From Victor.Rossier at unil.ch Mon Jul 4 10:38:40 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Mon, 4 Jul 2016 15:38:40 +0000 Subject: [maker-devel] Fasta index error Message-ID: <1467646720155.98154@unil.ch> Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jul 5 09:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:14 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <1467646720155.98154@unil.ch> References: <1467646720155.98154@unil.ch> Message-ID: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson > On Jul 4, 2016, at 9:38 AM, Victor Rossier wrote: > > Dear Maker, > > I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. > > Here is the error I get: > > WARNING: Cannot find >0, trying to re-index the fasta. > stop here:0 > ERROR: Fasta index error > at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. > GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 > Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 > eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 > Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 > Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 > Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 > --> rank=16, hostname=dee-serv04.vital-it.ch > ERROR: Failed while polishing alt-ESTs > ERROR: Chunk failed at level:6, tier_type:3 > FAILED CONTIG:scaffold52256_cov106 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:scaffold52256_cov106 > > Any thought how to solve this? > > Thanks in advance, > Victor Rossier > _______________________________________________ > 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 carsonhh at gmail.com Tue Jul 5 09:29:48 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:48 -0600 Subject: [maker-devel] Alternative genetic code In-Reply-To: <5773950C.8030102@icm.uu.se> References: <5773950C.8030102@icm.uu.se> Message-ID: <1D1B5FA1-E05E-49A9-BCEB-A4A859067CFE@gmail.com> Currently there is no support for alternate codon usage. ?Carson > On Jun 29, 2016, at 3:29 AM, Courtney Stairs wrote: > > Hello there, > > I noticed on the google group that someone has asked about using an alternative genetic code with Maker. Has such a function been implemented on the newer versions of Maker? I understand that this is not a straight-forward task. I am interested in using Maker on a genome that using code 6. > > Thank you very much for your time, > > Courtney > > -- > ------------------------------------ > Courtney Stairs, PhD > Post-doctoral fellow > Laboratory of Dr. Thijs Ettema > Institute for Cell and Molecular Biology > Uppsala University > Sweden > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From cjfields at illinois.edu Wed Jul 6 07:16:56 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 6 Jul 2016 12:16:56 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> Message-ID: I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Wed Jul 6 20:02:10 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: Thu, 07 Jul 2016 02:02:10 +0100 Subject: [maker-devel] Local representation needed Message-ID: <577DAA12.8050601@yandell-lab.org> Hello I am the personnel department manager and I am appealing to you in the name of the large-scale and first-rate partnership. Our company is engaged in different areas of activity, such as: - realtor - establishment and disestablishment of enterprises - bank account establishment and maintanance - logistics - private business support - etc. We are making a regional managers’ team now: - salary $4.600 + bonus - 1 - 2 working hours per day - flextime If you would like to be a regional manager visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Thu Jul 7 09:20:04 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: 7 Jul 2016 18:20:04 +0400 Subject: [maker-devel] Greetings Message-ID: <004601d1d85f$04bf9090$77bd7c9f$@yandell-lab.org> Compliments I’m addressing you on behalf of the HR department of a large company. Our company is engaged in different areas of activity, such as: - real estate - accounts opening - undertaking services - etc. There are vacant positions of regional managers: - salary $5.300 + bonus - underemployment - individual time-table If you would like to work with us, please provide us your contact information on visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 09:09:31 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 14:09:31 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <1467890724600.33833@unil.ch> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> Message-ID: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 11:17:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 10:17:11 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Message-ID: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson > On Jul 7, 2016, at 8:09 AM, Fields, Christopher J wrote: > > Victor, > > Can you post which version of MAKER you are using? > > chris > > >> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >> >> Thanks for the quick replies, >> >> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >> >> I renamed all transcripts and maker finished correctly! >> >> Thanks again, >> Victor Rossier >> >> De : Fields, Christopher J > >> Envoy? : mercredi 6 juillet 2016 14:16 >> ? : Carson Holt >> Cc : Victor Rossier; maker-devel at yandell-lab.org >> Objet : Re: [maker-devel] Fasta index error >> >> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >> >> chris >> >>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>> >>> You need to rename the contig. It is currently named 0 >>> >>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>> >>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>> >>> ?Carson >>> >>> >>> >>> >>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>> >>>> Dear Maker, >>>> >>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>> >>>> Here is the error I get: >>>> >>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>> stop here:0 >>>> ERROR: Fasta index error >>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>> ERROR: Failed while polishing alt-ESTs >>>> ERROR: Chunk failed at level:6, tier_type:3 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> Any thought how to solve this? >>>> >>>> Thanks in advance, >>>> Victor Rossier >>>> _______________________________________________ >>>> 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 >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 13:43:27 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 18:43:27 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> Message-ID: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 14:08:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 13:08:40 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson > On Jul 7, 2016, at 12:43 PM, Fields, Christopher J wrote: > > Easy enough to figure out when it snuck in: > > https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 > > Seems like it may have been in there a while. > > chris > >> On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: >> >> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? >> >> This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. >> >> ?Carson >> >> >> >>> On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: >>> >>> Victor, >>> >>> Can you post which version of MAKER you are using? >>> >>> chris >>> >>> >>>> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >>>> >>>> Thanks for the quick replies, >>>> >>>> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >>>> >>>> I renamed all transcripts and maker finished correctly! >>>> >>>> Thanks again, >>>> Victor Rossier >>>> >>>> De : Fields, Christopher J > >>>> Envoy? : mercredi 6 juillet 2016 14:16 >>>> ? : Carson Holt >>>> Cc : Victor Rossier; maker-devel at yandell-lab.org >>>> Objet : Re: [maker-devel] Fasta index error >>>> >>>> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >>>> >>>> chris >>>> >>>>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>>>> >>>>> You need to rename the contig. It is currently named 0 >>>>> >>>>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>>>> >>>>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>>>> >>>>> ?Carson >>>>> >>>>> >>>>> >>>>> >>>>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>>>> >>>>>> Dear Maker, >>>>>> >>>>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>>>> >>>>>> Here is the error I get: >>>>>> >>>>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>>>> stop here:0 >>>>>> ERROR: Fasta index error >>>>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>>>> ERROR: Failed while polishing alt-ESTs >>>>>> ERROR: Chunk failed at level:6, tier_type:3 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> ERROR: Chunk failed at level:4, tier_type:0 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> Any thought how to solve this? >>>>>> >>>>>> Thanks in advance, >>>>>> Victor Rossier >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From o.k.torresen at ibv.uio.no Thu Jul 7 16:29:54 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:29:54 +0000 Subject: [maker-devel] Fragmented annotation Message-ID: Hi all, I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. Thank you. Ole From dence at genetics.utah.edu Thu Jul 7 16:44:14 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:44:14 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: Message-ID: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > 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 Thu Jul 7 16:48:21 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:48:21 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 o.k.torresen at ibv.uio.no Thu Jul 7 16:55:01 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:55:01 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: , <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: <1467928535428.94166@ibv.uio.no> Hi Daniel, thank you for your prompt answer. I've created a repeat library using this approach: https://github.com/uio-cels/Repeats, which I hope is quite thorough, and used that in the annotation. I guess I could do model_org=all in addition. I guess I could and should look at bit more at the annotation in a genome browser, but it is hard to diagnosis something like this without knowing where to start. Thank you. Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:44 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From o.k.torresen at ibv.uio.no Thu Jul 7 16:56:39 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:56:39 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu>, Message-ID: <1467928633373.20514@ibv.uio.no> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:48 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 carsonhh at gmail.com Thu Jul 7 17:12:23 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 16:12:23 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: <8B6B4EA9-FE7E-443E-9B42-6110D93AACA1@gmail.com> Try the maker2eval_gtf script. It converts to GTF and adds explicit start/stop codons. ?Carson > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 From dence at genetics.utah.edu Thu Jul 7 17:13:18 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 22:13:18 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 o.k.torresen at ibv.uio.no Sat Jul 9 15:50:37 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Sat, 9 Jul 2016 20:50:37 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no>, Message-ID: <1468097477192.77639@ibv.uio.no> Daniel, Carson, I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. I guess the length of the genes/proteins could also be a factor I could look into. If the annotation would have been/is fragmented, what options could I try to tune? Thank you. Ole ________________________________________ From: Daniel Ence Sent: 08 July 2016 00:13 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 carsonhh at gmail.com Mon Jul 11 12:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 11 Jul 2016 11:29:14 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1468097477192.77639@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> <1468097477192.77639@ibv.uio.no> Message-ID: <953FC580-9A1D-4905-8E79-B98815BF5DDB@gmail.com> Most likely culprit is still that you have not properly masked repeats. Repeats encode real proteins (i.e. reverse transcriptase, etc.). So if they are not all masked they will be annotated as genes with start and stop codons. ?Carson > On Jul 9, 2016, at 2:50 PM, Ole Kristian T?rresen wrote: > > Daniel, Carson, > I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. > > I guess the length of the genes/proteins could also be a factor I could look into. > > If the annotation would have been/is fragmented, what options could I try to tune? > > Thank you. > > Ole > ________________________________________ > From: Daniel Ence > Sent: 08 July 2016 00:13 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. > > This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. > > ~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 > >> On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: >> >> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? >> >> Ole >> ________________________________________ >> From: Daniel Ence >> Sent: 07 July 2016 23:48 >> To: Ole Kristian T?rresen >> Cc: maker-devel at yandell-lab.org >> Subject: Re: [maker-devel] Fragmented annotation >> >> Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. >> >> ~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 >> >>> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >>> >>> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >>> >>> ~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 >>> >>>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>>> >>>> Hi all, >>>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>>> >>>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>>> >>>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>>> >>>> Thank you. >>>> >>>> Ole >>>> _______________________________________________ >>>> 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 From Victor.Rossier at unil.ch Thu Jul 7 06:25:24 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Thu, 7 Jul 2016 11:25:24 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> , Message-ID: <1467890724600.33833@unil.ch> Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I'll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it's the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. -Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Fri Jul 8 13:09:21 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 8 Jul 2016 18:09:21 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: It?s not terribly often sequence IDs are that short (let alone 0), though I could see it happening with raw assembler output. Usually we rename the seqs to something else. I?m still not terribly happy about the stringification overload but removing it would likely break things in terrible obscene ways (I found this out the hard way removing this behavior from the developer ontology modules). chris On Jul 7, 2016, at 2:08 PM, Carson Holt > wrote: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson On Jul 7, 2016, at 12:43 PM, Fields, Christopher J > wrote: Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 19:52:05 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 17:52:05 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Hi, I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. *Options I used include:* maker_gff=014_maker_Sacu_v1_s0008.gff est_pass=1 altest_pass=0 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 altest=alt_est.fasta snaphmm=snap.hmm trna=0 cpus=1 clean_try=0 clean_up=0 *Below are the last 50 lines in the stderr from the failed run.* running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ tblastx.pm:133 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: /share/apps/genomics/maker/bin/maker:979 ----------------------------------------------------------- --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local ERROR: Failed while collecting tblastx reports ERROR: Chunk failed at level:5, tier_type:3 FAILED CONTIG:Sacu_v1_s0008 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:Sacu_v1_s0008 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx did not finish on the last run and must be erased Maker is now finished!!! Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 22:20:43 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 20:20:43 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sun Jul 17 00:40:50 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sat, 16 Jul 2016 22:40:50 -0700 Subject: [maker-devel] MAKER output has different genes with same name Message-ID: I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: maker_gff=previous_run.gff est_pass=1 altest_pass=1 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: ------------------------------------- *Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* *Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 *Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* *Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* *Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 *Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 Here the models' headers from the maker.proteins.fasta: ------------------------------------- >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sun Jul 17 18:39:51 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sun, 17 Jul 2016 16:39:51 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. Matt On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > I have been using MAKER to iteratively update previous run's annotations > by running ab initios with fresh training and feeding the previous run's > GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > Along the way it seems that non-identical features with the same name, > some covering the same region and some not, accumulate. When I use > fasta_merge -d ...index.log I get sequences for the duplicates. Am I using > the control file options incorrectly? Any suggestions how to select final > models? Or should I redo the runs if I had some settings wrong? > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log > showing duplicate models: > > ------------------------------------- > > *Sacu_v1_s0077 maker gene 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* > > *Sacu_v1_s0077 maker mRNA 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* > > Sacu_v1_s0077 maker exon 138512 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > *Sacu_v1_s0077 maker gene 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* > > *Sacu_v1_s0077 maker mRNA 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* > > > > > *Sacu_v1_s0004 maker gene 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* > > *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > *Sacu_v1_s0004 maker gene 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* > > *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . > ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yincl2013 at 126.com Wed Jul 13 05:10:45 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Wed, 13 Jul 2016 18:10:45 +0800 Subject: [maker-devel] maker problem Message-ID: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China -------------- next part -------------- An HTML attachment was scrubbed... URL: From sebastien.moretti at unil.ch Tue Jul 12 03:35:43 2016 From: sebastien.moretti at unil.ch (Sebastien Moretti) Date: Tue, 12 Jul 2016 10:35:43 +0200 Subject: [maker-devel] Installation in a custom directory Message-ID: Hi I try to install maker in a custom directory following regular Perl commands with Build.PL. Unfortunately if I use perl Build.PL --installdirs= then ./Build install --destdir= build install fails with the error: Can't use an undefined value as a HASH reference at .../Module/Build/Base.pm line 3038. It does not happen if I don't use --installdirs Is there an "official" way to install maker in a custom directory? Also I found typos in the description of maker at http://www.yandell-lab.org/software/maker.html ouputs should be outputs seusequent should be ??? maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 Regards -- S?bastien Moretti Staff Scientist SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.org/ From carsonhh at gmail.com Mon Jul 18 09:48:28 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:48:28 -0600 Subject: [maker-devel] Installation in a custom directory In-Reply-To: References: Message-ID: <9A2E906F-F0B9-4CB3-9C18-CA57F4213D55@gmail.com> MAKER will by default put executables in ?/maker/bin. You should put ?/maker/bin into your PATH. The maker Build.PL is configured to install things in a set directory configuration to properly locate perl libraries, C shared objects, and data files. ?Carson > On Jul 12, 2016, at 2:35 AM, Sebastien Moretti wrote: > > Hi > > I try to install maker in a custom directory following regular Perl > commands with Build.PL. > > Unfortunately if I use > perl Build.PL --installdirs= > then > ./Build install --destdir= > build install fails with the error: > Can't use an undefined value as a HASH reference at > .../Module/Build/Base.pm line 3038. > > It does not happen if I don't use --installdirs > > > Is there an "official" way to install maker in a custom directory? > > > Also I found typos in the description of maker at > http://www.yandell-lab.org/software/maker.html > ouputs should be outputs > seusequent should be ??? > > > maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 > > Regards > > -- > S?bastien Moretti > Staff Scientist > SIB Vital-IT EMBnet, Quartier Sorge - Genopode > CH-1015 Lausanne, Switzerland > Tel.: +41 (21) 692 4079/4221 > http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.