based prediction, I use this data-set to train SNAP as well as Augustus predictions, followed by boot-strapping. I would typically expect 20-30K >>>>>>>genes however I am getting 8 times the expected gene count >>>>>>> indicating >>>>>>> too >>>>>>>many false positives. Is there a way to further refine these predication/script to retain predictions with AED score 1 and if yes >>>>>>>how >>>>>>>to go about this? >>>>>>>Thanks and regards, >>>>>>>Parul Kudtarkar >>>>>>>-- >>>>>>>Scientific Programmer >>>>>>>Center for Computational Regulatory Genomics >>>>>>>Beckman Institute, >>>>>>>California Institute of Technology >>>>>>>http://www.spbase.org >>>>>>>_______________________________________________ >>>>>>>maker-devel mailing list >>>>>>>maker-devel at box290.bluehost.com >>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.o rg >>>>> -- >>>>> Scientific Programmer >>>>> Center for Computational Regulatory Genomics >>>>> Beckman Institute, >>>>> California Institute of Technology >>>>> http://www.spbase.org >>>>-- >>>>Scientific Programmer >>>>Center for Computational Regulatory Genomics >>>>Beckman Institute, >>>>California Institute of Technology >>>>http://www.spbase.org >>>>_______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org _______________________________________________ >>>>maker-devel mailing list >>>>maker-devel at box290.bluehost.com >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>> _______________________________________________ >>> maker-devel mailing list >>> maker-devel at box290.bluehost.com >>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>-- >>Scientific Programmer >>Center for Computational Regulatory Genomics >>Beckman Institute, >>California Institute of Technology >>http://www.spbase.org > > > -- Scientific Programmer Center for Computational Regulatory Genomics Beckman Institute, California Institute of Technology http://www.spbase.org From carsonhh at gmail.com Thu Nov 29 18:39:31 2012 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 29 Nov 2012 20:39:31 -0500 Subject: [maker-devel] AED score In-Reply-To: <1344.131.215.15.234.1354235500.squirrel@webmail.caltech.edu> Message-ID: Wow 330,000 is a lot. a large portion of genes are likely to be partial at best. You should seriously consider using mRNAseq to capture those by using maker's est_gff option to pass in results from cufflinks or trinity. Also I wouldn't even try to annotate contigs less than 10kb in size, just have maker skip them by setting the min_contig filter in the maker_opts.ctl file. Thanks, Carson On 12-11-29 7:31 PM, "Parul Kudtarkar" wrote: >Thanks for the guidance Carson, total contig size is 330,611 with N50 of >39.17kb. I agree we have short ESTs. So this is the possible reason when >filtering based on AED score 0.75 there are no gene models predicted >despite the model_gff file has few genes with scores less than 0.75? > >Thanks and regards, >Parul Kudtarkar > >> There are certain characteristics that are apparent in this contig. >First >> it seems to be repeat rich with a very low gene density. You also have >very short ESTs, and because of the lengths you are probably getting >many >> of them to align spuriously which produces very short gene models that >are >> more than likely false positives or at the very least just a piece of a >gene. I would turn off est2genome as a predictor for this reason unless >you can get longer EST assemblies (i.e. From mRNAseq). Your protein >alignments also seem to be few and far between. You probably need to >add >> more proteins from a couple of related species, and you might consider >using protein2genome rather than est2genome as a predictor if you are >still working to generate a training set. Also est2genome produced >models >> almost always have an AED score near 0 so mixing est2genome with the >AED_threshold with such limited protein support does create an >artificial >> bias to get back very short and incomplete models. >> >> How many contigs do you have in total and what is the N50 value for the >assembly? If you have a large number of very short contigs, you will get >very inflated gene counts because you get genes split across contigs and >many contigs tend t be subtle rearrangements of other contigs just >assembled in a slightly different way (so you can get bits and pieces of >the same genes just rearranged). This scenario is another confounding >factor if using the est2genome predictor with short ESTs. I would >recommend running CEGMA to get an estimate for the genome completeness >as >> well as get an estimate of fragmentation as one of the statistics >produced >> is a percent of genes that are found complete (end to end) vs those that >are partial. CEGMA identifies house keeping genes that tend to be >shorter >> and less intron rich than other genes in the genome, so if CEGMA gives a >high partial percentage and a low complete percentage, then this pattern >can be expected to be even more exaggerated for other genes in the >genome. >> >> If your genome is highly fragmented or proteins do not align well then >there are other strategies. For example, some vertebrate genomes end up >having extremely fragmented assemblies (on the order of 100,000 >contigs), >> and if they