<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">The est2genome and protein2genome options are sufficient enough to get preliminary models to train a gene predictor. You can use then to train Augustus. Snap already has an HMM Oryza sativa you can probably use (look in Snap’s HMM folder).<div class=""><br class=""></div><div class="">Here is an old post that can help with Augustus training —> <a href="https://groups.google.com/forum/#!searchin/maker-devel/augustus$20train/maker-devel/7IdmQph98Js/agwL3J19b1QJ" class="">https://groups.google.com/forum/#!searchin/maker-devel/augustus$20train/maker-devel/7IdmQph98Js/agwL3J19b1QJ</a></div><div class=""><br class=""></div><div class="">Also look through the tutorial section on how to train gene predictors —> <a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors</a></div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Apr 14, 2015, at 5:36 AM, sangramjit basu <<a href="mailto:officialsjb@gmail.com" class="">officialsjb@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">I initially thought it would go for for gene prediction automatically but that was not the case (I realised after the run)..then I gave 1 for est2genome
and protein2genome in gene prediction section, is it sufficient ?? Because I would like augustus and snap prediction too...I got to give those options too, isn't it ??!! and I think we also have too train them first as Rice is not a model organism for any of them ???<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Apr 13, 2015 at 10:36 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class=""><div class="">Did you run with a gene predictor? Here is a quick tutorial guide on how to run MAKER and collect and view results at the end.</div><div class=""><br class=""></div><div class=""><a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Running_MAKER_with_example_data" target="_blank" class="">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Running_MAKER_with_example_data</a></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><br class=""><div class=""><blockquote type="cite" class=""><span class=""><div class="">On Apr 13, 2015, at 6:01 AM, sangramjit basu <<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>> wrote:</div><br class=""></span><div class=""><span class=""><div dir="ltr" class=""><div class="">hi,<br class=""></div>after the successful run I got the void folder, gff file and run.log ....is there any additional option to get the predicted protein fasta and transcript fasta file bcoz they weren't produced ??!!! and what does these mean : expressed_sequence_match, match_part, protein_match and translated_nucleotide_match ??? i mean which of them is to be considered "Genes" / "mRNA" and which one as "exons" ???<br class=""></div></span><div class="gmail_extra"><br class=""><div class="gmail_quote"><span class="">On Mon, Apr 13, 2015 at 10:15 AM, sangramjit basu <span dir="ltr" class=""><<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>></span> wrote:<br class=""></span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class="">Hello Carson,<br class="">I finally had a successful run on my rice data with MAKER...I extend my most sincere gratefulness for all the time you took out for me and all the help you gave...I am looking forward to a good-time MAKER-ing !!! <span class=""><330.gif></span><br class=""></div>-Sangram<br class=""></div><div class=""><div class="h5"><div class=""><div class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Sat, Apr 11, 2015 at 3:48 PM, sangramjit basu <span dir="ltr" class=""><<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">I took your advice Carson, this time there are no error on any required section but the contig is failing !!!! i'm attaching the output with -debug option, Please look into it.<br class=""></div><div class=""><div class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Apr 10, 2015 at 8:32 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">The specific module is DB_File (<a href="http://search.cpan.org/~pmqs/DB_File-1.835/DB_File.pm#Using_DB_File_with_Berkeley_DB_version_2_or_greater" target="_blank" class="">http://search.cpan.org/~pmqs/DB_File-1.835/DB_File.pm#Using_DB_File_with_Berkeley_DB_version_2_or_greater</a>). It normally comes preconfigured if you use the system perl. If you intstall your own Perl, then you may have to set everything up at Perl compile time or it will be ignored. Also you will have to reinstall MAKER if you update Perl or this module before trying to use it.<div class=""><br class=""></div><div class="">You can also run maker with the -debug flag to see the versions of all perl modules being used by MAKER. You may need to verify that the paths being used by MAEKR are the ones you expect. Don’t be surprised if you have multiple versions of some modules installed on your system (including BioPerl), and that those other copies are superseding the module you just installed.</div><span class=""><font color="#888888" class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class=""><div class=""><br class=""></div><div class=""><br class=""><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Apr 10, 2015, at 6:57 AM, sangramjit basu <<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class="">Now Carson I've upgraded perl version (5.14.2) along with updating bioperl ( CJFIELDS/BioPerl-1.6.924.tar.gz ) using cpan...I also seperately checked & installed the modules mentioned in gmod tutorial. Now i'm sure they are working fine but though I've installed BerkeleyDB from Oracle i'm not sure if it is visible to perl modules. Can you provide me a link or documentation of how to correctly manipulate this BerkeleyDB part. <br class=""></div>PS. The error is still persisting :( <br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Fri, Apr 10, 2015 at 2:05 AM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class=""><div class="">Basically there were two remaining possibilities. The first is that you are missing BerkleyDB support in your perl installation (this sometimes happens when people install their own version of perl rather than using the system perl). The second is that you have a broken version of BioPerl. BioPerl uses BerkleyDB to index the fasta files, and there are a couple of BioPerl versions with broken indexers. Make sure you do not use BioPerl-live from github. That is the unstable development version. You should use the stable version of BioPerl available through <a href="http://cpan.org/" target="_blank" class="">cpan.org</a> or via the cpan package manager that comes with perl.