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 Jul 18 09:53:09 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:53:09 -0600 Subject: [maker-devel] maker problem In-Reply-To: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson > On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: > > Hello, > > When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. > > Here is a part of main error log: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Can't get HSPs: data not collected. > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 > STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 > STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 > STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 > STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 > STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 > STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > ERROR: Failed while collecting blastx reports > ERROR: Chunk failed at level:9, tier_type:3 > FAILED CONTIG:QPacbio.Hiseq_683 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:QPacbio.Hiseq_683 > > examining contents of the fasta file and run log > Thanks! > > Best regards, > Ian > Department of Entomology, College of Plant Protection, Nanjing Agricultural University > No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 09:55:29 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:55:29 -0600 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: <7C44D0D0-D2CE-4899-9CE5-0050A928A6E0@gmail.com> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk. This will cause IO errors and partial result files because the operations done in TMP are not NFS safe. Thanks, Carson > On Jul 15, 2016, at 9:20 PM, Matt Simenc wrote: > > Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc > wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. > > Options I used include: > > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > > other_pass=0 > > > altest=alt_est.fasta > > > snaphmm=snap.hmm > > > trna=0 > > cpus=1 > > > clean_try=0 > > > clean_up=0 > > > > > > Below are the last 50 lines in the stderr from the failed run. > > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > > examining contents of the fasta file and run log > > > > --Next Contig-- > > > > Processing run.log file... > > MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > > Maker is now finished!!! > > > > > > Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 10:03:08 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:03:08 -0600 Subject: [maker-devel] maker problem In-Reply-To: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Message-ID: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson > On Jul 18, 2016, at 9:00 AM, Chuanlin Yin wrote: > > Thank you very much! > > I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. > > Thanks! > > Best wishes! > Ian > > 2016-07-18 > Chuanlin Yin > ????Carson Holt > > ?????2016-07-18 22:53 > ???Re: [maker-devel] maker problem > ????"Chuanlin Yin"> > ???"maker-devel"> > > The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. > > Thanks, > Carson > > >> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >> >> Hello, >> >> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >> >> Here is a part of main error log: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Can't get HSPs: data not collected. >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >> ----------------------------------------------------------- >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> ERROR: Failed while collecting blastx reports >> ERROR: Chunk failed at level:9, tier_type:3 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> ERROR: Chunk failed at level:4, tier_type:0 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> examining contents of the fasta file and run log >> Thanks! >> >> Best regards, >> Ian >> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >> >> >> _______________________________________________ >> 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 yincl2013 at 126.com Mon Jul 18 10:00:39 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Mon, 18 Jul 2016 23:00:39 +0800 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 Chuanlin Yin ????Carson Holt ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin" ???"maker-devel" The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 carsonhh at gmail.com Mon Jul 18 10:08:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:08:11 -0600 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Also with when trying 1, 2, or 3, run just the failed contig as a separate job or the old archived files will be reused rather than regenerating following the change (because MAKER archives partial results in theVoid directory). ?Carson > On Jul 18, 2016, at 9:03 AM, Carson Holt wrote: > > 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. > 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk > > ?Carson > > >> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >> >> Thank you very much! >> >> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >> >> Thanks! >> >> Best wishes! >> Ian >> >> 2016-07-18 >> Chuanlin Yin >> ????Carson Holt > >> ?????2016-07-18 22:53 >> ???Re: [maker-devel] maker problem >> ????"Chuanlin Yin"> >> ???"maker-devel"> >> >> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >> >> Thanks, >> Carson >> >> >>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>> >>> Hello, >>> >>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>> >>> Here is a part of main error log: >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Can't get HSPs: data not collected. >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> ERROR: Failed while collecting blastx reports >>> ERROR: Chunk failed at level:9, tier_type:3 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> ERROR: Chunk failed at level:4, tier_type:0 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> examining contents of the fasta file and run log >>> Thanks! >>> >>> Best regards, >>> Ian >>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>> >>> >>> _______________________________________________ >>> 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 mcsimenc at gmail.com Mon Jul 18 10:18:38 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:18:38 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! Matt On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 10:20:34 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:34 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Oops! I meant to reply to a different thread, not this one. That last message is related to a different problem. On Mon, Jul 18, 2016 at 8:18 AM, Matt Simenc wrote: > Update: > > So I isolated a single scaffold to run MAKER on and test different > parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire > assembly. There are still some duplicates. I tried using the -a command > line option and it reduced the number of duplicate IDs for different > features by 2, but I don't know what to do. It's important if I know maker > is keeping the features in order or if it's possible maker is mixing up > exons and CDSs between different gene and mRNA features. > > Thanks! > Matt > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > >> Hi, >> >> I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I >> isolated this scaffold from my assembly after maker successfully annotated >> all other scaffolds in the assembly but failed on this one, and failed on >> successive retries. >> >> I fed this maker run a maker-generated gff from a prior successful run. >> This is the first run on which I have added transcript sequences from a >> closely related species. The only ab initio program I'm running here was >> SNAP. >> >> *Options I used include:* >> >> maker_gff=014_maker_Sacu_v1_s0008.gff >> >> est_pass=1 >> >> altest_pass=0 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> altest=alt_est.fasta >> >> snaphmm=snap.hmm >> >> trna=0 >> >> cpus=1 >> >> clean_try=0 >> >> clean_up=0 >> >> >> >> *Below are the last 50 lines in the stderr from the failed run.* >> >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> >> MSG: Can't get HSPs: data not collected. >> >> STACK: Error::throw >> >> STACK: Bio::Root::Root::throw >> /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 >> >> STACK: Bio::Search::Hit::PhatHit::Base::hsps >> /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> >> STACK: Widget::tblastx::keepers >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 >> >> STACK: Widget::tblastx::parse >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 >> >> STACK: GI::reblast_merged_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:469 >> >> STACK: GI::merge_resolve_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:289 >> >> STACK: Process::MpiChunk::_go >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 >> >> STACK: Process::MpiChunk::run >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 >> >> STACK: /share/apps/genomics/maker/bin/maker:979 >> >> ----------------------------------------------------------- >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> ERROR: Failed while collecting tblastx reports >> >> ERROR: Chunk failed at level:5, tier_type:3 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> ERROR: Chunk failed at level:4, tier_type:0 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> examining contents of the fasta file and run log >> >> >> --Next Contig-- >> >> >> Processing run.log file... >> >> MAKER WARNING: The file >> Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> did not finish on the last run and must be erased >> >> >> Maker is now finished!!! >> >> >> >> Any help would be appreciated, please let me know if any other >> information about this run would be helpful in diagnosing the problem(s). >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 10:20:44 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:44 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that > set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > >> I have been using MAKER to iteratively update previous run's annotations >> by running ab initios with fresh training and feeding the previous run's >> GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> Along the way it seems that non-identical features with the same name, >> some covering the same region and some not, accumulate. When I use >> fasta_merge -d ...index.log I get sequences for the duplicates. Am I using >> the control file options incorrectly? Any suggestions how to select final >> models? Or should I redo the runs if I had some settings wrong? >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log >> showing duplicate models: >> >> ------------------------------------- >> >> *Sacu_v1_s0077 maker gene 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* >> >> *Sacu_v1_s0077 maker mRNA 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> *Sacu_v1_s0077 maker gene 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* >> >> *Sacu_v1_s0077 maker mRNA 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* >> >> >> >> >> *Sacu_v1_s0004 maker gene 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* >> >> *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> *Sacu_v1_s0004 maker gene 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* >> >> *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . >> ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 10:29:54 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:29:54 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. ?Carson > On Jul 18, 2016, at 9:20 AM, Matt Simenc wrote: > > Update: > > So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. > > Thanks! > > On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: > I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > > Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? > > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: > > ------------------------------------- > > Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 > > Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 > > Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 > > > Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 > > > > > > > > Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 > > Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > > > Thanks! > > Matt > > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 10:35:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:35:40 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> References: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Message-ID: <3A0272F5-F6C3-4546-BF5F-E859C191713C@gmail.com> Also from your previous STDERR log you have /state/partition1/ set as your TMP directory. If that is a network mounted location, then you can get duplicate writes from separate threads to output files because of failed locks. The TMP directory should normally be set to /tmp as it is usually a locally mounted disk that will be independent and inaccessible to other nodes. Duplicate entries are often a sign of this type of IO error, especially if there is a certain degree of randomness to who gets duplicated. ?Carson > On Jul 18, 2016, at 9:29 AM, Carson Holt wrote: > > Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. > > Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. > > Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. > > ?Carson > > > > >> On Jul 18, 2016, at 9:20 AM, Matt Simenc > wrote: >> >> Update: >> >> So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. >> >> However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. >> >> Thanks! >> >> On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: >> Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. >> >> Matt >> >> On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: >> I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> >> Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? >> >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: >> >> ------------------------------------- >> >> Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 >> >> Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 >> >> >> Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 >> >> >> >> >> >> >> >> Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 >> >> Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> >> >> Thanks! >> >> Matt >> >> >> >> _______________________________________________ >> 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 cjfields at illinois.edu Mon Jul 18 12:46:52 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 18 Jul 2016 17:46:52 +0000 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. chris 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 ________________________________ Chuanlin Yin ________________________________ ????Carson Holt > ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin"> ???"maker-devel"> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 12:58:46 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 11:58:46 -0600 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Nothing specific I?m aware. Their error is occurring immediately following the blast report parse. The hit is defined, but the hash key of the object holding the HSPs is not defined. Half the time I see an error that come up through the BioPerl Bio::Root::Root::throw mechanism it goes away when the user installs the current CPAN version of BioPerl (they either have really old BioPerl or are using the live version). So I always have the user check that first. The other half of the time it ends up being an IO error (truncated file because they used NFS for temporary file space). Truncated can cause failures in multiple ways. Then less often it is a blast issue (there are a handful of subversions of blast+ that give frequent failures). ?Carson > On Jul 18, 2016, at 11:46 AM, Fields, Christopher J wrote: > > >> On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: >> >> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > > Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. > > chris > >> 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. >> 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk >> >> ?Carson >> >> >>> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >>> >>> Thank you very much! >>> >>> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >>> >>> Thanks! >>> >>> Best wishes! >>> Ian >>> >>> 2016-07-18 >>> Chuanlin Yin >>> ????Carson Holt > >>> ?????2016-07-18 22:53 >>> ???Re: [maker-devel] maker problem >>> ????"Chuanlin Yin"> >>> ???"maker-devel"> >>> >>> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >>> >>> Thanks, >>> Carson >>> >>> >>>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>>> >>>> Hello, >>>> >>>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>>> >>>> Here is a part of main error log: >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Can't get HSPs: data not collected. >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> ERROR: Failed while collecting blastx reports >>>> ERROR: Chunk failed at level:9, tier_type:3 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> examining contents of the fasta file and run log >>>> Thanks! >>>> >>>> Best regards, >>>> Ian >>>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>>> >>>> >>>> _______________________________________________ >>>> 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Victor.Rossier at unil.ch Mon Jul 4 09:38:40 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Mon, 4 Jul 2016 15:38:40 +0000 Subject: [maker-devel] Fasta index error Message-ID: <1467646720155.98154@unil.ch> Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jul 5 08:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:14 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <1467646720155.98154@unil.ch> References: <1467646720155.98154@unil.ch> Message-ID: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson > On Jul 4, 2016, at 9:38 AM, Victor Rossier wrote: > > Dear Maker, > > I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. > > Here is the error I get: > > WARNING: Cannot find >0, trying to re-index the fasta. > stop here:0 > ERROR: Fasta index error > at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. > GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 > Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 > eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 > Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 > Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 > Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 > --> rank=16, hostname=dee-serv04.vital-it.ch > ERROR: Failed while polishing alt-ESTs > ERROR: Chunk failed at level:6, tier_type:3 > FAILED CONTIG:scaffold52256_cov106 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:scaffold52256_cov106 > > Any thought how to solve this? > > Thanks in advance, > Victor Rossier > _______________________________________________ > 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 carsonhh at gmail.com Tue Jul 5 08:29:48 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:48 -0600 Subject: [maker-devel] Alternative genetic code In-Reply-To: <5773950C.8030102@icm.uu.se> References: <5773950C.8030102@icm.uu.se> Message-ID: <1D1B5FA1-E05E-49A9-BCEB-A4A859067CFE@gmail.com> Currently there is no support for alternate codon usage. ?Carson > On Jun 29, 2016, at 3:29 AM, Courtney Stairs wrote: > > Hello there, > > I noticed on the google group that someone has asked about using an alternative genetic code with Maker. Has such a function been implemented on the newer versions of Maker? I understand that this is not a straight-forward task. I am interested in using Maker on a genome that using code 6. > > Thank you very much for your time, > > Courtney > > -- > ------------------------------------ > Courtney Stairs, PhD > Post-doctoral fellow > Laboratory of Dr. Thijs Ettema > Institute for Cell and Molecular Biology > Uppsala University > Sweden > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From cjfields at illinois.edu Wed Jul 6 06:16:56 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 6 Jul 2016 12:16:56 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> Message-ID: I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Wed Jul 6 19:02:10 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: Thu, 07 Jul 2016 02:02:10 +0100 Subject: [maker-devel] Local representation needed Message-ID: <577DAA12.8050601@yandell-lab.org> Hello I am the personnel department manager and I am appealing to you in the name of the large-scale and first-rate partnership. Our company is engaged in different areas of activity, such as: - realtor - establishment and disestablishment of enterprises - bank account establishment and maintanance - logistics - private business support - etc. We are making a regional managers’ team now: - salary $4.600 + bonus - 1 - 2 working hours per day - flextime If you would like to be a regional manager visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Thu Jul 7 08:20:04 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: 7 Jul 2016 18:20:04 +0400 Subject: [maker-devel] Greetings Message-ID: <004601d1d85f$04bf9090$77bd7c9f$@yandell-lab.org> Compliments I’m addressing you on behalf of the HR department of a large company. Our company is engaged in different areas of activity, such as: - real estate - accounts opening - undertaking services - etc. There are vacant positions of regional managers: - salary $5.300 + bonus - underemployment - individual time-table If you would like to work with us, please provide us your contact information on visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 08:09:31 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 14:09:31 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <1467890724600.33833@unil.ch> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> Message-ID: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 10:17:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 10:17:11 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Message-ID: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson > On Jul 7, 2016, at 8:09 AM, Fields, Christopher J wrote: > > Victor, > > Can you post which version of MAKER you are using? > > chris > > >> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >> >> Thanks for the quick replies, >> >> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >> >> I renamed all transcripts and maker finished correctly! >> >> Thanks again, >> Victor Rossier >> >> De : Fields, Christopher J > >> Envoy? : mercredi 6 juillet 2016 14:16 >> ? : Carson Holt >> Cc : Victor Rossier; maker-devel at yandell-lab.org >> Objet : Re: [maker-devel] Fasta index error >> >> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >> >> chris >> >>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>> >>> You need to rename the contig. It is currently named 0 >>> >>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>> >>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>> >>> ?Carson >>> >>> >>> >>> >>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>> >>>> Dear Maker, >>>> >>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>> >>>> Here is the error I get: >>>> >>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>> stop here:0 >>>> ERROR: Fasta index error >>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>> ERROR: Failed while polishing alt-ESTs >>>> ERROR: Chunk failed at level:6, tier_type:3 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> Any thought how to solve this? >>>> >>>> Thanks in advance, >>>> Victor Rossier >>>> _______________________________________________ >>>> 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 >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 12:43:27 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 18:43:27 