are distantly related to other annotated species few >proteins >> may align to the contigs because the introns in the alignments tend to >be >> so long and exons so short that it pushes down the significance scores >too >> much. In those cases heavy mRNAseq seems to be the best if not only way >to get enough evidence to stitch gene models together. >> >> Thanks, >> Carson >> >> >> >> On 12-11-28 4:40 PM, "Parul Kudtarkar" wrote: >> >>>Dear Carson and Daniel, >>>Thanks. I ran sample file for filtering genes based on AED score. The >input gff3 file was provided to option model_pred(see attached file >Scaffold1.gff), the cutoff AED score was set to 0.75. There are at least >>> 5 >>>genes with AED score less than 0.75. However there were no genes >>> predicted >>>in the output file(see attached file Scaffold1_out). I have also >attached >>>the maker_opts.ctl. Could you please advice on this. >>>Thanks and regards, >>>Parul Kudtarkar >>>> Use the AED_threshold option in the maker_opts.ctl file if you just >>>>want >>>> to restrict final gene models to close matches directly within maker. >>>>On >>>> the other hand, if you are trying to build a dataset for training gene >predictors, use the maker2zff script for generating a filtered dataset >>>>for >>>> SNAP training. There are a number of filters available. Just call the >script once without parameters to see the options. >>>> Thanks, >>>> Carson >>>> On 12-11-27 5:55 PM, "Daniel Ence" wrote: >>>>>Hi Parul, >>>>>I think the way you described (with the maker_opts.ctl file) is how >you >>>>>want to proceed. You still need to give the genome too. >>>>>Daniel >>>>>Daniel Ence >>>>>Graduate Student >>>>>Eccles Institute of Human Genetics >>>>>University of Utah >>>>>15 North 2030 East, Room 2100 >>>>>Salt Lake City, UT 84112-5330 >>>>>________________________________________ >>>>>From: maker-devel-bounces at yandell-lab.org >>>>>[maker-devel-bounces at yandell-lab.org] on behalf of Parul Kudtarkar >[parulk at caltech.edu] >>>>>Sent: Tuesday, November 27, 2012 3:41 PM >>>>>To: Parul Kudtarkar >>>>>Cc: maker-devel at yandell-lab.org >>>>>Subject: Re: [maker-devel] AED score >>>>>Also, are there any other parameters that are required when filtering >based on AED score? >>>>>> Hello Carson, >>>>>> Just to confirm, Is there a script that would filter gene models at >specific AED score. >>>>>> Alternatively if I were to do this within maker with regards to >>>>>>parameters >>>>>> in maker_opts.ctl file I would have to provide my predicted genes >>>>>>gff3 >>>>>> file to model_gff and set AED_threshold at desired threshold? >Thanks and regards, >>>>>> Parul Kudtarkar >>>>>>> AED score with 1 are the ones you don't want. 0 is best and 1 is >worst >>>>>>> as >>>>>>> it is a distance metric. You can use the AED_threshold parameter >to >>>>>>> require better matching to the evidence by setting it closer to 0. >>>>>>>You >>>>>>> can >>>>>>> also try to increase protein homology evidence as some of your >calls >>>>>>>may >>>>>>> be split genes due to lack of evidence linking them. >>>>>>> --Carson >>>>>>> On 12-11-26 4:35 PM, "Parul Kudtarkar" wrote: >>>>>>>>Dear Maker community, >>>>>>>>For gene-prediction I get training data-set from evidence based >prediction, I use this data-set to train SNAP as well as Augustus >predictions, followed by boot-strapping. I would typically expect >20-30K >>>>>>>>genes however I am getting 8 times the expected gene count >>>>>>>> indicating >>>>>>>> too >>>>>>>>many false positives. Is there a way to further refine these >predication/script to retain predictions with AED score 1 and if >yes >>>>>>>>how >>>>>>>>to go about this? >>>>>>>>Thanks and regards, >>>>>>>>Parul Kudtarkar >>>>>>>>-- >>>>>>>>Scientific Programmer >>>>>>>>Center for Computational Regulatory Genomics >>>>>>>>Beckman Institute, >>>>>>>>California Institute of Technology >>>>>>>>http://www.spbase.org >>>>>>>>_______________________________________________ >>>>>>>>maker-devel mailing list >>>>>>>>maker-devel at box290.bluehost.com >>>>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab >>>>>>>>.o >rg >>>>>> -- >>>>>> Scientific Programmer >>>>>> Center for Computational Regulatory Genomics >>>>>> Beckman Institute, >>>>>> California Institute of Technology >>>>>> http://www.spbase.org >>>>>-- >>>>>Scientific Programmer >>>>>Center for Computational Regulatory Genomics >>>>>Beckman Institute, >>>>>California Institute of Technology >>>>>http://www.spbase.org >>>>>_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >_______________________________________________ >>>>>maker-devel mailing list >>>>>maker-devel at box290.bluehost.com >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or >>>>>g >>>> _______________________________________________ >>>> maker-devel mailing list >>>> maker-devel at box290.bluehost.com >>>> >>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org >>>-- >>>Scientific Programmer >>>Center for Computational Regulatory Genomics >>>Beckman Institute, >>>California Institute of Technology >>>http://www.spbase.org >> >> >> > > >-- >Scientific Programmer >Center for Computational Regulatory Genomics >Beckman Institute, >California Institute of Technology >http://www.spbase.org > > > >