</div><span class=""><font color="#888888" class=""><div class=""><br class=""></div><div class="">—Carson</div></font></span><div class=""><div class=""><div class=""><br class=""></div><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Apr 9, 2015, at 2:27 PM, sangramjit basu <<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>> wrote:</div><br class=""><div class=""><p dir="ltr" class="">Yes Carson thats the line I get wen i do which perl…in one of gmod mailing list solution i saw a similiar problem like mine though the error lines looked little differnt bt the prob essentialy was same, there you suggested to update bioperl…do you think i shud try that ???!!!</p>
<div class="gmail_quote">On Apr 9, 2015 7:44 PM, "Carson Holt" <<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>> wrote:<br type="attribution" class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Are you by any chance using a non-system perl? When you type 'which perl’ on the command line, is the path /usr/bin/perl?<div class=""><br class=""></div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""><div class=""><div class=""><blockquote type="cite" class=""><div class="">On Apr 9, 2015, at 1:58 AM, sangramjit basu <<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">I did that Carson...infact I made all the ctl files freshly...still it is giving this error:<br class=""><br class="">STATUS: Parsing control files...<br class="">WARNING: RepBase is not installed for RepeatMasker. This limits<br class="">RepeatMasker's functionality and makes the model_org option in the<br class="">control files virtually meaningless. MAKER will now reconfigure<br class="">for simple repeat masking only.<br class="">STATUS: Processing and indexing input FASTA files...<br class="">STATUS: Setting up database for any GFF3 input...<br class="">A data structure will be created for you at:<br class="">/opt/maker/hsap_contig.maker.output/hsap_contig_datastore<br class=""><br class="">To access files for individual sequences use the datastore index:<br class="">/opt/maker/hsap_contig.maker.output/hsap_contig_master_datastore_index.log<br class=""><br class="">STATUS: Now running MAKER...<br class="">examining contents of the fasta file and run log<br class=""><br class=""><br class=""><br class="">--Next Contig--<br class=""><br class="">MAKER WARNING: All old files will be erased before continuing<br class="">#---------------------------------------------------------------------<br class="">Skipping the contig because it is too short!!<br class="">SeqID: NT_010783.15<br class="">Length: 0<br class="">#---------------------------------------------------------------------<br class=""><br class=""><br class=""><br class=""><br class="">Maker is now finished!!!<br class=""><br class=""><br class=""><br class="">Start_time: 1428565629<br class="">End_time: 1428565633<br class="">Elapsed: 4<br class=""></div><br class=""></div>This is really confusing...Is it because of hardware limitation ?? why is this line coming: Skipping the contig because it is too short!! ??? what is the minimum contig length required ?<br class=""></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Apr 8, 2015 at 8:22 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Rerun with the -f options. You probably have some truncated files hanging around from your last failed run.<div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class=""><div class=""><div class="">On Apr 8, 2015, at 5:22 AM, sangramjit basu <<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>> wrote:</div><br class=""></div></div><div class=""><div class=""><div class=""><div dir="ltr" class=""><div class=""><div class="">Hello Carson,<br class=""></div>I took your advice and indeed on cleaning tmp drive it ran. But now the problem is that whatever file i am giving it (be it dpp_contig.fa or hsap_contig.fa from test dataset or my rice chromosome 1 even human chr1 ) it is always showing the following error:<br class="">STATUS: Parsing control files...<br class="">STATUS: Processing and indexing input FASTA files...<br class="">STATUS: Setting up database for any GFF3 input...<br class="">A data structure will be created for you at:<br class="">/opt/maker/chr1.maker.output/chr1_datastore<br class=""><br class="">To access files for individual sequences use the datastore index:<br class="">/opt/maker/chr1.maker.output/chr1_master_datastore_index.log<br class=""><br class="">STATUS: Now running MAKER...<br class="">examining contents of the fasta file and run log<br class=""><br class=""><br class=""><br class="">--Next Contig--<br class=""><br class="">MAKER WARNING: All old files will be erased before continuing<br class="">#---------------------------------------------------------------------<br class="">Skipping the contig because it is too short!!<br class="">SeqID: chr1<br class="">Length: 0<br class="">#---------------------------------------------------------------------<br class=""><br class=""><br class=""><br class=""><br class="">Maker is now finished!!!