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> Message-ID: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 13:08:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 13:08:40 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson > On Jul 7, 2016, at 12:43 PM, Fields, Christopher J wrote: > > Easy enough to figure out when it snuck in: > > https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 > > Seems like it may have been in there a while. > > chris > >> On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: >> >> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? >> >> This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. >> >> ?Carson >> >> >> >>> On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: >>> >>> Victor, >>> >>> Can you post which version of MAKER you are using? >>> >>> chris >>> >>> >>>> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >>>> >>>> Thanks for the quick replies, >>>> >>>> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >>>> >>>> I renamed all transcripts and maker finished correctly! >>>> >>>> Thanks again, >>>> Victor Rossier >>>> >>>> De : Fields, Christopher J > >>>> Envoy? : mercredi 6 juillet 2016 14:16 >>>> ? : Carson Holt >>>> Cc : Victor Rossier; maker-devel at yandell-lab.org >>>> Objet : Re: [maker-devel] Fasta index error >>>> >>>> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >>>> >>>> chris >>>> >>>>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>>>> >>>>> You need to rename the contig. It is currently named 0 >>>>> >>>>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>>>> >>>>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>>>> >>>>> ?Carson >>>>> >>>>> >>>>> >>>>> >>>>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>>>> >>>>>> Dear Maker, >>>>>> >>>>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>>>> >>>>>> Here is the error I get: >>>>>> >>>>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>>>> stop here:0 >>>>>> ERROR: Fasta index error >>>>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>>>> ERROR: Failed while polishing alt-ESTs >>>>>> ERROR: Chunk failed at level:6, tier_type:3 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> ERROR: Chunk failed at level:4, tier_type:0 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> Any thought how to solve this? >>>>>> >>>>>> Thanks in advance, >>>>>> Victor Rossier >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From o.k.torresen at ibv.uio.no Thu Jul 7 15:29:54 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:29:54 +0000 Subject: [maker-devel] Fragmented annotation Message-ID: Hi all, I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. Thank you. Ole From dence at genetics.utah.edu Thu Jul 7 15:44:14 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:44:14 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: Message-ID: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > 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 Thu Jul 7 15:48:21 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:48:21 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 o.k.torresen at ibv.uio.no Thu Jul 7 15:55:01 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:55:01 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: , <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: <1467928535428.94166@ibv.uio.no> Hi Daniel, thank you for your prompt answer. I've created a repeat library using this approach: https://github.com/uio-cels/Repeats, which I hope is quite thorough, and used that in the annotation. I guess I could do model_org=all in addition. I guess I could and should look at bit more at the annotation in a genome browser, but it is hard to diagnosis something like this without knowing where to start. Thank you. Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:44 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From o.k.torresen at ibv.uio.no Thu Jul 7 15:56:39 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:56:39 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu>, Message-ID: <1467928633373.20514@ibv.uio.no> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:48 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 carsonhh at gmail.com Thu Jul 7 16:12:23 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 16:12:23 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: <8B6B4EA9-FE7E-443E-9B42-6110D93AACA1@gmail.com> Try the maker2eval_gtf script. It converts to GTF and adds explicit start/stop codons. ?Carson > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 From dence at genetics.utah.edu Thu Jul 7 16:13:18 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 22:13:18 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 o.k.torresen at ibv.uio.no Sat Jul 9 14:50:37 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Sat, 9 Jul 2016 20:50:37 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no>, Message-ID: <1468097477192.77639@ibv.uio.no> Daniel, Carson, I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. I guess the length of the genes/proteins could also be a factor I could look into. If the annotation would have been/is fragmented, what options could I try to tune? Thank you. Ole ________________________________________ From: Daniel Ence Sent: 08 July 2016 00:13 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 carsonhh at gmail.com Mon Jul 11 11:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 11 Jul 2016 11:29:14 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1468097477192.77639@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> <1468097477192.77639@ibv.uio.no> Message-ID: <953FC580-9A1D-4905-8E79-B98815BF5DDB@gmail.com> Most likely culprit is still that you have not properly masked repeats. Repeats encode real proteins (i.e. reverse transcriptase, etc.). So if they are not all masked they will be annotated as genes with start and stop codons. ?Carson > On Jul 9, 2016, at 2:50 PM, Ole Kristian T?rresen wrote: > > Daniel, Carson, > I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. > > I guess the length of the genes/proteins could also be a factor I could look into. > > If the annotation would have been/is fragmented, what options could I try to tune? > > Thank you. > > Ole > ________________________________________ > From: Daniel Ence > Sent: 08 July 2016 00:13 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. > > This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. > > ~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 > >> On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: >> >> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? >> >> Ole >> ________________________________________ >> From: Daniel Ence >> Sent: 07 July 2016 23:48 >> To: Ole Kristian T?rresen >> Cc: maker-devel at yandell-lab.org >> Subject: Re: [maker-devel] Fragmented annotation >> >> Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. >> >> ~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 >> >>> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >>> >>> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >>> >>> ~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 >>> >>>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>>> >>>> Hi all, >>>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>>> >>>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>>> >>>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>>> >>>> Thank you. >>>> >>>> Ole >>>> _______________________________________________ >>>> 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 From Victor.Rossier at unil.ch Thu Jul 7 05:25:24 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Thu, 7 Jul 2016 11:25:24 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> , Message-ID: <1467890724600.33833@unil.ch> Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I'll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it's the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. -Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Fri Jul 8 12:09:21 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 8 Jul 2016 18:09:21 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: It?s not terribly often sequence IDs are that short (let alone 0), though I could see it happening with raw assembler output. Usually we rename the seqs to something else. I?m still not terribly happy about the stringification overload but removing it would likely break things in terrible obscene ways (I found this out the hard way removing this behavior from the developer ontology modules). chris On Jul 7, 2016, at 2:08 PM, Carson Holt > wrote: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson On Jul 7, 2016, at 12:43 PM, Fields, Christopher J > wrote: Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 18:52:05 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 17:52:05 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Hi, I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. *Options I used include:* maker_gff=014_maker_Sacu_v1_s0008.gff est_pass=1 altest_pass=0 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 altest=alt_est.fasta snaphmm=snap.hmm trna=0 cpus=1 clean_try=0 clean_up=0 *Below are the last 50 lines in the stderr from the failed run.* running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ tblastx.pm:133 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: /share/apps/genomics/maker/bin/maker:979 ----------------------------------------------------------- --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local ERROR: Failed while collecting tblastx reports ERROR: Chunk failed at level:5, tier_type:3 FAILED CONTIG:Sacu_v1_s0008 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:Sacu_v1_s0008 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx did not finish on the last run and must be erased Maker is now finished!!! Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 21:20:43 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 20:20:43 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sat Jul 16 23:40:50 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sat, 16 Jul 2016 22:40:50 -0700 Subject: [maker-devel] MAKER output has different genes with same name Message-ID: I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: maker_gff=previous_run.gff est_pass=1 altest_pass=1 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: ------------------------------------- *Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* *Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 *Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* *Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* *Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 *Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 Here the models' headers from the maker.proteins.fasta: ------------------------------------- >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sun Jul 17 17:39:51 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sun, 17 Jul 2016 16:39:51 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. Matt On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > I have been using MAKER to iteratively update previous run's annotations > by running ab initios with fresh training and feeding the previous run's > GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > Along the way it seems that non-identical features with the same name, > some covering the same region and some not, accumulate. When I use > fasta_merge -d ...index.log I get sequences for the duplicates. Am I using > the control file options incorrectly? Any suggestions how to select final > models? Or should I redo the runs if I had some settings wrong? > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log > showing duplicate models: > > ------------------------------------- > > *Sacu_v1_s0077 maker gene 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* > > *Sacu_v1_s0077 maker mRNA 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* > > Sacu_v1_s0077 maker exon 138512 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > *Sacu_v1_s0077 maker gene 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* > > *Sacu_v1_s0077 maker mRNA 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* > > > > > *Sacu_v1_s0004 maker gene 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* > > *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > *Sacu_v1_s0004 maker gene 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* > > *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . > ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yincl2013 at 126.com Wed Jul 13 04:10:45 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Wed, 13 Jul 2016 18:10:45 +0800 Subject: [maker-devel] maker problem Message-ID: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China -------------- next part -------------- An HTML attachment was scrubbed... URL: From sebastien.moretti at unil.ch Tue Jul 12 02:35:43 2016 From: sebastien.moretti at unil.ch (Sebastien Moretti) Date: Tue, 12 Jul 2016 10:35:43 +0200 Subject: [maker-devel] Installation in a custom directory Message-ID: Hi I try to install maker in a custom directory following regular Perl commands with Build.PL. Unfortunately if I use perl Build.PL --installdirs= then ./Build install --destdir= build install fails with the error: Can't use an undefined value as a HASH reference at .../Module/Build/Base.pm line 3038. It does not happen if I don't use --installdirs Is there an "official" way to install maker in a custom directory? Also I found typos in the description of maker at http://www.yandell-lab.org/software/maker.html ouputs should be outputs seusequent should be ??? maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 Regards -- S?bastien Moretti Staff Scientist SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.org/ From carsonhh at gmail.com Mon Jul 18 08:48:28 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:48:28 -0600 Subject: [maker-devel] Installation in a custom directory In-Reply-To: References: Message-ID: <9A2E906F-F0B9-4CB3-9C18-CA57F4213D55@gmail.com> MAKER will by default put executables in ?/maker/bin. You should put ?/maker/bin into your PATH. The maker Build.PL is configured to install things in a set directory configuration to properly locate perl libraries, C shared objects, and data files. ?Carson > On Jul 12, 2016, at 2:35 AM, Sebastien Moretti wrote: > > Hi > > I try to install maker in a custom directory following regular Perl > commands with Build.PL. > > Unfortunately if I use > perl Build.PL --installdirs= > then > ./Build install --destdir= > build install fails with the error: > Can't use an undefined value as a HASH reference at > .../Module/Build/Base.pm line 3038. > > It does not happen if I don't use --installdirs > > > Is there an "official" way to install maker in a custom directory? > > > Also I found typos in the description of maker at > http://www.yandell-lab.org/software/maker.html > ouputs should be outputs > seusequent should be ??? > > > maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 > > Regards > > -- > S?bastien Moretti > Staff Scientist > SIB Vital-IT EMBnet, Quartier Sorge - Genopode > CH-1015 Lausanne, Switzerland > Tel.: +41 (21) 692 4079/4221 > http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.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 Jul 18 08:53:09 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:53:09 -0600 Subject: [maker-devel] maker problem In-Reply-To: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson > On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: > > Hello, > > When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. > > Here is a part of main error log: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Can't get HSPs: data not collected. > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 > STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 > STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 > STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 > STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 > STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 > STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > ERROR: Failed while collecting blastx reports > ERROR: Chunk failed at level:9, tier_type:3 > FAILED CONTIG:QPacbio.Hiseq_683 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:QPacbio.Hiseq_683 > > examining contents of the fasta file and run log > Thanks! > > Best regards, > Ian > Department of Entomology, College of Plant Protection, Nanjing Agricultural University > No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 08:55:29 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:55:29 -0600 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: <7C44D0D0-D2CE-4899-9CE5-0050A928A6E0@gmail.com> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk. This will cause IO errors and partial result files because the operations done in TMP are not NFS safe. Thanks, Carson > On Jul 15, 2016, at 9:20 PM, Matt Simenc wrote: > > Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc > wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. > > Options I used include: > > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > > other_pass=0 > > > altest=alt_est.fasta > > > snaphmm=snap.hmm > > > trna=0 > > cpus=1 > > > clean_try=0 > > > clean_up=0 > > > > > > Below are the last 50 lines in the stderr from the failed run. > > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > > examining contents of the fasta file and run log > > > > --Next Contig-- > > > > Processing run.log file... > > MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > > Maker is now finished!!! > > > > > > Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 09:03:08 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:03:08 -0600 Subject: [maker-devel] maker problem In-Reply-To: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Message-ID: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson > On Jul 18, 2016, at 9:00 AM, Chuanlin Yin wrote: > > Thank you very much! > > I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. > > Thanks! > > Best wishes! > Ian > > 2016-07-18 > Chuanlin Yin > ????Carson Holt > > ?????2016-07-18 22:53 > ???Re: [maker-devel] maker problem > ????"Chuanlin Yin"> > ???"maker-devel"> > > The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. > > Thanks, > Carson > > >> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >> >> Hello, >> >> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >> >> Here is a part of main error log: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Can't get HSPs: data not collected. >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >> ----------------------------------------------------------- >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> ERROR: Failed while collecting blastx reports >> ERROR: Chunk failed at level:9, tier_type:3 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> ERROR: Chunk failed at level:4, tier_type:0 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> examining contents of the fasta file and run log >> Thanks! >> >> Best regards, >> Ian >> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >> >> >> _______________________________________________ >> 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 yincl2013 at 126.com Mon Jul 18 09:00:39 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Mon, 18 Jul 2016 23:00:39 +0800 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 Chuanlin Yin ????Carson Holt ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin" ???"maker-devel" The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 carsonhh at gmail.com Mon Jul 18 09:08:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:08:11 -0600 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Also with when trying 1, 2, or 3, run just the failed contig as a separate job or the old archived files will be reused rather than regenerating following the change (because MAKER archives partial results in theVoid directory). ?Carson > On Jul 18, 2016, at 9:03 AM, Carson Holt wrote: > > 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. > 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk > > ?Carson > > >> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >> >> Thank you very much! >> >> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >> >> Thanks! >> >> Best wishes! >> Ian >> >> 2016-07-18 >> Chuanlin Yin >> ????Carson Holt > >> ?????2016-07-18 22:53 >> ???Re: [maker-devel] maker problem >> ????"Chuanlin Yin"> >> ???"maker-devel"> >> >> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >> >> Thanks, >> Carson >> >> >>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>> >>> Hello, >>> >>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>> >>> Here is a part of main error log: >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Can't get HSPs: data not collected. >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> ERROR: Failed while collecting blastx reports >>> ERROR: Chunk failed at level:9, tier_type:3 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> ERROR: Chunk failed at level:4, tier_type:0 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> examining contents of the fasta file and run log >>> Thanks! >>> >>> Best regards, >>> Ian >>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>> >>> >>> _______________________________________________ >>> 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 mcsimenc at gmail.com Mon Jul 18 09:18:38 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:18:38 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! Matt On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 09:20:34 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:34 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Oops! I meant to reply to a different thread, not this one. That last message is related to a different problem. On Mon, Jul 18, 2016 at 8:18 AM, Matt Simenc wrote: > Update: > > So I isolated a single scaffold to run MAKER on and test different > parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire > assembly. There are still some duplicates. I tried using the -a command > line option and it reduced the number of duplicate IDs for different > features by 2, but I don't know what to do. It's important if I know maker > is keeping the features in order or if it's possible maker is mixing up > exons and CDSs between different gene and mRNA features. > > Thanks! > Matt > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > >> Hi, >> >> I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I >> isolated this scaffold from my assembly after maker successfully annotated >> all other scaffolds in the assembly but failed on this one, and failed on >> successive retries. >> >> I fed this maker run a maker-generated gff from a prior successful run. >> This is the first run on which I have added transcript sequences from a >> closely related species. The only ab initio program I'm running here was >> SNAP. >> >> *Options I used include:* >> >> maker_gff=014_maker_Sacu_v1_s0008.gff >> >> est_pass=1 >> >> altest_pass=0 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> altest=alt_est.fasta >> >> snaphmm=snap.hmm >> >> trna=0 >> >> cpus=1 >> >> clean_try=0 >> >> clean_up=0 >> >> >> >> *Below are the last 50 lines in the stderr from the failed run.