[maker-devel] (no subject)
Carson Holt
carsonhh at gmail.com
Tue Apr 14 09:42:31 MDT 2015
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).
Here is an old post that can help with Augustus training —> https://groups.google.com/forum/#!searchin/maker-devel/augustus$20train/maker-devel/7IdmQph98Js/agwL3J19b1QJ <https://groups.google.com/forum/#!searchin/maker-devel/augustus$20train/maker-devel/7IdmQph98Js/agwL3J19b1QJ>
Also look through the tutorial section on how to train gene predictors —> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Training_ab_initio_Gene_Predictors>
—Carson
> On Apr 14, 2015, at 5:36 AM, sangramjit basu <officialsjb at gmail.com> wrote:
>
> 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 ???
>
> On Mon, Apr 13, 2015 at 10:36 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
> 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.
>
> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Running_MAKER_with_example_data <http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_GMOD_Online_Training_2014#Running_MAKER_with_example_data>
>
> —Carson
>
>
>
>> On Apr 13, 2015, at 6:01 AM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>>
>> hi,
>> 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" ???
>>
>> On Mon, Apr 13, 2015 at 10:15 AM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>> Hello Carson,
>> 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 !!! <330.gif>
>> -Sangram
>>
>> On Sat, Apr 11, 2015 at 3:48 PM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>> 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.
>>
>> On Fri, Apr 10, 2015 at 8:32 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>> The specific module is DB_File (http://search.cpan.org/~pmqs/DB_File-1.835/DB_File.pm#Using_DB_File_with_Berkeley_DB_version_2_or_greater <http://search.cpan.org/~pmqs/DB_File-1.835/DB_File.pm#Using_DB_File_with_Berkeley_DB_version_2_or_greater>). 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.
>>
>> 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.
>>
>> —Carson
>>
>>
>>
>>> On Apr 10, 2015, at 6:57 AM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>>>
>>> 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.
>>> PS. The error is still persisting :(
>>>
>>> On Fri, Apr 10, 2015 at 2:05 AM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>>> 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 cpan.org <http://cpan.org/> or via the cpan package manager that comes with perl.
>>>
>>> —Carson
>>>
>>>
>>>> On Apr 9, 2015, at 2:27 PM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>>>>
>>>> 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 ???!!!
>>>>
>>>> On Apr 9, 2015 7:44 PM, "Carson Holt" <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>>>> 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?
>>>>
>>>>
>>>> —Carson
>>>>
>>>>> On Apr 9, 2015, at 1:58 AM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>>>>>
>>>>> I did that Carson...infact I made all the ctl files freshly...still it is giving this error:
>>>>>
>>>>> STATUS: Parsing control files...
>>>>> WARNING: RepBase is not installed for RepeatMasker. This limits
>>>>> RepeatMasker's functionality and makes the model_org option in the
>>>>> control files virtually meaningless. MAKER will now reconfigure
>>>>> for simple repeat masking only.
>>>>> STATUS: Processing and indexing input FASTA files...
>>>>> STATUS: Setting up database for any GFF3 input...
>>>>> A data structure will be created for you at:
>>>>> /opt/maker/hsap_contig.maker.output/hsap_contig_datastore
>>>>>
>>>>> To access files for individual sequences use the datastore index:
>>>>> /opt/maker/hsap_contig.maker.output/hsap_contig_master_datastore_index.log
>>>>>
>>>>> STATUS: Now running MAKER...
>>>>> examining contents of the fasta file and run log
>>>>>
>>>>>
>>>>>
>>>>> --Next Contig--
>>>>>
>>>>> MAKER WARNING: All old files will be erased before continuing
>>>>> #---------------------------------------------------------------------
>>>>> Skipping the contig because it is too short!!
>>>>> SeqID: NT_010783.15
>>>>> Length: 0
>>>>> #---------------------------------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Maker is now finished!!!
>>>>>
>>>>>
>>>>>
>>>>> Start_time: 1428565629
>>>>> End_time: 1428565633
>>>>> Elapsed: 4
>>>>>
>>>>> 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 ?
>>>>>
>>>>> On Wed, Apr 8, 2015 at 8:22 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>>>>> Rerun with the -f options. You probably have some truncated files hanging around from your last failed run.
>>>>>
>>>>> —Carson
>>>>>
>>>>>
>>>>>
>>>>>> On Apr 8, 2015, at 5:22 AM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>>>>>>
>>>>>> Hello Carson,
>>>>>> 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:
>>>>>> 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:
>>>>>> /opt/maker/chr1.maker.output/chr1_datastore
>>>>>>
>>>>>> To access files for individual sequences use the datastore index:
>>>>>> /opt/maker/chr1.maker.output/chr1_master_datastore_index.log
>>>>>>
>>>>>> STATUS: Now running MAKER...