<br class=""><br class=""><br class=""><br class="">Start_time: 1428491050<br class="">End_time: 1428491080<br class="">Elapsed: 30<br class=""><br class=""></div><b class="">How can a full chromosome be short contig !!!</b> <b class="">i am attaching my option control file please take a look at it and see if something is going wrong parameter-wise</b>. Thank you in advance :)<br class=""><div class=""> </div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Apr 8, 2015 at 11:26 AM, sangramjit basu <span dir="ltr" class=""><<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class=""><div class=""><div class="">Hello Scott and Carson,<br class=""></div>Thank you so much for your time and prompt reply. Carson's point seems the problem actually, I hope to get it right this time and will get back to you with the outcome.<br class=""></div>With best regards<span class=""><font color="#888888" class=""><br class=""></font></span></div><span class=""><font color="#888888" class="">Sangramjit<br class=""></font></span></div><div class=""><div class=""><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Apr 7, 2015 at 9:57 PM, Carson Holt <span dir="ltr" class=""><<a href="mailto:carsonhh@gmail.com" target="_blank" class="">carsonhh@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word" class="">Hi Sangramjit,<div class=""><br class=""></div><div class="">Where the error occured means either one of your input files is not formatted correctly (i.e. not correct fasta format or not correct GFF3 format). Or the drive with your temporary directory is full (usually /tmp), and MAKER can’t write the temporary files it needs to run. Or you set the TMP= option in the control files to an NFS mounted location. Some parts of MAKER cannot run in NFS drives because of the way they handle file locks.</div><div class=""><br class=""></div><div class="">—Carson</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On Apr 7, 2015, at 8:30 AM, Scott Cain <<a href="mailto:scott@scottcain.net" target="_blank" class="">scott@scottcain.net</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Hi Sangramjit,<div class=""><br class=""></div><div class="">I'm cc'ing the MAKER mailing list, where they should be able to help you out.</div><div class=""><br class=""></div><div class="">Scott</div><div class=""><br class=""></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Tue, Apr 7, 2015 at 3:57 AM, sangramjit basu <span dir="ltr" class=""><<a href="mailto:officialsjb@gmail.com" target="_blank" class="">officialsjb@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class=""><div class=""><div class=""><b class="">Hello Sir/Madam,<br class=""><br class=""></b></div><b class="">I am Bioinformatician trainee on NGS platform. I have been trying to use Maker to annotate rice genome (Oryza sativa indica), but have been facing a error that i cannot understand:<br class=""></b><br class="">setting up GFF3 output and fasta chunks<br class="">doing repeat masking<br class="">ERROR: Not a SCALAR reference<br class=""> at /opt/maker/bin/../lib/Fasta.pm line 382.<br class=""> Fasta::_formatSeq(FastaSeq=HASH(0x4219e18), 60) called at /opt/maker/bin/../lib/Fasta.pm line 369<br class=""> Fasta::toFastaRef(">1 CHUNK number:0 size:100000 offset:0", REF(0x4207be0)) called at /opt/maker/bin/../lib/FastaChunk.pm line 217<br class=""> FastaChunk::fasta_ref(FastaChunk=HASH(0x417e968)) called at /opt/maker/bin/../lib/FastaChunk.pm line 168<br class=""> FastaChunk::write_file(FastaChunk=HASH(0x417e968), "/opt/maker/Oryza_indica.ASM465v1.25.dna.chromosome.1.maker.ou"...) called at /opt/maker/bin/../lib/GI.pm line 3138<br class=""> GI::repeatmask(FastaChunk=HASH(0x417e968), "/opt/maker/Oryza_indica.ASM465v1.25.dna.chromosome.1.maker.ou"..., 1, "simple", "/opt/RepeatMasker/RepeatMasker", "", 1, runlog=HASH(0x4207cb8)) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 769<br class=""> Process::MpiChunk::__ANON__() called at /opt/maker/bin/../lib/Error.pm line 415<br class=""> eval {...} called at /opt/maker/bin/../lib/Error.pm line 407<br class=""> Error::subs::try(CODE(0x417fce0), HASH(0x4195a48)) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 4224<br class=""> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x417fc80), "run", HASH(0x4208f70), 0, 1) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 341<br class=""> Process::MpiChunk::run(Process::MpiChunk=HASH(0x417fc80), 0) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 357<br class=""> Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x417fc80), 0) called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287<br class=""> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x417fc20), 0) called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287<br class=""> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x4102ba8), 0) called at /opt/maker/bin/maker line 686<br class="">--> rank=NA, hostname=nucleome01-Lenovo-H520S<br class="">ERROR: Failed while doing repeat masking<br class="">ERROR: Chunk failed at level:0, tier_type:1<br class="">FAILED CONTIG:1<br class=""><br class="">ERROR: Chunk failed at level:2, tier_type:0<br class="">FAILED CONTIG:1<br class=""><br class=""></div><b class="">P.S. : I have low hard disk space, is it because of that ??</b><br class=""></div>
</blockquote></div><br class=""><br clear="all" class=""><span class=""><font color="#888888" class=""><div class=""><br class=""></div>-- <br class=""><div class="">------------------------------------------------------------------------<br class="">Scott Cain, Ph. D. scott at scottcain dot net<br class="">GMOD Coordinator (<a href="http://gmod.org/" target="_blank" class="">http://gmod.org/</a>) 216-392-3087<br class="">Ontario Institute for Cancer Research</div>
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