* >> >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> >> MSG: Can't get HSPs: data not collected. >> >> STACK: Error::throw >> >> STACK: Bio::Root::Root::throw >> /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 >> >> STACK: Bio::Search::Hit::PhatHit::Base::hsps >> /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> >> STACK: Widget::tblastx::keepers >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 >> >> STACK: Widget::tblastx::parse >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 >> >> STACK: GI::reblast_merged_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:469 >> >> STACK: GI::merge_resolve_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:289 >> >> STACK: Process::MpiChunk::_go >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 >> >> STACK: Process::MpiChunk::run >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 >> >> STACK: /share/apps/genomics/maker/bin/maker:979 >> >> ----------------------------------------------------------- >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> ERROR: Failed while collecting tblastx reports >> >> ERROR: Chunk failed at level:5, tier_type:3 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> ERROR: Chunk failed at level:4, tier_type:0 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> examining contents of the fasta file and run log >> >> >> --Next Contig-- >> >> >> Processing run.log file... >> >> MAKER WARNING: The file >> Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> did not finish on the last run and must be erased >> >> >> Maker is now finished!!! >> >> >> >> Any help would be appreciated, please let me know if any other >> information about this run would be helpful in diagnosing the problem(s). >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 09:20:44 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:44 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that > set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > >> I have been using MAKER to iteratively update previous run's annotations >> by running ab initios with fresh training and feeding the previous run's >> GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> Along the way it seems that non-identical features with the same name, >> some covering the same region and some not, accumulate. When I use >> fasta_merge -d ...index.log I get sequences for the duplicates. Am I using >> the control file options incorrectly? Any suggestions how to select final >> models? Or should I redo the runs if I had some settings wrong? >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log >> showing duplicate models: >> >> ------------------------------------- >> >> *Sacu_v1_s0077 maker gene 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* >> >> *Sacu_v1_s0077 maker mRNA 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> *Sacu_v1_s0077 maker gene 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* >> >> *Sacu_v1_s0077 maker mRNA 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* >> >> >> >> >> *Sacu_v1_s0004 maker gene 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* >> >> *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> *Sacu_v1_s0004 maker gene 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* >> >> *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . >> ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 09:29:54 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:29:54 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. ?Carson > On Jul 18, 2016, at 9:20 AM, Matt Simenc wrote: > > Update: > > So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. > > Thanks! > > On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: > I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > > Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? > > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: > > ------------------------------------- > > Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 > > Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 > > Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 > > > Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 > > > > > > > > Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 > > Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > > > Thanks! > > Matt > > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 09:35:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:35:40 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> References: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Message-ID: <3A0272F5-F6C3-4546-BF5F-E859C191713C@gmail.com> Also from your previous STDERR log you have /state/partition1/ set as your TMP directory. If that is a network mounted location, then you can get duplicate writes from separate threads to output files because of failed locks. The TMP directory should normally be set to /tmp as it is usually a locally mounted disk that will be independent and inaccessible to other nodes. Duplicate entries are often a sign of this type of IO error, especially if there is a certain degree of randomness to who gets duplicated. ?Carson > On Jul 18, 2016, at 9:29 AM, Carson Holt wrote: > > Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. > > Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. > > Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. > > ?Carson > > > > >> On Jul 18, 2016, at 9:20 AM, Matt Simenc > wrote: >> >> Update: >> >> So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. >> >> However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. >> >> Thanks! >> >> On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: >> Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. >> >> Matt >> >> On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: >> I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> >> Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? >> >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: >> >> ------------------------------------- >> >> Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 >> >> Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 >> >> >> Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 >> >> >> >> >> >> >> >> Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 >> >> Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> >> >> Thanks! >> >> Matt >> >> >> >> _______________________________________________ >> 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 cjfields at illinois.edu Mon Jul 18 11:46:52 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 18 Jul 2016 17:46:52 +0000 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. chris 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 ________________________________ Chuanlin Yin ________________________________ ????Carson Holt > ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin"> ???"maker-devel"> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 11:58:46 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 11:58:46 -0600 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Nothing specific I?m aware. Their error is occurring immediately following the blast report parse. The hit is defined, but the hash key of the object holding the HSPs is not defined. Half the time I see an error that come up through the BioPerl Bio::Root::Root::throw mechanism it goes away when the user installs the current CPAN version of BioPerl (they either have really old BioPerl or are using the live version). So I always have the user check that first. The other half of the time it ends up being an IO error (truncated file because they used NFS for temporary file space). Truncated can cause failures in multiple ways. Then less often it is a blast issue (there are a handful of subversions of blast+ that give frequent failures). ?Carson > On Jul 18, 2016, at 11:46 AM, Fields, Christopher J wrote: > > >> On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: >> >> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > > Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. > > chris > >> 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. >> 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk >> >> ?Carson >> >> >>> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >>> >>> Thank you very much! >>> >>> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >>> >>> Thanks! >>> >>> Best wishes! >>> Ian >>> >>> 2016-07-18 >>> Chuanlin Yin >>> ????Carson Holt > >>> ?????2016-07-18 22:53 >>> ???Re: [maker-devel] maker problem >>> ????"Chuanlin Yin"> >>> ???"maker-devel"> >>> >>> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >>> >>> Thanks, >>> Carson >>> >>> >>>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>>> >>>> Hello, >>>> >>>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>>> >>>> Here is a part of main error log: >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Can't get HSPs: data not collected. >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> ERROR: Failed while collecting blastx reports >>>> ERROR: Chunk failed at level:9, tier_type:3 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> examining contents of the fasta file and run log >>>> Thanks! >>>> >>>> Best regards, >>>> Ian >>>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>>> >>>> >>>> _______________________________________________ >>>> 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Victor.Rossier at unil.ch Mon Jul 4 09:38:40 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Mon, 4 Jul 2016 15:38:40 +0000 Subject: [maker-devel] Fasta index error Message-ID: <1467646720155.98154@unil.ch> Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jul 5 08:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:14 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <1467646720155.98154@unil.ch> References: <1467646720155.98154@unil.ch> Message-ID: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson > On Jul 4, 2016, at 9:38 AM, Victor Rossier wrote: > > Dear Maker, > > I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. > > Here is the error I get: > > WARNING: Cannot find >0, trying to re-index the fasta. > stop here:0 > ERROR: Fasta index error > at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. > GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 > Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 > eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 > Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 > Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 > Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 > --> rank=16, hostname=dee-serv04.vital-it.ch > ERROR: Failed while polishing alt-ESTs > ERROR: Chunk failed at level:6, tier_type:3 > FAILED CONTIG:scaffold52256_cov106 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:scaffold52256_cov106 > > Any thought how to solve this? > > Thanks in advance, > Victor Rossier > _______________________________________________ > 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 carsonhh at gmail.com Tue Jul 5 08:29:48 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:48 -0600 Subject: [maker-devel] Alternative genetic code In-Reply-To: <5773950C.8030102@icm.uu.se> References: <5773950C.8030102@icm.uu.se> Message-ID: <1D1B5FA1-E05E-49A9-BCEB-A4A859067CFE@gmail.com> Currently there is no support for alternate codon usage. ?Carson > On Jun 29, 2016, at 3:29 AM, Courtney Stairs wrote: > > Hello there, > > I noticed on the google group that someone has asked about using an alternative genetic code with Maker. Has such a function been implemented on the newer versions of Maker? I understand that this is not a straight-forward task. I am interested in using Maker on a genome that using code 6. > > Thank you very much for your time, > > Courtney > > -- > ------------------------------------ > Courtney Stairs, PhD > Post-doctoral fellow > Laboratory of Dr. Thijs Ettema > Institute for Cell and Molecular Biology > Uppsala University > Sweden > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From cjfields at illinois.edu Wed Jul 6 06:16:56 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 6 Jul 2016 12:16:56 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> Message-ID: I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Wed Jul 6 19:02:10 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: Thu, 07 Jul 2016 02:02:10 +0100 Subject: [maker-devel] Local representation needed Message-ID: <577DAA12.8050601@yandell-lab.org> Hello I am the personnel department manager and I am appealing to you in the name of the large-scale and first-rate partnership. Our company is engaged in different areas of activity, such as: - realtor - establishment and disestablishment of enterprises - bank account establishment and maintanance - logistics - private business support - etc. We are making a regional managers’ team now: - salary $4.600 + bonus - 1 - 2 working hours per day - flextime If you would like to be a regional manager visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Thu Jul 7 08:20:04 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: 7 Jul 2016 18:20:04 +0400 Subject: [maker-devel] Greetings Message-ID: <004601d1d85f$04bf9090$77bd7c9f$@yandell-lab.org> Compliments I’m addressing you on behalf of the HR department of a large company. Our company is engaged in different areas of activity, such as: - real estate - accounts opening - undertaking services - etc. There are vacant positions of regional managers: - salary $5.300 + bonus - underemployment - individual time-table If you would like to work with us, please provide us your contact information on visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 08:09:31 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 14:09:31 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <1467890724600.33833@unil.ch> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> Message-ID: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 10:17:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 10:17:11 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Message-ID: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson > On Jul 7, 2016, at 8:09 AM, Fields, Christopher J wrote: > > Victor, > > Can you post which version of MAKER you are using? > > chris > > >> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >> >> Thanks for the quick replies, >> >> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >> >> I renamed all transcripts and maker finished correctly! >> >> Thanks again, >> Victor Rossier >> >> De : Fields, Christopher J > >> Envoy? : mercredi 6 juillet 2016 14:16 >> ? : Carson Holt >> Cc : Victor Rossier; maker-devel at yandell-lab.org >> Objet : Re: [maker-devel] Fasta index error >> >> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >> >> chris >> >>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>> >>> You need to rename the contig. It is currently named 0 >>> >>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>> >>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>> >>> ?Carson >>> >>> >>> >>> >>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>> >>>> Dear Maker, >>>> >>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>> >>>> Here is the error I get: >>>> >>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>> stop here:0 >>>> ERROR: Fasta index error >>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>> ERROR: Failed while polishing alt-ESTs >>>> ERROR: Chunk failed at level:6, tier_type:3 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> Any thought how to solve this? >>>> >>>> Thanks in advance, >>>> Victor Rossier >>>> _______________________________________________ >>>> 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 >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 12:43:27 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 18:43:27 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> Message-ID: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 13:08:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 13:08:40 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson > On Jul 7, 2016, at 12:43 PM, Fields, Christopher J wrote: > > Easy enough to figure out when it snuck in: > > https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 > > Seems like it may have been in there a while. > > chris > >> On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: >> >> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? >> >> This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. >> >> ?Carson >> >> >> >>> On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: >>> >>> Victor, >>> >>> Can you post which version of MAKER you are using? >>> >>> chris >>> >>> >>>> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >>>> >>>> Thanks for the quick replies, >>>> >>>> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >>>> >>>> I renamed all transcripts and maker finished correctly! >>>> >>>> Thanks again, >>>> Victor Rossier >>>> >>>> De : Fields, Christopher J > >>>> Envoy? : mercredi 6 juillet 2016 14:16 >>>> ? : Carson Holt >>>> Cc : Victor Rossier; maker-devel at yandell-lab.org >>>> Objet : Re: [maker-devel] Fasta index error >>>> >>>> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >>>> >>>> chris >>>> >>>>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>>>> >>>>> You need to rename the contig. It is currently named 0 >>>>> >>>>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>>>> >>>>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>>>> >>>>> ?Carson >>>>> >>>>> >>>>> >>>>> >>>>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>>>> >>>>>> Dear Maker, >>>>>> >>>>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>>>> >>>>>> Here is the error I get: >>>>>> >>>>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>>>> stop here:0 >>>>>> ERROR: Fasta index error >>>>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>>>> ERROR: Failed while polishing alt-ESTs >>>>>> ERROR: Chunk failed at level:6, tier_type:3 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> ERROR: Chunk failed at level:4, tier_type:0 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> Any thought how to solve this? >>>>>> >>>>>> Thanks in advance, >>>>>> Victor Rossier >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From o.k.torresen at ibv.uio.no Thu Jul 7 15:29:54 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:29:54 +0000 Subject: [maker-devel] Fragmented annotation Message-ID: Hi all, I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. Thank you. Ole From dence at genetics.utah.edu Thu Jul 7 15:44:14 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:44:14 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: Message-ID: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > 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 Thu Jul 7 15:48:21 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:48:21 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 o.k.torresen at ibv.uio.no Thu Jul 7 15:55:01 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:55:01 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: , <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: <1467928535428.94166@ibv.uio.no> Hi Daniel, thank you for your prompt answer. I've created a repeat library using this approach: https://github.com/uio-cels/Repeats, which I hope is quite thorough, and used that in the annotation. I guess I could do model_org=all in addition. I guess I could and should look at bit more at the annotation in a genome browser, but it is hard to diagnosis something like this without knowing where to start. Thank you. Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:44 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From o.k.torresen at ibv.uio.no Thu Jul 7 15:56:39 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:56:39 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu>, Message-ID: <1467928633373.20514@ibv.uio.no> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:48 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 carsonhh at gmail.com Thu Jul 7 16:12:23 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 16:12:23 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: <8B6B4EA9-FE7E-443E-9B42-6110D93AACA1@gmail.com> Try the maker2eval_gtf script. It converts to GTF and adds explicit start/stop codons. ?Carson > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 From dence at genetics.utah.edu Thu Jul 7 16:13:18 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 22:13:18 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 o.k.torresen at ibv.uio.no Sat Jul 9 14:50:37 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Sat, 9 Jul 2016 20:50:37 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no>, Message-ID: <1468097477192.77639@ibv.uio.no> Daniel, Carson, I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. I guess the length of the genes/proteins could also be a factor I could look into. If the annotation would have been/is fragmented, what options could I try to tune? Thank you. Ole ________________________________________ From: Daniel Ence Sent: 08 July 2016 00:13 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 carsonhh at gmail.com Mon Jul 11 11:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 11 Jul 2016 11:29:14 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1468097477192.77639@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> <1468097477192.77639@ibv.uio.no> Message-ID: <953FC580-9A1D-4905-8E79-B98815BF5DDB@gmail.com> Most likely culprit is still that you have not properly masked repeats. Repeats encode real proteins (i.e. reverse transcriptase, etc.). So if they are not all masked they will be annotated as genes with start and stop codons. ?Carson > On Jul 9, 2016, at 2:50 PM, Ole Kristian T?rresen wrote: > > Daniel, Carson, > I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. > > I guess the length of the genes/proteins could also be a factor I could look into. > > If the annotation would have been/is fragmented, what options could I try to tune? > > Thank you. > > Ole > ________________________________________ > From: Daniel Ence > Sent: 08 July 2016 00:13 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. > > This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. > > ~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 > >> On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: >> >> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? >> >> Ole >> ________________________________________ >> From: Daniel Ence >> Sent: 07 July 2016 23:48 >> To: Ole Kristian T?rresen >> Cc: maker-devel at yandell-lab.org >> Subject: Re: [maker-devel] Fragmented annotation >> >> Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. >> >> ~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 >> >>> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >>> >>> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >>> >>> ~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 >>> >>>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>>> >>>> Hi all, >>>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>>> >>>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>>> >>>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>>> >>>> Thank you. >>>> >>>> Ole >>>> _______________________________________________ >>>> 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 From Victor.Rossier at unil.ch Thu Jul 7 05:25:24 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Thu, 7 Jul 2016 11:25:24 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> , Message-ID: <1467890724600.33833@unil.ch> Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I'll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it's the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. -Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Fri Jul 8 12:09:21 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 8 Jul 2016 18:09:21 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: It?s not terribly often sequence IDs are that short (let alone 0), though I could see it happening with raw assembler output. Usually we rename the seqs to something else. I?m still not terribly happy about the stringification overload but removing it would likely break things in terrible obscene ways (I found this out the hard way removing this behavior from the developer ontology modules). chris On Jul 7, 2016, at 2:08 PM, Carson Holt > wrote: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson On Jul 7, 2016, at 12:43 PM, Fields, Christopher J > wrote: Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 18:52:05 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 17:52:05 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Hi, I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. *Options I used include:* maker_gff=014_maker_Sacu_v1_s0008.gff est_pass=1 altest_pass=0 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 altest=alt_est.fasta snaphmm=snap.hmm trna=0 cpus=1 clean_try=0 clean_up=0 *Below are the last 50 lines in the stderr from the failed run.