>>>>>> examining contents of the fasta file and run log
>>>>>>
>>>>>>
>>>>>>
>>>>>> --Next Contig--
>>>>>>
>>>>>> MAKER WARNING: All old files will be erased before continuing
>>>>>> #---------------------------------------------------------------------
>>>>>> Skipping the contig because it is too short!!
>>>>>> SeqID: chr1
>>>>>> Length: 0
>>>>>> #---------------------------------------------------------------------
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> Maker is now finished!!!
>>>>>>
>>>>>>
>>>>>>
>>>>>> Start_time: 1428491050
>>>>>> End_time: 1428491080
>>>>>> Elapsed: 30
>>>>>>
>>>>>> How can a full chromosome be short contig !!! i am attaching my option control file please take a look at it and see if something is going wrong parameter-wise. Thank you in advance :)
>>>>>>
>>>>>>
>>>>>> On Wed, Apr 8, 2015 at 11:26 AM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>>>>>> Hello Scott and Carson,
>>>>>> 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.
>>>>>> With best regards
>>>>>> Sangramjit
>>>>>>
>>>>>> On Tue, Apr 7, 2015 at 9:57 PM, Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>>>>>> Hi Sangramjit,
>>>>>>
>>>>>> 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.
>>>>>>
>>>>>> —Carson
>>>>>>
>>>>>>
>>>>>>
>>>>>>> On Apr 7, 2015, at 8:30 AM, Scott Cain <scott at scottcain.net <mailto:scott at scottcain.net>> wrote:
>>>>>>>
>>>>>>> Hi Sangramjit,
>>>>>>>
>>>>>>> I'm cc'ing the MAKER mailing list, where they should be able to help you out.
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Apr 7, 2015 at 3:57 AM, sangramjit basu <officialsjb at gmail.com <mailto:officialsjb at gmail.com>> wrote:
>>>>>>> Hello Sir/Madam,
>>>>>>>
>>>>>>> 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:
>>>>>>>
>>>>>>> setting up GFF3 output and fasta chunks
>>>>>>> doing repeat masking
>>>>>>> ERROR: Not a SCALAR reference
>>>>>>> at /opt/maker/bin/../lib/Fasta.pm line 382.
>>>>>>> Fasta::_formatSeq(FastaSeq=HASH(0x4219e18), 60) called at /opt/maker/bin/../lib/Fasta.pm line 369
>>>>>>> Fasta::toFastaRef(">1 CHUNK number:0 size:100000 offset:0", REF(0x4207be0)) called at /opt/maker/bin/../lib/FastaChunk.pm line 217
>>>>>>> FastaChunk::fasta_ref(FastaChunk=HASH(0x417e968)) called at /opt/maker/bin/../lib/FastaChunk.pm line 168
>>>>>>> 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
>>>>>>> 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
>>>>>>> Process::MpiChunk::__ANON__() called at /opt/maker/bin/../lib/Error.pm line 415
>>>>>>> eval {...} called at /opt/maker/bin/../lib/Error.pm line 407
>>>>>>> Error::subs::try(CODE(0x417fce0), HASH(0x4195a48)) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 4224
>>>>>>> Process::MpiChunk::_go(Process::MpiChunk=HASH(0x417fc80), "run", HASH(0x4208f70), 0, 1) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 341
>>>>>>> Process::MpiChunk::run(Process::MpiChunk=HASH(0x417fc80), 0) called at /opt/maker/bin/../lib/Process/MpiChunk.pm line 357
>>>>>>> Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x417fc80), 0) called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287
>>>>>>> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x417fc20), 0) called at /opt/maker/bin/../lib/Process/MpiTiers.pm line 287
>>>>>>> Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x4102ba8), 0) called at /opt/maker/bin/maker line 686
>>>>>>> --> rank=NA, hostname=nucleome01-Lenovo-H520S
>>>>>>> ERROR: Failed while doing repeat masking
>>>>>>> ERROR: Chunk failed at level:0, tier_type:1
>>>>>>> FAILED CONTIG:1
>>>>>>>
>>>>>>> ERROR: Chunk failed at level:2, tier_type:0
>>>>>>> FAILED CONTIG:1
>>>>>>>
>>>>>>> P.S. : I have low hard disk space, is it because of that ??
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D. scott at scottcain dot net
>>>>>>> GMOD Coordinator (http://gmod.org/ <http://gmod.org/>) 216-392-3087
>>>>>>> Ontario Institute for Cancer Research
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>>>>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
>>>>>>
>>>>>>
>>>>>>
>>>>>> <maker_exe.ctl><maker_opts.ctl>
>>>>>
>>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>
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