* running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ tblastx.pm:133 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: /share/apps/genomics/maker/bin/maker:979 ----------------------------------------------------------- --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local ERROR: Failed while collecting tblastx reports ERROR: Chunk failed at level:5, tier_type:3 FAILED CONTIG:Sacu_v1_s0008 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:Sacu_v1_s0008 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx did not finish on the last run and must be erased Maker is now finished!!! Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 21:20:43 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 20:20:43 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sat Jul 16 23:40:50 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sat, 16 Jul 2016 22:40:50 -0700 Subject: [maker-devel] MAKER output has different genes with same name Message-ID: I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: maker_gff=previous_run.gff est_pass=1 altest_pass=1 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: ------------------------------------- *Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* *Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 *Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* *Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* *Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 *Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 Here the models' headers from the maker.proteins.fasta: ------------------------------------- >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sun Jul 17 17:39:51 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sun, 17 Jul 2016 16:39:51 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. Matt On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > I have been using MAKER to iteratively update previous run's annotations > by running ab initios with fresh training and feeding the previous run's > GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > Along the way it seems that non-identical features with the same name, > some covering the same region and some not, accumulate. When I use > fasta_merge -d ...index.log I get sequences for the duplicates. Am I using > the control file options incorrectly? Any suggestions how to select final > models? Or should I redo the runs if I had some settings wrong? > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log > showing duplicate models: > > ------------------------------------- > > *Sacu_v1_s0077 maker gene 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* > > *Sacu_v1_s0077 maker mRNA 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* > > Sacu_v1_s0077 maker exon 138512 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > *Sacu_v1_s0077 maker gene 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* > > *Sacu_v1_s0077 maker mRNA 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* > > > > > *Sacu_v1_s0004 maker gene 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* > > *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > *Sacu_v1_s0004 maker gene 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* > > *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . > ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yincl2013 at 126.com Wed Jul 13 04:10:45 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Wed, 13 Jul 2016 18:10:45 +0800 Subject: [maker-devel] maker problem Message-ID: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China -------------- next part -------------- An HTML attachment was scrubbed... URL: From sebastien.moretti at unil.ch Tue Jul 12 02:35:43 2016 From: sebastien.moretti at unil.ch (Sebastien Moretti) Date: Tue, 12 Jul 2016 10:35:43 +0200 Subject: [maker-devel] Installation in a custom directory Message-ID: Hi I try to install maker in a custom directory following regular Perl commands with Build.PL. Unfortunately if I use perl Build.PL --installdirs= then ./Build install --destdir= build install fails with the error: Can't use an undefined value as a HASH reference at .../Module/Build/Base.pm line 3038. It does not happen if I don't use --installdirs Is there an "official" way to install maker in a custom directory? Also I found typos in the description of maker at http://www.yandell-lab.org/software/maker.html ouputs should be outputs seusequent should be ??? maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 Regards -- S?bastien Moretti Staff Scientist SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.org/ From carsonhh at gmail.com Mon Jul 18 08:48:28 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:48:28 -0600 Subject: [maker-devel] Installation in a custom directory In-Reply-To: References: Message-ID: <9A2E906F-F0B9-4CB3-9C18-CA57F4213D55@gmail.com> MAKER will by default put executables in ?/maker/bin. You should put ?/maker/bin into your PATH. The maker Build.PL is configured to install things in a set directory configuration to properly locate perl libraries, C shared objects, and data files. ?Carson > On Jul 12, 2016, at 2:35 AM, Sebastien Moretti wrote: > > Hi > > I try to install maker in a custom directory following regular Perl > commands with Build.PL. > > Unfortunately if I use > perl Build.PL --installdirs= > then > ./Build install --destdir= > build install fails with the error: > Can't use an undefined value as a HASH reference at > .../Module/Build/Base.pm line 3038. > > It does not happen if I don't use --installdirs > > > Is there an "official" way to install maker in a custom directory? > > > Also I found typos in the description of maker at > http://www.yandell-lab.org/software/maker.html > ouputs should be outputs > seusequent should be ??? > > > maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 > > Regards > > -- > S?bastien Moretti > Staff Scientist > SIB Vital-IT EMBnet, Quartier Sorge - Genopode > CH-1015 Lausanne, Switzerland > Tel.: +41 (21) 692 4079/4221 > http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.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 Jul 18 08:53:09 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:53:09 -0600 Subject: [maker-devel] maker problem In-Reply-To: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson > On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: > > Hello, > > When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. > > Here is a part of main error log: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Can't get HSPs: data not collected. > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 > STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 > STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 > STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 > STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 > STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 > STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > ERROR: Failed while collecting blastx reports > ERROR: Chunk failed at level:9, tier_type:3 > FAILED CONTIG:QPacbio.Hiseq_683 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:QPacbio.Hiseq_683 > > examining contents of the fasta file and run log > Thanks! > > Best regards, > Ian > Department of Entomology, College of Plant Protection, Nanjing Agricultural University > No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 08:55:29 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:55:29 -0600 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: <7C44D0D0-D2CE-4899-9CE5-0050A928A6E0@gmail.com> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk. This will cause IO errors and partial result files because the operations done in TMP are not NFS safe. Thanks, Carson > On Jul 15, 2016, at 9:20 PM, Matt Simenc wrote: > > Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc > wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. > > Options I used include: > > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > > other_pass=0 > > > altest=alt_est.fasta > > > snaphmm=snap.hmm > > > trna=0 > > cpus=1 > > > clean_try=0 > > > clean_up=0 > > > > > > Below are the last 50 lines in the stderr from the failed run. > > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > > examining contents of the fasta file and run log > > > > --Next Contig-- > > > > Processing run.log file... > > MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > > Maker is now finished!!! > > > > > > Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 09:03:08 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:03:08 -0600 Subject: [maker-devel] maker problem In-Reply-To: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Message-ID: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson > On Jul 18, 2016, at 9:00 AM, Chuanlin Yin wrote: > > Thank you very much! > > I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. > > Thanks! > > Best wishes! > Ian > > 2016-07-18 > Chuanlin Yin > ????Carson Holt > > ?????2016-07-18 22:53 > ???Re: [maker-devel] maker problem > ????"Chuanlin Yin"> > ???"maker-devel"> > > The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. > > Thanks, > Carson > > >> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >> >> Hello, >> >> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >> >> Here is a part of main error log: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Can't get HSPs: data not collected. >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >> ----------------------------------------------------------- >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> ERROR: Failed while collecting blastx reports >> ERROR: Chunk failed at level:9, tier_type:3 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> ERROR: Chunk failed at level:4, tier_type:0 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> examining contents of the fasta file and run log >> Thanks! >> >> Best regards, >> Ian >> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >> >> >> _______________________________________________ >> 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 yincl2013 at 126.com Mon Jul 18 09:00:39 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Mon, 18 Jul 2016 23:00:39 +0800 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 Chuanlin Yin ????Carson Holt ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin" ???"maker-devel" The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 carsonhh at gmail.com Mon Jul 18 09:08:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:08:11 -0600 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Also with when trying 1, 2, or 3, run just the failed contig as a separate job or the old archived files will be reused rather than regenerating following the change (because MAKER archives partial results in theVoid directory). ?Carson > On Jul 18, 2016, at 9:03 AM, Carson Holt wrote: > > 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. > 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk > > ?Carson > > >> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >> >> Thank you very much! >> >> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >> >> Thanks! >> >> Best wishes! >> Ian >> >> 2016-07-18 >> Chuanlin Yin >> ????Carson Holt > >> ?????2016-07-18 22:53 >> ???Re: [maker-devel] maker problem >> ????"Chuanlin Yin"> >> ???"maker-devel"> >> >> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >> >> Thanks, >> Carson >> >> >>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>> >>> Hello, >>> >>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>> >>> Here is a part of main error log: >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Can't get HSPs: data not collected. >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> ERROR: Failed while collecting blastx reports >>> ERROR: Chunk failed at level:9, tier_type:3 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> ERROR: Chunk failed at level:4, tier_type:0 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> examining contents of the fasta file and run log >>> Thanks! >>> >>> Best regards, >>> Ian >>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>> >>> >>> _______________________________________________ >>> 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 mcsimenc at gmail.com Mon Jul 18 09:18:38 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:18:38 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! Matt On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 09:20:34 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:34 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Oops! I meant to reply to a different thread, not this one. That last message is related to a different problem. On Mon, Jul 18, 2016 at 8:18 AM, Matt Simenc wrote: > Update: > > So I isolated a single scaffold to run MAKER on and test different > parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire > assembly. There are still some duplicates. I tried using the -a command > line option and it reduced the number of duplicate IDs for different > features by 2, but I don't know what to do. It's important if I know maker > is keeping the features in order or if it's possible maker is mixing up > exons and CDSs between different gene and mRNA features. > > Thanks! > Matt > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > >> Hi, >> >> I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I >> isolated this scaffold from my assembly after maker successfully annotated >> all other scaffolds in the assembly but failed on this one, and failed on >> successive retries. >> >> I fed this maker run a maker-generated gff from a prior successful run. >> This is the first run on which I have added transcript sequences from a >> closely related species. The only ab initio program I'm running here was >> SNAP. >> >> *Options I used include:* >> >> maker_gff=014_maker_Sacu_v1_s0008.gff >> >> est_pass=1 >> >> altest_pass=0 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> altest=alt_est.fasta >> >> snaphmm=snap.hmm >> >> trna=0 >> >> cpus=1 >> >> clean_try=0 >> >> clean_up=0 >> >> >> >> *Below are the last 50 lines in the stderr from the failed run.* >> >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> >> MSG: Can't get HSPs: data not collected. >> >> STACK: Error::throw >> >> STACK: Bio::Root::Root::throw >> /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 >> >> STACK: Bio::Search::Hit::PhatHit::Base::hsps >> /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> >> STACK: Widget::tblastx::keepers >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 >> >> STACK: Widget::tblastx::parse >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 >> >> STACK: GI::reblast_merged_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:469 >> >> STACK: GI::merge_resolve_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:289 >> >> STACK: Process::MpiChunk::_go >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 >> >> STACK: Process::MpiChunk::run >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 >> >> STACK: /share/apps/genomics/maker/bin/maker:979 >> >> ----------------------------------------------------------- >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> ERROR: Failed while collecting tblastx reports >> >> ERROR: Chunk failed at level:5, tier_type:3 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> ERROR: Chunk failed at level:4, tier_type:0 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> examining contents of the fasta file and run log >> >> >> --Next Contig-- >> >> >> Processing run.log file... >> >> MAKER WARNING: The file >> Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> did not finish on the last run and must be erased >> >> >> Maker is now finished!!! >> >> >> >> Any help would be appreciated, please let me know if any other >> information about this run would be helpful in diagnosing the problem(s). >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 09:20:44 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:44 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that > set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > >> I have been using MAKER to iteratively update previous run's annotations >> by running ab initios with fresh training and feeding the previous run's >> GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> Along the way it seems that non-identical features with the same name, >> some covering the same region and some not, accumulate. When I use >> fasta_merge -d ...index.log I get sequences for the duplicates. Am I using >> the control file options incorrectly? Any suggestions how to select final >> models? Or should I redo the runs if I had some settings wrong? >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log >> showing duplicate models: >> >> ------------------------------------- >> >> *Sacu_v1_s0077 maker gene 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* >> >> *Sacu_v1_s0077 maker mRNA 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> *Sacu_v1_s0077 maker gene 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* >> >> *Sacu_v1_s0077 maker mRNA 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* >> >> >> >> >> *Sacu_v1_s0004 maker gene 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* >> >> *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> *Sacu_v1_s0004 maker gene 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* >> >> *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . >> ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 09:29:54 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:29:54 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. ?Carson > On Jul 18, 2016, at 9:20 AM, Matt Simenc wrote: > > Update: > > So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. > > Thanks! > > On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: > I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > > Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? > > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: > > ------------------------------------- > > Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 > > Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 > > Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 > > > Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 > > > > > > > > Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 > > Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > > > Thanks! > > Matt > > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 09:35:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:35:40 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> References: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Message-ID: <3A0272F5-F6C3-4546-BF5F-E859C191713C@gmail.com> Also from your previous STDERR log you have /state/partition1/ set as your TMP directory. If that is a network mounted location, then you can get duplicate writes from separate threads to output files because of failed locks. The TMP directory should normally be set to /tmp as it is usually a locally mounted disk that will be independent and inaccessible to other nodes. Duplicate entries are often a sign of this type of IO error, especially if there is a certain degree of randomness to who gets duplicated. ?Carson > On Jul 18, 2016, at 9:29 AM, Carson Holt wrote: > > Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. > > Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. > > Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. > > ?Carson > > > > >> On Jul 18, 2016, at 9:20 AM, Matt Simenc > wrote: >> >> Update: >> >> So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. >> >> However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. >> >> Thanks! >> >> On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: >> Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. >> >> Matt >> >> On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: >> I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> >> Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? >> >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: >> >> ------------------------------------- >> >> Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 >> >> Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 >> >> >> Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 >> >> >> >> >> >> >> >> Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 >> >> Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> >> >> Thanks! >> >> Matt >> >> >> >> _______________________________________________ >> 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 cjfields at illinois.edu Mon Jul 18 11:46:52 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 18 Jul 2016 17:46:52 +0000 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. chris 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 ________________________________ Chuanlin Yin ________________________________ ????Carson Holt > ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin"> ???"maker-devel"> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 11:58:46 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 11:58:46 -0600 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Nothing specific I?m aware. Their error is occurring immediately following the blast report parse. The hit is defined, but the hash key of the object holding the HSPs is not defined. Half the time I see an error that come up through the BioPerl Bio::Root::Root::throw mechanism it goes away when the user installs the current CPAN version of BioPerl (they either have really old BioPerl or are using the live version). So I always have the user check that first. The other half of the time it ends up being an IO error (truncated file because they used NFS for temporary file space). Truncated can cause failures in multiple ways. Then less often it is a blast issue (there are a handful of subversions of blast+ that give frequent failures). ?Carson > On Jul 18, 2016, at 11:46 AM, Fields, Christopher J wrote: > > >> On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: >> >> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > > Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. > > chris > >> 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. >> 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk >> >> ?Carson >> >> >>> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >>> >>> Thank you very much! >>> >>> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >>> >>> Thanks! >>> >>> Best wishes! >>> Ian >>> >>> 2016-07-18 >>> Chuanlin Yin >>> ????Carson Holt > >>> ?????2016-07-18 22:53 >>> ???Re: [maker-devel] maker problem >>> ????"Chuanlin Yin"> >>> ???"maker-devel"> >>> >>> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >>> >>> Thanks, >>> Carson >>> >>> >>>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>>> >>>> Hello, >>>> >>>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>>> >>>> Here is a part of main error log: >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Can't get HSPs: data not collected. >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> ERROR: Failed while collecting blastx reports >>>> ERROR: Chunk failed at level:9, tier_type:3 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> examining contents of the fasta file and run log >>>> Thanks! >>>> >>>> Best regards, >>>> Ian >>>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>>> >>>> >>>> _______________________________________________ >>>> 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Victor.Rossier at unil.ch Mon Jul 4 09:38:40 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Mon, 4 Jul 2016 15:38:40 +0000 Subject: [maker-devel] Fasta index error Message-ID: <1467646720155.98154@unil.ch> Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Tue Jul 5 08:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:14 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <1467646720155.98154@unil.ch> References: <1467646720155.98154@unil.ch> Message-ID: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson > On Jul 4, 2016, at 9:38 AM, Victor Rossier wrote: > > Dear Maker, > > I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. > > Here is the error I get: > > WARNING: Cannot find >0, trying to re-index the fasta. > stop here:0 > ERROR: Fasta index error > at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. > GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 > Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 > eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 > Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 > Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 > Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 > --> rank=16, hostname=dee-serv04.vital-it.ch > ERROR: Failed while polishing alt-ESTs > ERROR: Chunk failed at level:6, tier_type:3 > FAILED CONTIG:scaffold52256_cov106 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:scaffold52256_cov106 > > Any thought how to solve this? > > Thanks in advance, > Victor Rossier > _______________________________________________ > 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 carsonhh at gmail.com Tue Jul 5 08:29:48 2016 From: carsonhh at gmail.com (Carson Holt) Date: Tue, 5 Jul 2016 08:29:48 -0600 Subject: [maker-devel] Alternative genetic code In-Reply-To: <5773950C.8030102@icm.uu.se> References: <5773950C.8030102@icm.uu.se> Message-ID: <1D1B5FA1-E05E-49A9-BCEB-A4A859067CFE@gmail.com> Currently there is no support for alternate codon usage. ?Carson > On Jun 29, 2016, at 3:29 AM, Courtney Stairs wrote: > > Hello there, > > I noticed on the google group that someone has asked about using an alternative genetic code with Maker. Has such a function been implemented on the newer versions of Maker? I understand that this is not a straight-forward task. I am interested in using Maker on a genome that using code 6. > > Thank you very much for your time, > > Courtney > > -- > ------------------------------------ > Courtney Stairs, PhD > Post-doctoral fellow > Laboratory of Dr. Thijs Ettema > Institute for Cell and Molecular Biology > Uppsala University > Sweden > > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From cjfields at illinois.edu Wed Jul 6 06:16:56 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 6 Jul 2016 12:16:56 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> Message-ID: I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Wed Jul 6 19:02:10 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: Thu, 07 Jul 2016 02:02:10 +0100 Subject: [maker-devel] Local representation needed Message-ID: <577DAA12.8050601@yandell-lab.org> Hello I am the personnel department manager and I am appealing to you in the name of the large-scale and first-rate partnership. Our company is engaged in different areas of activity, such as: - realtor - establishment and disestablishment of enterprises - bank account establishment and maintanance - logistics - private business support - etc. We are making a regional managers’ team now: - salary $4.600 + bonus - 1 - 2 working hours per day - flextime If you would like to be a regional manager visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From maker-devel at yandell-lab.org Thu Jul 7 08:20:04 2016 From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org) Date: 7 Jul 2016 18:20:04 +0400 Subject: [maker-devel] Greetings Message-ID: <004601d1d85f$04bf9090$77bd7c9f$@yandell-lab.org> Compliments I’m addressing you on behalf of the HR department of a large company. Our company is engaged in different areas of activity, such as: - real estate - accounts opening - undertaking services - etc. There are vacant positions of regional managers: - salary $5.300 + bonus - underemployment - individual time-table If you would like to work with us, please provide us your contact information on visit our web page. -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 08:09:31 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 14:09:31 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <1467890724600.33833@unil.ch> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> Message-ID: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 10:17:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 10:17:11 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> Message-ID: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson > On Jul 7, 2016, at 8:09 AM, Fields, Christopher J wrote: > > Victor, > > Can you post which version of MAKER you are using? > > chris > > >> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >> >> Thanks for the quick replies, >> >> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >> >> I renamed all transcripts and maker finished correctly! >> >> Thanks again, >> Victor Rossier >> >> De : Fields, Christopher J > >> Envoy? : mercredi 6 juillet 2016 14:16 >> ? : Carson Holt >> Cc : Victor Rossier; maker-devel at yandell-lab.org >> Objet : Re: [maker-devel] Fasta index error >> >> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >> >> chris >> >>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>> >>> You need to rename the contig. It is currently named 0 >>> >>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>> >>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>> >>> ?Carson >>> >>> >>> >>> >>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>> >>>> Dear Maker, >>>> >>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>> >>>> Here is the error I get: >>>> >>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>> stop here:0 >>>> ERROR: Fasta index error >>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>> ERROR: Failed while polishing alt-ESTs >>>> ERROR: Chunk failed at level:6, tier_type:3 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:scaffold52256_cov106 >>>> >>>> Any thought how to solve this? >>>> >>>> Thanks in advance, >>>> Victor Rossier >>>> _______________________________________________ >>>> 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 >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Thu Jul 7 12:43:27 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Thu, 7 Jul 2016 18:43:27 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> Message-ID: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu Jul 7 13:08:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 13:08:40 -0600 Subject: [maker-devel] Fasta index error In-Reply-To: <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson > On Jul 7, 2016, at 12:43 PM, Fields, Christopher J wrote: > > Easy enough to figure out when it snuck in: > > https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 > > Seems like it may have been in there a while. > > chris > >> On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: >> >> I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? >> >> This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. >> >> ?Carson >> >> >> >>> On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: >>> >>> Victor, >>> >>> Can you post which version of MAKER you are using? >>> >>> chris >>> >>> >>>> On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: >>>> >>>> Thanks for the quick replies, >>>> >>>> It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. >>>> >>>> I renamed all transcripts and maker finished correctly! >>>> >>>> Thanks again, >>>> Victor Rossier >>>> >>>> De : Fields, Christopher J > >>>> Envoy? : mercredi 6 juillet 2016 14:16 >>>> ? : Carson Holt >>>> Cc : Victor Rossier; maker-devel at yandell-lab.org >>>> Objet : Re: [maker-devel] Fasta index error >>>> >>>> I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. >>>> >>>> chris >>>> >>>>> On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: >>>>> >>>>> You need to rename the contig. It is currently named 0 >>>>> >>>>> The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. >>>>> >>>>> You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. >>>>> >>>>> ?Carson >>>>> >>>>> >>>>> >>>>> >>>>>> On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: >>>>>> >>>>>> Dear Maker, >>>>>> >>>>>> I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. >>>>>> >>>>>> Here is the error I get: >>>>>> >>>>>> WARNING: Cannot find >0, trying to re-index the fasta. >>>>>> stop here:0 >>>>>> ERROR: Fasta index error >>>>>> at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. >>>>>> GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 >>>>>> Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 >>>>>> eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 >>>>>> Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 >>>>>> Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 >>>>>> Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 >>>>>> --> rank=16, hostname=dee-serv04.vital-it.ch >>>>>> ERROR: Failed while polishing alt-ESTs >>>>>> ERROR: Chunk failed at level:6, tier_type:3 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> ERROR: Chunk failed at level:4, tier_type:0 >>>>>> FAILED CONTIG:scaffold52256_cov106 >>>>>> >>>>>> Any thought how to solve this? >>>>>> >>>>>> Thanks in advance, >>>>>> Victor Rossier >>>>>> _______________________________________________ >>>>>> 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 >>>> >>>> >>> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From o.k.torresen at ibv.uio.no Thu Jul 7 15:29:54 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:29:54 +0000 Subject: [maker-devel] Fragmented annotation Message-ID: Hi all, I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. Thank you. Ole From dence at genetics.utah.edu Thu Jul 7 15:44:14 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:44:14 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: Message-ID: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > 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 Thu Jul 7 15:48:21 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 21:48:21 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 o.k.torresen at ibv.uio.no Thu Jul 7 15:55:01 2016 From: o.k.torresen at ibv.uio.no (=?iso-8859-1?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:55:01 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> References: , <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> Message-ID: <1467928535428.94166@ibv.uio.no> Hi Daniel, thank you for your prompt answer. I've created a repeat library using this approach: https://github.com/uio-cels/Repeats, which I hope is quite thorough, and used that in the annotation. I guess I could do model_org=all in addition. I guess I could and should look at bit more at the annotation in a genome browser, but it is hard to diagnosis something like this without knowing where to start. Thank you. Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:44 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? ~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 > On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: > > Hi all, > I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. > > However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? > > I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. > > Thank you. > > Ole > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From o.k.torresen at ibv.uio.no Thu Jul 7 15:56:39 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Thu, 7 Jul 2016 21:56:39 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu>, Message-ID: <1467928633373.20514@ibv.uio.no> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? Ole ________________________________________ From: Daniel Ence Sent: 07 July 2016 23:48 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. ~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 > On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: > > Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? > > ~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 > >> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >> >> Hi all, >> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >> >> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >> >> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >> >> Thank you. >> >> Ole >> _______________________________________________ >> 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 carsonhh at gmail.com Thu Jul 7 16:12:23 2016 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 7 Jul 2016 16:12:23 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: <8B6B4EA9-FE7E-443E-9B42-6110D93AACA1@gmail.com> Try the maker2eval_gtf script. It converts to GTF and adds explicit start/stop codons. ?Carson > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 From dence at genetics.utah.edu Thu Jul 7 16:13:18 2016 From: dence at genetics.utah.edu (Daniel Ence) Date: Thu, 7 Jul 2016 22:13:18 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1467928633373.20514@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> Message-ID: That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 o.k.torresen at ibv.uio.no Sat Jul 9 14:50:37 2016 From: o.k.torresen at ibv.uio.no (=?Windows-1252?Q?Ole_Kristian_T=F8rresen?=) Date: Sat, 9 Jul 2016 20:50:37 +0000 Subject: [maker-devel] Fragmented annotation In-Reply-To: References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no>, Message-ID: <1468097477192.77639@ibv.uio.no> Daniel, Carson, I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. I guess the length of the genes/proteins could also be a factor I could look into. If the annotation would have been/is fragmented, what options could I try to tune? Thank you. Ole ________________________________________ From: Daniel Ence Sent: 08 July 2016 00:13 To: Ole Kristian T?rresen Cc: maker-devel at yandell-lab.org Subject: Re: [maker-devel] Fragmented annotation That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. ~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 > On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: > > Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? > > Ole > ________________________________________ > From: Daniel Ence > Sent: 07 July 2016 23:48 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. > > ~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 > >> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >> >> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >> >> ~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 >> >>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>> >>> Hi all, >>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>> >>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>> >>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>> >>> Thank you. >>> >>> Ole >>> _______________________________________________ >>> 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 carsonhh at gmail.com Mon Jul 11 11:29:14 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 11 Jul 2016 11:29:14 -0600 Subject: [maker-devel] Fragmented annotation In-Reply-To: <1468097477192.77639@ibv.uio.no> References: <229CC642-8B16-493A-92F2-36247A89B780@genetics.utah.edu> <1467928633373.20514@ibv.uio.no> <1468097477192.77639@ibv.uio.no> Message-ID: <953FC580-9A1D-4905-8E79-B98815BF5DDB@gmail.com> Most likely culprit is still that you have not properly masked repeats. Repeats encode real proteins (i.e. reverse transcriptase, etc.). So if they are not all masked they will be annotated as genes with start and stop codons. ?Carson > On Jul 9, 2016, at 2:50 PM, Ole Kristian T?rresen wrote: > > Daniel, Carson, > I haven't been able to spend much time on this yet, but a quick gft conversion shows that with 96576 genes, 91089 has a stop codon, and 91984 a start codon. > > I guess the length of the genes/proteins could also be a factor I could look into. > > If the annotation would have been/is fragmented, what options could I try to tune? > > Thank you. > > Ole > ________________________________________ > From: Daniel Ence > Sent: 08 July 2016 00:13 > To: Ole Kristian T?rresen > Cc: maker-devel at yandell-lab.org > Subject: Re: [maker-devel] Fragmented annotation > > That?s what I was thinking. If you have the fasta files of the transcripts, then you can do a fast pattern match on the beginning and end of each sequence. > > This is also the kind of thing that can quickly become clear in a browser like you already suggested. In the old desktop Apollo genome browser, incomplete genes were highlighted with orange arrows. I don?t know how other browsers handle that. > > ~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 > >> On Jul 7, 2016, at 3:56 PM, Ole Kristian T?rresen wrote: >> >> Sure, but is there a quick way of doing this? With UTRs and such, I am unsure how to parse the gff properly. Three first bases of each CDS for each gene, or something like that? And the three last for the last CDS for a gene? >> >> Ole >> ________________________________________ >> From: Daniel Ence >> Sent: 07 July 2016 23:48 >> To: Ole Kristian T?rresen >> Cc: maker-devel at yandell-lab.org >> Subject: Re: [maker-devel] Fragmented annotation >> >> Addressing your suspicion that your genes are fragmented, can you check how many of the protein or transcript sequeces begin and end with canonical start and stop codons? That might tell you whether you have ?gene-parts? rather than full genes. >> >> ~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 >> >>> On Jul 7, 2016, at 3:44 PM, Daniel Ence wrote: >>> >>> Hi Ole, when I hear that a genome had too many genes annotated, one of the first things I think of is masking repetitive elements in the genome. Those can contribute a large number of spurious gene annotations which are originating from transposable elements. What did you use for repeat masking for your genome? Did you run MAKER on a pre-masked version of the assembly? >>> >>> ~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 >>> >>>> On Jul 7, 2016, at 3:29 PM, Ole Kristian T?rresen wrote: >>>> >>>> Hi all, >>>> I have annotated a fish genome (about 700 Mbp total, 90 kbp N50 contig, 270 kbp N50 scaffold), where I get 96576 gene models, 67917 with default filtering (quality_filter.pl -d) and 67917 with standard filtering (quality_filter.pl -s). I chose to report all genes with AED less than 0.5 (27437) as the high quality set. >>>> >>>> However, I wonder a bit. One thing is that 70k genes cannot be correct for this species (it is not polyploid), and the correct number of genes should be a bit more than 20k I think. I suspect that many of my genes are fragmented, how can I fix this? I have tried searching the forum, but cannot find any good answers. Is there some parameters I can adjust? >>>> >>>> I have used SwissProt/UniProt and a Trinity assembly of reads from several stages of embryo development as evidence. I used SNAP with CEGMA, AUGUSTUS trained with BUSCO actinoptergyrii genes and GeneMark-ES in first pass, SNAP trained on first pass annotation and AUGUSTUS trained on the transcriptome and first pass annotation together with GeneMark for second pass annotation. >>>> >>>> Thank you. >>>> >>>> Ole >>>> _______________________________________________ >>>> 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 From Victor.Rossier at unil.ch Thu Jul 7 05:25:24 2016 From: Victor.Rossier at unil.ch (Victor Rossier) Date: Thu, 7 Jul 2016 11:25:24 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> , Message-ID: <1467890724600.33833@unil.ch> Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I'll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it's the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. -Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From cjfields at illinois.edu Fri Jul 8 12:09:21 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Fri, 8 Jul 2016 18:09:21 +0000 Subject: [maker-devel] Fasta index error In-Reply-To: References: <1467646720155.98154@unil.ch> <1467890724600.33833@unil.ch> <5285C11D-F9BE-4398-B44A-5516C7D46859@illinois.edu> <5B008EE9-14AA-433C-9E3F-E84ADC07BEC2@gmail.com> <9DC2D5B7-9408-4BBA-BB5E-90DA6A71AEE1@illinois.edu> Message-ID: It?s not terribly often sequence IDs are that short (let alone 0), though I could see it happening with raw assembler output. Usually we rename the seqs to something else. I?m still not terribly happy about the stringification overload but removing it would likely break things in terrible obscene ways (I found this out the hard way removing this behavior from the developer ontology modules). chris On Jul 7, 2016, at 2:08 PM, Carson Holt > wrote: Thanks. I?ve updated the test inside MAKER, so it now checks both that ref type equals 'Bio::PrimarySeq::Fasta? and the value is defined. I?m surprised I haven?t seen this come up before. ?Carson On Jul 7, 2016, at 12:43 PM, Fields, Christopher J > wrote: Easy enough to figure out when it snuck in: https://github.com/bioperl/bioperl-live/blame/master/Bio/DB/Fasta.pm#L358 Seems like it may have been in there a while. chris On Jul 7, 2016, at 11:17 AM, Carson Holt > wrote: I made a test case, and apparently the issue is that Bio::PrimarySeq::Fasta has been function overloaded to return the ID in scalar context. So if you do 'print' to a Bio::PrimarySeq::Fasta object it prints the ID rather than the object reference. Is this something recently changed? This means that the test for the object existing in MAKER now fails because it sees the ID. I can change the test. ?Carson On Jul 7, 2016, at 8:09 AM, Fields, Christopher J > wrote: Victor, Can you post which version of MAKER you are using? chris On Jul 7, 2016, at 6:25 AM, Victor Rossier > wrote: Thanks for the quick replies, It was actually the first cufflink transcript (used as altest in the maker_opts.ctl) that was named '>0'. I renamed all transcripts and maker finished correctly! Thanks again, Victor Rossier ________________________________ De : Fields, Christopher J > Envoy? : mercredi 6 juillet 2016 14:16 ? : Carson Holt Cc : Victor Rossier; maker-devel at yandell-lab.org Objet : Re: [maker-devel] Fasta index error I?ll go ahead and post this as a bug for Bio::DB::Fasta and will try to come up with a test case. chris On Jul 5, 2016, at 9:29 AM, Carson Holt > wrote: You need to rename the contig. It is currently named 0 The value 0 is the same as false in a most programing languages and is likely causing the BioPerl indexer to not return a result. This would technically be a bug in the BioPerl indexer, but it?s the kind of thing that has the potential to cause errors in several libraries and third party tools, so it would still be best to rename the contig. You can also try updating BioPerl as it may already be fixed. You may want to submit a bug report to the BioPerl developer community. At the point of failure, MAKER is testing for the existence of the object reference and not on the ID itself. So BioPerl has returned an empty reference. ?Carson On Jul 4, 2016, at 9:38 AM, Victor Rossier > wrote: Dear Maker, I did run maker for the annotation of a denovo genome assembly. It works great for all scaffolds but 1. Here is the error I get: WARNING: Cannot find >0, trying to re-index the fasta. stop here:0 ERROR: Fasta index error at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/GI.pm line 1622. GI::polish_exonerate('FastaChunk=HASH(0x5fd22b8)', 'FastaSeq=HASH(0x4607540)', 211829, '>scaffold52256_cov106', 'ARRAY(0x62a2240)', 'ARRAY(0x629f198)', '/scratch/beegfs/monthly/vrossier/temp/aoc_denovo_maker/Aocell...', 'a', '/software/SequenceAnalysis/SequenceAlignment/exonerate/2.2.0/...', ...) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 2491 Process::MpiChunk::__ANON__() called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 415 eval {...} called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Error.pm line 407 Error::subs::try('CODE(0x45d40a8)', 'HASH(0x5fe4930)') called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 4224 Process::MpiChunk::_go('Process::MpiChunk=HASH(0x45ddfb0)', 'run', 'HASH(0x4e3c540)', 6, 3) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/../lib/Process/MpiChunk.pm line 341 Process::MpiChunk::run('Process::MpiChunk=HASH(0x45ddfb0)', 16) called at /scratch/beegfs/monthly/vrossier/SOFT/MAKER2/maker_mpich/bin/maker line 979 --> rank=16, hostname=dee-serv04.vital-it.ch ERROR: Failed while polishing alt-ESTs ERROR: Chunk failed at level:6, tier_type:3 FAILED CONTIG:scaffold52256_cov106 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:scaffold52256_cov106 Any thought how to solve this? Thanks in advance, Victor Rossier _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 18:52:05 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 17:52:05 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Hi, I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. *Options I used include:* maker_gff=014_maker_Sacu_v1_s0008.gff est_pass=1 altest_pass=0 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 altest=alt_est.fasta snaphmm=snap.hmm trna=0 cpus=1 clean_try=0 clean_up=0 *Below are the last 50 lines in the stderr from the failed run.* running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# running blast search. #--------- command -------------# Widget::tblastx: /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx #-------------------------------# ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ tblastx.pm:133 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: /share/apps/genomics/maker/bin/maker:979 ----------------------------------------------------------- --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local --> rank=31, hostname=kepler-0-8.local ERROR: Failed while collecting tblastx reports ERROR: Chunk failed at level:5, tier_type:3 FAILED CONTIG:Sacu_v1_s0008 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:Sacu_v1_s0008 examining contents of the fasta file and run log --Next Contig-- Processing run.log file... MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx did not finish on the last run and must be erased Maker is now finished!!! Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Fri Jul 15 21:20:43 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Fri, 15 Jul 2016 20:20:43 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully Message-ID: Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sat Jul 16 23:40:50 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sat, 16 Jul 2016 22:40:50 -0700 Subject: [maker-devel] MAKER output has different genes with same name Message-ID: I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: maker_gff=previous_run.gff est_pass=1 altest_pass=1 protein_pass=1 rm_pass=1 model_pass=1 pred_pass=1 other_pass=0 Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: ------------------------------------- *Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* *Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 *Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* *Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* *Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 *Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 Here the models' headers from the maker.proteins.fasta: ------------------------------------- >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 Thanks! Matt -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Sun Jul 17 17:39:51 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Sun, 17 Jul 2016 16:39:51 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. Matt On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > I have been using MAKER to iteratively update previous run's annotations > by running ab initios with fresh training and feeding the previous run's > GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > Along the way it seems that non-identical features with the same name, > some covering the same region and some not, accumulate. When I use > fasta_merge -d ...index.log I get sequences for the duplicates. Am I using > the control file options incorrectly? Any suggestions how to select final > models? Or should I redo the runs if I had some settings wrong? > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log > showing duplicate models: > > ------------------------------------- > > *Sacu_v1_s0077 maker gene 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* > > *Sacu_v1_s0077 maker mRNA 136647 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* > > Sacu_v1_s0077 maker exon 138512 138568 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > *Sacu_v1_s0077 maker gene 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* > > *Sacu_v1_s0077 maker mRNA 98236 98541 . - . > ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* > > > > > *Sacu_v1_s0004 maker gene 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* > > *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > *Sacu_v1_s0004 maker gene 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* > > *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 > ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . > ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 > eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From yincl2013 at 126.com Wed Jul 13 04:10:45 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Wed, 13 Jul 2016 18:10:45 +0800 Subject: [maker-devel] maker problem Message-ID: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China -------------- next part -------------- An HTML attachment was scrubbed... URL: From sebastien.moretti at unil.ch Tue Jul 12 02:35:43 2016 From: sebastien.moretti at unil.ch (Sebastien Moretti) Date: Tue, 12 Jul 2016 10:35:43 +0200 Subject: [maker-devel] Installation in a custom directory Message-ID: Hi I try to install maker in a custom directory following regular Perl commands with Build.PL. Unfortunately if I use perl Build.PL --installdirs= then ./Build install --destdir= build install fails with the error: Can't use an undefined value as a HASH reference at .../Module/Build/Base.pm line 3038. It does not happen if I don't use --installdirs Is there an "official" way to install maker in a custom directory? Also I found typos in the description of maker at http://www.yandell-lab.org/software/maker.html ouputs should be outputs seusequent should be ??? maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 Regards -- S?bastien Moretti Staff Scientist SIB Vital-IT EMBnet, Quartier Sorge - Genopode CH-1015 Lausanne, Switzerland Tel.: +41 (21) 692 4079/4221 http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.org/ From carsonhh at gmail.com Mon Jul 18 08:48:28 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:48:28 -0600 Subject: [maker-devel] Installation in a custom directory In-Reply-To: References: Message-ID: <9A2E906F-F0B9-4CB3-9C18-CA57F4213D55@gmail.com> MAKER will by default put executables in ?/maker/bin. You should put ?/maker/bin into your PATH. The maker Build.PL is configured to install things in a set directory configuration to properly locate perl libraries, C shared objects, and data files. ?Carson > On Jul 12, 2016, at 2:35 AM, Sebastien Moretti wrote: > > Hi > > I try to install maker in a custom directory following regular Perl > commands with Build.PL. > > Unfortunately if I use > perl Build.PL --installdirs= > then > ./Build install --destdir= > build install fails with the error: > Can't use an undefined value as a HASH reference at > .../Module/Build/Base.pm line 3038. > > It does not happen if I don't use --installdirs > > > Is there an "official" way to install maker in a custom directory? > > > Also I found typos in the description of maker at > http://www.yandell-lab.org/software/maker.html > ouputs should be outputs > seusequent should be ??? > > > maker 2.31.8, Linux x86_64 2.6.32, Perl 5.18.2 > > Regards > > -- > S?bastien Moretti > Staff Scientist > SIB Vital-IT EMBnet, Quartier Sorge - Genopode > CH-1015 Lausanne, Switzerland > Tel.: +41 (21) 692 4079/4221 > http://www.vital-it.ch/ http://myhits.vital-it.ch/ http://MetaNetX.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 Jul 18 08:53:09 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:53:09 -0600 Subject: [maker-devel] maker problem In-Reply-To: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson > On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: > > Hello, > > When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. > > Here is a part of main error log: > ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Can't get HSPs: data not collected. > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 > STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 > STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 > STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 > STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 > STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 > STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 > STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 > STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 > STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 > ----------------------------------------------------------- > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > --> rank=NA, hostname=localhost.localdomain > ERROR: Failed while collecting blastx reports > ERROR: Chunk failed at level:9, tier_type:3 > FAILED CONTIG:QPacbio.Hiseq_683 > > ERROR: Chunk failed at level:4, tier_type:0 > FAILED CONTIG:QPacbio.Hiseq_683 > > examining contents of the fasta file and run log > Thanks! > > Best regards, > Ian > Department of Entomology, College of Plant Protection, Nanjing Agricultural University > No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 08:55:29 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 08:55:29 -0600 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: <7C44D0D0-D2CE-4899-9CE5-0050A928A6E0@gmail.com> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk. This will cause IO errors and partial result files because the operations done in TMP are not NFS safe. Thanks, Carson > On Jul 15, 2016, at 9:20 PM, Matt Simenc wrote: > > Update: I re-ran the annotation but left out the transcripts from the related species in the altest parameter and the annotation completed successfully. I would like to use these altest transcripts if possible, but this is better than nothing! Any ideas? > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc > wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I isolated this scaffold from my assembly after maker successfully annotated all other scaffolds in the assembly but failed on this one, and failed on successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. This is the first run on which I have added transcript sequences from a closely related species. The only ab initio program I'm running here was SNAP. > > Options I used include: > > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > > other_pass=0 > > > altest=alt_est.fasta > > > snaphmm=snap.hmm > > > trna=0 > > cpus=1 > > > clean_try=0 > > > clean_up=0 > > > > > > Below are the last 50 lines in the stderr from the failed run. > > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking true -show_gis -out /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > > examining contents of the fasta file and run log > > > > --Next Contig-- > > > > Processing run.log file... > > MAKER WARNING: The file Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > > Maker is now finished!!! > > > > > > Any help would be appreciated, please let me know if any other information about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 09:03:08 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:03:08 -0600 Subject: [maker-devel] maker problem In-Reply-To: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Message-ID: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson > On Jul 18, 2016, at 9:00 AM, Chuanlin Yin wrote: > > Thank you very much! > > I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. > > Thanks! > > Best wishes! > Ian > > 2016-07-18 > Chuanlin Yin > ????Carson Holt > > ?????2016-07-18 22:53 > ???Re: [maker-devel] maker problem > ????"Chuanlin Yin"> > ???"maker-devel"> > > The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. > > Thanks, > Carson > > >> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >> >> Hello, >> >> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >> >> Here is a part of main error log: >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> MSG: Can't get HSPs: data not collected. >> STACK: Error::throw >> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >> ----------------------------------------------------------- >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> --> rank=NA, hostname=localhost.localdomain >> ERROR: Failed while collecting blastx reports >> ERROR: Chunk failed at level:9, tier_type:3 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> ERROR: Chunk failed at level:4, tier_type:0 >> FAILED CONTIG:QPacbio.Hiseq_683 >> >> examining contents of the fasta file and run log >> Thanks! >> >> Best regards, >> Ian >> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >> >> >> _______________________________________________ >> 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 yincl2013 at 126.com Mon Jul 18 09:00:39 2016 From: yincl2013 at 126.com (Chuanlin Yin) Date: Mon, 18 Jul 2016 23:00:39 +0800 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> Message-ID: <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 Chuanlin Yin ????Carson Holt ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin" ???"maker-devel" The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 carsonhh at gmail.com Mon Jul 18 09:08:11 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:08:11 -0600 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Also with when trying 1, 2, or 3, run just the failed contig as a separate job or the old archived files will be reused rather than regenerating following the change (because MAKER archives partial results in theVoid directory). ?Carson > On Jul 18, 2016, at 9:03 AM, Carson Holt wrote: > > 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. > 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk > > ?Carson > > >> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >> >> Thank you very much! >> >> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >> >> Thanks! >> >> Best wishes! >> Ian >> >> 2016-07-18 >> Chuanlin Yin >> ????Carson Holt > >> ?????2016-07-18 22:53 >> ???Re: [maker-devel] maker problem >> ????"Chuanlin Yin"> >> ???"maker-devel"> >> >> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >> >> Thanks, >> Carson >> >> >>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>> >>> Hello, >>> >>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>> >>> Here is a part of main error log: >>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>> MSG: Can't get HSPs: data not collected. >>> STACK: Error::throw >>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>> ----------------------------------------------------------- >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> --> rank=NA, hostname=localhost.localdomain >>> ERROR: Failed while collecting blastx reports >>> ERROR: Chunk failed at level:9, tier_type:3 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> ERROR: Chunk failed at level:4, tier_type:0 >>> FAILED CONTIG:QPacbio.Hiseq_683 >>> >>> examining contents of the fasta file and run log >>> Thanks! >>> >>> Best regards, >>> Ian >>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>> >>> >>> _______________________________________________ >>> 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 mcsimenc at gmail.com Mon Jul 18 09:18:38 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:18:38 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! Matt On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > Hi, > > I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I > isolated this scaffold from my assembly after maker successfully annotated > all other scaffolds in the assembly but failed on this one, and failed on > successive retries. > > I fed this maker run a maker-generated gff from a prior successful run. > This is the first run on which I have added transcript sequences from a > closely related species. The only ab initio program I'm running here was > SNAP. > > *Options I used include:* > > maker_gff=014_maker_Sacu_v1_s0008.gff > > est_pass=1 > > altest_pass=0 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > altest=alt_est.fasta > > snaphmm=snap.hmm > > trna=0 > > cpus=1 > > clean_try=0 > > clean_up=0 > > > > *Below are the last 50 lines in the stderr from the failed run.* > > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > running blast search. > > #--------- command -------------# > > Widget::tblastx: > > /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db > /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 > -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 > -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking > true -show_gis -out > /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > #-------------------------------# > > > ------------- EXCEPTION: Bio::Root::Exception ------------- > > MSG: Can't get HSPs: data not collected. > > STACK: Error::throw > > STACK: Bio::Root::Root::throw > /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 > > STACK: Bio::Search::Hit::PhatHit::Base::hsps > /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 > > STACK: Widget::tblastx::keepers > /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 > > STACK: Widget::tblastx::parse /share/apps/genomics/maker/bin/../lib/Widget/ > tblastx.pm:133 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 > > STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 > > STACK: GI::reblast_merged_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:469 > > STACK: GI::merge_resolve_hits > /share/apps/genomics/maker/bin/../lib/GI.pm:289 > > STACK: Process::MpiChunk::_go > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 > > STACK: Process::MpiChunk::run > /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 > > STACK: /share/apps/genomics/maker/bin/maker:979 > > ----------------------------------------------------------- > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > --> rank=31, hostname=kepler-0-8.local > > ERROR: Failed while collecting tblastx reports > > ERROR: Chunk failed at level:5, tier_type:3 > > FAILED CONTIG:Sacu_v1_s0008 > > > ERROR: Chunk failed at level:4, tier_type:0 > > FAILED CONTIG:Sacu_v1_s0008 > > > examining contents of the fasta file and run log > > > --Next Contig-- > > > Processing run.log file... > > MAKER WARNING: The file > Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx > > did not finish on the last run and must be erased > > > Maker is now finished!!! > > > > Any help would be appreciated, please let me know if any other information > about this run would be helpful in diagnosing the problem(s). Thanks! > > Matt > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 09:20:34 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:34 -0700 Subject: [maker-devel] Maker failed annotating single scaffold, other scaffolds in assembly annotated successfully In-Reply-To: References: Message-ID: Oops! I meant to reply to a different thread, not this one. That last message is related to a different problem. On Mon, Jul 18, 2016 at 8:18 AM, Matt Simenc wrote: > Update: > > So I isolated a single scaffold to run MAKER on and test different > parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire > assembly. There are still some duplicates. I tried using the -a command > line option and it reduced the number of duplicate IDs for different > features by 2, but I don't know what to do. It's important if I know maker > is keeping the features in order or if it's possible maker is mixing up > exons and CDSs between different gene and mRNA features. > > Thanks! > Matt > > On Fri, Jul 15, 2016 at 5:52 PM, Matt Simenc wrote: > >> Hi, >> >> I'm running MAKER 2.31.8 using MPI, annotating a single scaffold. I >> isolated this scaffold from my assembly after maker successfully annotated >> all other scaffolds in the assembly but failed on this one, and failed on >> successive retries. >> >> I fed this maker run a maker-generated gff from a prior successful run. >> This is the first run on which I have added transcript sequences from a >> closely related species. The only ab initio program I'm running here was >> SNAP. >> >> *Options I used include:* >> >> maker_gff=014_maker_Sacu_v1_s0008.gff >> >> est_pass=1 >> >> altest_pass=0 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> altest=alt_est.fasta >> >> snaphmm=snap.hmm >> >> trna=0 >> >> cpus=1 >> >> clean_try=0 >> >> clean_up=0 >> >> >> >> *Below are the last 50 lines in the stderr from the failed run.* >> >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> running blast search. >> >> #--------- command -------------# >> >> Widget::tblastx: >> >> /share/apps/genomics/maker/bin/../exe/blast/bin/tblastx -db >> /state/partition1/maker_8Leu2i/db.2883882-2921215.for_tblastx.fasta -query >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0 >> -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -dbsize 1000 >> -searchsp 500000000 -num_threads 1 -lcase_masking -seg yes -soft_masking >> true -show_gis -out >> /home/joshd/data/salvinia/annotation/v.2_SUMMER2016/maker/018_2016_07_11_SNAP_round4_using_014_results_allGenes_andAzfiEST/Sacu_v1_s0008_rerun/Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> #-------------------------------# >> >> >> ------------- EXCEPTION: Bio::Root::Exception ------------- >> >> MSG: Can't get HSPs: data not collected. >> >> STACK: Error::throw >> >> STACK: Bio::Root::Root::throw >> /share/apps/perl5/perls/perl-5.22.0/lib/site_perl/5.22.0/Bio/Root/Root.pm:449 >> >> STACK: Bio::Search::Hit::PhatHit::Base::hsps >> /share/apps/genomics/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >> >> STACK: Widget::tblastx::keepers >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:192 >> >> STACK: Widget::tblastx::parse >> /share/apps/genomics/maker/bin/../lib/Widget/tblastx.pm:133 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2952 >> >> STACK: GI::tblastx /share/apps/genomics/maker/bin/../lib/GI.pm:2961 >> >> STACK: GI::reblast_merged_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:469 >> >> STACK: GI::merge_resolve_hits >> /share/apps/genomics/maker/bin/../lib/GI.pm:289 >> >> STACK: Process::MpiChunk::_go >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:2361 >> >> STACK: Process::MpiChunk::run >> /share/apps/genomics/maker/bin/../lib/Process/MpiChunk.pm:341 >> >> STACK: /share/apps/genomics/maker/bin/maker:979 >> >> ----------------------------------------------------------- >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> --> rank=31, hostname=kepler-0-8.local >> >> ERROR: Failed while collecting tblastx reports >> >> ERROR: Chunk failed at level:5, tier_type:3 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> ERROR: Chunk failed at level:4, tier_type:0 >> >> FAILED CONTIG:Sacu_v1_s0008 >> >> >> examining contents of the fasta file and run log >> >> >> --Next Contig-- >> >> >> Processing run.log file... >> >> MAKER WARNING: The file >> Sacu_v1_s0008.maker.output/Sacu_v1_s0008_datastore/CF/CA/Sacu_v1_s0008//theVoid.Sacu_v1_s0008/2/Sacu_v1_s0008.2883882.2921215.0.db%2E2883882-2921215%2Efor_tblastx%2Efasta.tblastx >> >> did not finish on the last run and must be erased >> >> >> Maker is now finished!!! >> >> >> >> Any help would be appreciated, please let me know if any other >> information about this run would be helpful in diagnosing the problem(s). >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mcsimenc at gmail.com Mon Jul 18 09:20:44 2016 From: mcsimenc at gmail.com (Matt Simenc) Date: Mon, 18 Jul 2016 08:20:44 -0700 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: Update: So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. Thanks! On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that > set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc wrote: > >> I have been using MAKER to iteratively update previous run's annotations >> by running ab initios with fresh training and feeding the previous run's >> GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> Along the way it seems that non-identical features with the same name, >> some covering the same region and some not, accumulate. When I use >> fasta_merge -d ...index.log I get sequences for the duplicates. Am I using >> the control file options incorrectly? Any suggestions how to select final >> models? Or should I redo the runs if I had some settings wrong? >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log >> showing duplicate models: >> >> ------------------------------------- >> >> *Sacu_v1_s0077 maker gene 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704* >> >> *Sacu_v1_s0077 maker mRNA 136647 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704* >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> *Sacu_v1_s0077 maker gene 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18* >> >> *Sacu_v1_s0077 maker mRNA 98236 98541 . - . >> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18* >> >> >> >> >> *Sacu_v1_s0004 maker gene 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976* >> >> *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976* >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> *Sacu_v1_s0004 maker gene 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624* >> >> *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624* >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 >> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . >> ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 >> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> Thanks! >> >> Matt >> > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 09:29:54 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:29:54 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: References: Message-ID: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. ?Carson > On Jul 18, 2016, at 9:20 AM, Matt Simenc wrote: > > Update: > > So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. > > However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. > > Thanks! > > On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: > Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. > > Matt > > On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: > I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: > > maker_gff=previous_run.gff > > est_pass=1 > > altest_pass=1 > > protein_pass=1 > > rm_pass=1 > > model_pass=1 > > pred_pass=1 > > other_pass=0 > > > > Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? > > > > Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: > > ------------------------------------- > > Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 > > Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 > > Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 > > Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 > > > Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 > > > > > > > > Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 > > Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 > > Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 > > Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 > > > Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 > > > > Here the models' headers from the maker.proteins.fasta: > > ------------------------------------- > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 > > > >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 > > > >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 > > > > > > Thanks! > > Matt > > > > _______________________________________________ > 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 carsonhh at gmail.com Mon Jul 18 09:35:40 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 09:35:40 -0600 Subject: [maker-devel] MAKER output has different genes with same name In-Reply-To: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> References: <768DBFAF-2958-4969-B9FF-3250D97AC7B2@gmail.com> Message-ID: <3A0272F5-F6C3-4546-BF5F-E859C191713C@gmail.com> Also from your previous STDERR log you have /state/partition1/ set as your TMP directory. If that is a network mounted location, then you can get duplicate writes from separate threads to output files because of failed locks. The TMP directory should normally be set to /tmp as it is usually a locally mounted disk that will be independent and inaccessible to other nodes. Duplicate entries are often a sign of this type of IO error, especially if there is a certain degree of randomness to who gets duplicated. ?Carson > On Jul 18, 2016, at 9:29 AM, Carson Holt wrote: > > Normally a second run should be done in the same directory as opposed to passing in the previous GFF3. Using GFF3 passthrough is meant as a round about way of getting previous results into a new run (for example a previous version of an annotation set where you need to keep the old annoations for some reason and don?t have access to the original data files). You actually lose certain info that was available in the BLAST reports but cannot be recovered from the GFF3 for example. > > Both model_pass and pred_pass should probably be set to 0 if you are letting things rerun by providing snaphmm. > > Also check your input GFF3 for duplicates, as those will iteratively feed into the next run. > > ?Carson > > > > >> On Jul 18, 2016, at 9:20 AM, Matt Simenc > wrote: >> >> Update: >> >> So I isolated a single scaffold to run MAKER on and test different parameters. With map_forward=1 the duplicates disappeared. >> >> However this does not entirely take care of the issue with the entire assembly. There are still some duplicates. I tried using the -a command line option and it reduced the number of duplicate IDs for different features by 2, but I don't know what to do. It's important if I know maker is keeping the features in order or if it's possible maker is mixing up exons and CDSs between different gene and mRNA features. >> >> Thanks! >> >> On Sun, Jul 17, 2016 at 4:39 PM, Matt Simenc > wrote: >> Hi, I figured out the problem. I needed to use map_forward=1. With that set, no duplicates. >> >> Matt >> >> On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc > wrote: >> I have been using MAKER to iteratively update previous run's annotations by running ab initios with fresh training and feeding the previous run's GFF using the maker_gff option like this: >> >> maker_gff=previous_run.gff >> >> est_pass=1 >> >> altest_pass=1 >> >> protein_pass=1 >> >> rm_pass=1 >> >> model_pass=1 >> >> pred_pass=1 >> >> other_pass=0 >> >> >> >> Along the way it seems that non-identical features with the same name, some covering the same region and some not, accumulate. When I use fasta_merge -d ...index.log I get sequences for the duplicates. Am I using the control file options incorrectly? Any suggestions how to select final models? Or should I redo the runs if I had some settings wrong? >> >> >> >> Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models: >> >> ------------------------------------- >> >> Sacu_v1_s0077 maker gene 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704 >> >> Sacu_v1_s0077 maker mRNA 136647 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704 >> >> Sacu_v1_s0077 maker exon 138512 138568 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 138297 138361 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137723 137786 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 137578 137643 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker exon 136647 136871 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138512 138568 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 138297 138361 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137723 137786 . - 1 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 137578 137643 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker CDS 136647 136871 . - 0 ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 >> >> Sacu_v1_s0077 maker gene 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18 >> >> >> Sacu_v1_s0077 maker mRNA 98236 98541 . - . ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18 >> >> >> >> >> >> >> >> Sacu_v1_s0004 maker gene 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976 >> >> Sacu_v1_s0004 maker mRNA 4775142 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976 >> >> Sacu_v1_s0004 maker exon 4775142 4775330 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker exon 4775354 4775554 . + . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker gene 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker mRNA 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624 >> >> Sacu_v1_s0004 maker exon 4767976 4768158 . - . ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0 ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 >> >> >> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + . ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976 >> >> >> >> Here the models' headers from the maker.proteins.fasta: >> >> ------------------------------------- >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|2|0|129 >> >> >> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60 >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|0|0|0|1|1|5|0|158 >> >> >> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00 eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101 >> >> >> >> >> >> Thanks! >> >> Matt >> >> >> >> _______________________________________________ >> 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 cjfields at illinois.edu Mon Jul 18 11:46:52 2016 From: cjfields at illinois.edu (Fields, Christopher J) Date: Mon, 18 Jul 2016 17:46:52 +0000 Subject: [maker-devel] maker problem In-Reply-To: <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. chris 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk ?Carson On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: Thank you very much! I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. Thanks! Best wishes! Ian 2016-07-18 ________________________________ Chuanlin Yin ________________________________ ????Carson Holt > ?????2016-07-18 22:53 ???Re: [maker-devel] maker problem ????"Chuanlin Yin"> ???"maker-devel"> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. Thanks, Carson On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: Hello, When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. Here is a part of main error log: ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Can't get HSPs: data not collected. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 ----------------------------------------------------------- --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain --> rank=NA, hostname=localhost.localdomain ERROR: Failed while collecting blastx reports ERROR: Chunk failed at level:9, tier_type:3 FAILED CONTIG:QPacbio.Hiseq_683 ERROR: Chunk failed at level:4, tier_type:0 FAILED CONTIG:QPacbio.Hiseq_683 examining contents of the fasta file and run log Thanks! Best regards, Ian Department of Entomology, College of Plant Protection, Nanjing Agricultural University No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China _______________________________________________ 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon Jul 18 11:58:46 2016 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 18 Jul 2016 11:58:46 -0600 Subject: [maker-devel] maker problem In-Reply-To: References: <1b052523.2559.155e3bcc89d.Coremail.yincl2013@126.com> <63f81872.550b.155fe85f634.Coremail.yincl2013@126.com> <04016DA2-5210-4869-A5F3-4384043A6020@gmail.com> Message-ID: Nothing specific I?m aware. Their error is occurring immediately following the blast report parse. The hit is defined, but the hash key of the object holding the HSPs is not defined. Half the time I see an error that come up through the BioPerl Bio::Root::Root::throw mechanism it goes away when the user installs the current CPAN version of BioPerl (they either have really old BioPerl or are using the live version). So I always have the user check that first. The other half of the time it ends up being an IO error (truncated file because they used NFS for temporary file space). Truncated can cause failures in multiple ways. Then less often it is a blast issue (there are a handful of subversions of blast+ that give frequent failures). ?Carson > On Jul 18, 2016, at 11:46 AM, Fields, Christopher J wrote: > > >> On Jul 18, 2016, at 10:03 AM, Carson Holt > wrote: >> >> 1. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. > > Just curious, is there anything broken w/ bioperl-live we need to know about? We?re about to release BioPerl v1.7.0 (I?m already on RC5), it would be nice to know if we?re missing anything that would potentially break downstream applications. > > chris > >> 2. Try installing a different version of BLAST incase the BLAST report is somehow not created correctly. >> 3. Make sure TMP= in the maker_opts.ctl file is not set to a network mounted disk >> >> ?Carson >> >> >>> On Jul 18, 2016, at 9:00 AM, Chuanlin Yin > wrote: >>> >>> Thank you very much! >>> >>> I know the error is saying that there is a hit with no HSPs, but why other scaffolds are all OK except that one. I have checked that scaffold for many times and the format is correct. >>> >>> Thanks! >>> >>> Best wishes! >>> Ian >>> >>> 2016-07-18 >>> Chuanlin Yin >>> ????Carson Holt > >>> ?????2016-07-18 22:53 >>> ???Re: [maker-devel] maker problem >>> ????"Chuanlin Yin"> >>> ???"maker-devel"> >>> >>> The error is saying that there is a hit with no HSPs. Make sure you are using the current CPAN version of BioPerl, and not BioPerl live. Also you can try a different version of BLAST if the BLAST report is somehow not created correctly. Finally do not set your TMP= location to a network mounted disk (on many clusters your home directory is network mounted). This will cause IO errors and partial result files. I can?t tell what your temporary directory is set to because your STDERR is truncated. >>> >>> Thanks, >>> Carson >>> >>> >>>> On Jul 13, 2016, at 4:10 AM, Chuanlin Yin > wrote: >>>> >>>> Hello, >>>> >>>> When I use the maker for geomic annotation pipeline, I met a very big problem. My genome has 7282 scaffolds, all is success but for one scaffold is failed. I don?t konw why and I have check the log, but I still can't fix the problem. So I need you help, and I will appreciate it very much. >>>> >>>> Here is a part of main error log: >>>> ------------- EXCEPTION: Bio::Root::Exception ------------- >>>> MSG: Can't get HSPs: data not collected. >>>> STACK: Error::throw >>>> STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:449 >>>> STACK: Bio::Search::Hit::PhatHit::Base::hsps /disk/home/yincl/software/maker/maker/bin/../lib/Bio/Search/Hit/PhatHit/Base.pm:552 >>>> STACK: Widget::blastx::keepers /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:190 >>>> STACK: Widget::blastx::parse /disk/home/yincl/software/maker/maker/bin/../lib/Widget/blastx.pm:132 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2622 >>>> STACK: GI::blastx /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:2631 >>>> STACK: GI::reblast_merged_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:445 >>>> STACK: GI::merge_resolve_hits /disk/home/yincl/software/maker/maker/bin/../lib/GI.pm:289 >>>> STACK: Process::MpiChunk::_go /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:2821 >>>> STACK: Process::MpiChunk::run /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:341 >>>> STACK: Process::MpiChunk::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiChunk.pm:357 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: Process::MpiTiers::run_all /disk/home/yincl/software/maker/maker/bin/../lib/Process/MpiTiers.pm:287 >>>> STACK: /disk/home/yincl/software/maker/maker/bin/maker:686 >>>> ----------------------------------------------------------- >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> --> rank=NA, hostname=localhost.localdomain >>>> ERROR: Failed while collecting blastx reports >>>> ERROR: Chunk failed at level:9, tier_type:3 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> ERROR: Chunk failed at level:4, tier_type:0 >>>> FAILED CONTIG:QPacbio.Hiseq_683 >>>> >>>> examining contents of the fasta file and run log >>>> Thanks! >>>> >>>> Best regards, >>>> Ian >>>> Department of Entomology, College of Plant Protection, Nanjing Agricultural University >>>> No. 1, Weigang Road, Xuanwu District, Nanjing, Jiangsu 210095, China >>>> >>>> >>>> _______________________________________________ >>>> 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: