From patrick.tranvan at unil.ch Wed May 1 05:25:09 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Wed, 1 May 2019 10:25:09 +0000 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? Message-ID: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Hi Carson and Maker dev team, Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 I cite: "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " I am wondering: 1) Where did you find these statistics ? 2) Do you have new statistics for 2019 ? 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? Thanks. Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon May 6 11:26:18 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 6 May 2019 10:26:18 -0600 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? In-Reply-To: <92f0dde60f734f259c92feb1a085d31b@unil.ch> References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <0C9F80D5-E0DB-4024-9E34-C510E7033034@gmail.com> Those numbers came from https://gold.jgi.doe.gov You can download their tables and filter the data on different attributes. ?Carson > On May 1, 2019, at 4:25 AM, Patrick Tran Van wrote: > > Hi Carson and Maker dev team, > > Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 > > I cite: > > "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " > > "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " > > I am wondering: > > 1) Where did you find these statistics ? > > 2) Do you have new statistics for 2019 ? > > 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? > > Thanks. > > > Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.ence at ufl.edu Mon May 13 08:12:13 2019 From: d.ence at ufl.edu (Ence,daniel) Date: Mon, 13 May 2019 13:12:13 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: References: Message-ID: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Mon May 13 08:50:26 2019 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 13 May 2019 13:50:26 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> References: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Message-ID: <181B8E01-422F-4685-AEEC-A66DEB7B88ED@umail.utah.edu> Hey Dan, How?s life? What are you up to these days? --mark From: maker-devel on behalf of "Ence,daniel" Date: Monday, May 13, 2019 at 7:21 AM To: Christian Ayala Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Running out of time in MAKER Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 14 03:12:09 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 14 May 2019 08:12:09 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch>, Message-ID: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed May 15 10:49:43 2019 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 15 May 2019 09:49:43 -0600 Subject: [maker-devel] Redundant FASTA headers In-Reply-To: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> References: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> Message-ID: <59A2492E-2568-4326-9EC3-BE19D0EE79CC@gmail.com> Headers are used to pull individual sequences out for exonerate polishing. So non-unique headers could result in the wrong sequence being pulled out (it makes the fasta index ambiguous). ?Carson > On Apr 24, 2019, at 1:42 AM, Bastian Schiffthaler wrote: > > Hi, > > I'm running the MPI version of MAKER and I'm supplying seven different trinity assemblies (different experiments) as evidence. Now trinity will not generate unique FASTA headers >across< files, so I'm wondering if there could be an issue with ID collision? What does MAKER use the headers for? Could it create race conditions in temp files? > > Thanks in advance, > Bastian > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Wed May 15 23:42:20 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Thu, 16 May 2019 14:42:20 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Fri May 17 09:30:27 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Fri, 17 May 2019 10:30:27 -0400 Subject: [maker-devel] genome annnotation by maker Message-ID: Hello, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Sat May 18 23:10:23 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Sun, 19 May 2019 04:10:23 +0000 Subject: [maker-devel] Maker errors In-Reply-To: References: <3345C6C6-07A5-41A1-8486-37C3005915E5@genetics.utah.edu> Message-ID: On May 18, 2019, at 10:10 PM, Carson Hinton Holt > wrote: Hi Samia, I?ve CC?d my reply to the devel list as well. MAKER can annotate gene positions on prokaryotes although it?s best suited for eukaryotic genomes. It does only support canonical codon usage though (so would not be usful if the prakaryote you are interested has any other codon table). You need to train a predictor like genemark first, although the protein2genome prediction option works relatively well in prokaryotes. Output is in fasta and GFF3 format. If you need GeneBank format (what you have below) you will need to convert. There are tools out there like GAG that can help convert MAKER output for GenBank submission. ?Carson On May 17, 2019, at 2:30 AM, djerroud samia > wrote: Hello, thank you for your answer, I suscribed to the mailing list, but seems that it will take a little time. My question is quite urgent. IF you can answer to my answers from here it would be cool. Well, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia Le jeu. 16 mai 2019 ? 14:25, Carson Hinton Holt > a ?crit : You can post error to the MAKER devel mailing list ?> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org You can search for previous posts to the devel list here (FYI, the google group used is an archive, you must still post original questions to the list above) ?> http://groups.google.com/group/maker-devel Also general info is at wiki here ?> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page ?Carson On May 16, 2019, at 7:13 AM, djerroud samia > wrote: Hello, I am very new in using maker, I get some errors. can you tell me who is the person who deals with the technical problems of maker Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 21 06:25:33 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 21 May 2019 11:25:33 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> , Message-ID: Hi Xavier I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. By the way, I would like to show you my training steps with augustus, in order to know if they are correct: zff2augustus_gbk.pl export.ann export.dna > final_genes.gb randomSplit.pl final_genes.gb 500 new_species.pl --species=Demo etraining --species=Demo final_genes.gb optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test etraining --species=Demo final_genes.gb I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. Thank you in advance Pedro Seoane ________________________________ De: Xabier V?zquez-Campos Enviado: jueves, 16 de mayo de 2019 4:42 Para: p sz Cc: maker-devel at yandell-lab.org Asunto: Re: [maker-devel] RV: Problem training agustus Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz > wrote: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Xabier V?zquez-Campos, PhD Research Associate NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Tue May 21 07:11:18 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Tue, 21 May 2019 08:11:18 -0400 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... My problem is I don't know the pipeline I should follow to get all this informaitions thank you, Samia Le mar. 21 mai 2019 ? 07:25, p sz a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 xvazquezc at gmail.com Tue May 21 18:56:31 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 22 May 2019 09:56:31 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, this is what I did the last time I run it. I had RNAseq, the genome is soft-masked and the training set is the one from zff2augustus_gbk.pl. You only need one step with autoAug.pl, it should be included with your installation of AUGUSTUS AUG_TRAIN= #workingdir MYSP= #name used for the gene model in the augustus config folder RNA_SEQ= #assembled RNAseq data GENOME= #soft-masked genome TRAIN=${BASE}/snap1/pugra.train1.gb mkdir -p ${AUG_TRAIN} cd ${AUG_TRAIN} autoAug.pl --noninteractive -v -v -v \ --cpus=${PBS_NUM_PPN} \ --maxIntronLen=3000 \ --species=${MYSP} \ --genome=${GENOME} \ --cdna=${RNA_SEQ} \ --trainingset=${TRAIN} \ --optrounds=5 \ --workingdir=${AUG_TRAIN} On Tue, 21 May 2019 at 21:25, p sz wrote: > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From liqing850104 at gmail.com Wed May 22 11:18:06 2019 From: liqing850104 at gmail.com (=?UTF-8?B?5p2O6Z2SIExpLCBRaW5n?=) Date: Wed, 22 May 2019 10:18:06 -0600 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila wrote: > Dear Maker group > My name is Nazila, I am a Ph.D. student at Miami University. I'm working > on *Phrynosoma platyrhinos *genome annotation and I'm trying to use > MAKER. So as a requirement I'm trying to use tRNAscan. First I used the > latest version (2.0) and I got the first -q file but I faced a warning like > this: > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > And I tried overwrite and append but it just froze and didn't work anymore. > So I tried to use an older version (1.3.1) but this one is hard to make it > work too. I'm getting an error: > > Can't locate object method "new" via package "tRNAscanSE::Constants" > (perhaps you forgot to load "tRNAscanSE::Constants"?) at > /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. > > Would you please help me with it? Which version should I use? And how > could I solve the problem for that version? > Looking forward for your reply; > Thanks, > Nazila > -------------- next part -------------- An HTML attachment was scrubbed... URL: From atalgarni at gmail.com Wed May 22 06:51:29 2019 From: atalgarni at gmail.com (Abdulmalek Algarni) Date: Wed, 22 May 2019 14:51:29 +0300 Subject: [maker-devel] Failed to run maker after install Message-ID: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Hi there, I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h Couldn't find an appropriate DIRECTORY for Inline to use. at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. Compilation failed in require at (eval 27) line 2. ...propagated at /System/Library/Perl/5.18/base.pm line 84. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. Compilation failed in require at ./maker line 62. BEGIN failed--compilation aborted at ./maker line 62. For the other excutables here is an example : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff Usage: cegma2zff This script converts the output GFF file from CEGMA into ZFF format for use in SNAP training. Output files are always genome.ann and genome.dna. Best regards, Abdulmalek -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 23 11:44:11 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 May 2019 10:44:11 -0600 Subject: [maker-devel] Failed to run maker after install In-Reply-To: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> References: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Message-ID: <47C0BDC5-5B9A-4562-B9D6-3BC74A10BCFC@gmail.com> Install live version of BioPerl, then reinsall MAKER against that ?> https://github.com/bioperl/bioperl-live There is a BioPerl related issue with Inline::C that has been fixed. ?Carson > On May 22, 2019, at 5:51 AM, Abdulmalek Algarni wrote: > > Hi there, > > I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : > > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h > Couldn't find an appropriate DIRECTORY for Inline to use. > > at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. > Compilation failed in require at (eval 27) line 2. > ...propagated at /System/Library/Perl/5.18/base.pm line 84. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. > Compilation failed in require at ./maker line 62. > BEGIN failed--compilation aborted at ./maker line 62. > > > For the other excutables here is an example : > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff > > Usage: > cegma2zff > > This script converts the output GFF file from CEGMA into ZFF format > for use in SNAP training. Output files are always genome.ann and > genome.dna. > > > > Best regards, > > Abdulmalek > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Thu May 23 21:12:22 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Fri, 24 May 2019 02:12:22 +0000 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: <6700FDE9-0114-4774-A578-8F30DEB8BE3B@genetics.utah.edu> Use version 1.3.1 (last stable version for 1.X series), we haven?t updated maker to handle tRNAscan version 2 options and output yet. All version here ?> http://trna.ucsc.edu/software/ ?Carson On May 22, 2019, at 10:18 AM, ?? Li, Qing > wrote: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila > wrote: Dear Maker group My name is Nazila, I am a Ph.D. student at Miami University. I'm working on Phrynosoma platyrhinos genome annotation and I'm trying to use MAKER. So as a requirement I'm trying to use tRNAscan. First I used the latest version (2.0) and I got the first -q file but I faced a warning like this: WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? And I tried overwrite and append but it just froze and didn't work anymore. So I tried to use an older version (1.3.1) but this one is hard to make it work too. I'm getting an error: Can't locate object method "new" via package "tRNAscanSE::Constants" (perhaps you forgot to load "tRNAscanSE::Constants"?) at /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. Would you please help me with it? Which version should I use? And how could I solve the problem for that version? Looking forward for your reply; Thanks, Nazila -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 30 13:09:20 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 30 May 2019 12:09:20 -0600 Subject: [maker-devel] Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <3180F4FE-30B1-4A32-B367-850B9219E456@gmail.com> If you are looking to submit to Genebank, tools like GAL are good (https://github.com/The-Sequence-Ontology/GAL ). Things like accession which you listed below only exist inside of GeneBank (i.e. after you submit). They are not produced by pipelines or format converters. ?Carson > On May 21, 2019, at 6:11 AM, djerroud samia wrote: > > Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations > > cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... > My problem is I don't know the pipeline I should follow to get all this informaitions > > thank you, Samia > > Le mar. 21 mai 2019 ? 07:25, p sz > a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > De: Xabier V?zquez-Campos > > Enviado: jueves, 16 de mayo de 2019 4:42 > Para: p sz > Cc: maker-devel at yandell-lab.org > Asunto: Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl . I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz > wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- > Xabier V?zquez-Campos, PhD > Research Associate > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 eduardoconrados at gmail.com Fri May 31 14:27:14 2019 From: eduardoconrados at gmail.com (Eduardo Conrado Souza Queiroz Nascimento) Date: Fri, 31 May 2019 19:27:14 -0000 Subject: [maker-devel] Problems with ipr_update_gff Message-ID: Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Wed May 1 04:25:09 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Wed, 1 May 2019 10:25:09 +0000 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? Message-ID: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Hi Carson and Maker dev team, Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 I cite: "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " I am wondering: 1) Where did you find these statistics ? 2) Do you have new statistics for 2019 ? 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? Thanks. Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon May 6 10:26:18 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 6 May 2019 10:26:18 -0600 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? In-Reply-To: <92f0dde60f734f259c92feb1a085d31b@unil.ch> References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <0C9F80D5-E0DB-4024-9E34-C510E7033034@gmail.com> Those numbers came from https://gold.jgi.doe.gov You can download their tables and filter the data on different attributes. ?Carson > On May 1, 2019, at 4:25 AM, Patrick Tran Van wrote: > > Hi Carson and Maker dev team, > > Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 > > I cite: > > "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " > > "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " > > I am wondering: > > 1) Where did you find these statistics ? > > 2) Do you have new statistics for 2019 ? > > 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? > > Thanks. > > > Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.ence at ufl.edu Mon May 13 07:12:13 2019 From: d.ence at ufl.edu (Ence,daniel) Date: Mon, 13 May 2019 13:12:13 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: References: Message-ID: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Mon May 13 07:50:26 2019 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 13 May 2019 13:50:26 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> References: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Message-ID: <181B8E01-422F-4685-AEEC-A66DEB7B88ED@umail.utah.edu> Hey Dan, How?s life? What are you up to these days? --mark From: maker-devel on behalf of "Ence,daniel" Date: Monday, May 13, 2019 at 7:21 AM To: Christian Ayala Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Running out of time in MAKER Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 14 02:12:09 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 14 May 2019 08:12:09 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch>, Message-ID: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed May 15 09:49:43 2019 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 15 May 2019 09:49:43 -0600 Subject: [maker-devel] Redundant FASTA headers In-Reply-To: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> References: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> Message-ID: <59A2492E-2568-4326-9EC3-BE19D0EE79CC@gmail.com> Headers are used to pull individual sequences out for exonerate polishing. So non-unique headers could result in the wrong sequence being pulled out (it makes the fasta index ambiguous). ?Carson > On Apr 24, 2019, at 1:42 AM, Bastian Schiffthaler wrote: > > Hi, > > I'm running the MPI version of MAKER and I'm supplying seven different trinity assemblies (different experiments) as evidence. Now trinity will not generate unique FASTA headers >across< files, so I'm wondering if there could be an issue with ID collision? What does MAKER use the headers for? Could it create race conditions in temp files? > > Thanks in advance, > Bastian > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Wed May 15 22:42:20 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Thu, 16 May 2019 14:42:20 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Fri May 17 08:30:27 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Fri, 17 May 2019 10:30:27 -0400 Subject: [maker-devel] genome annnotation by maker Message-ID: Hello, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Sat May 18 22:10:23 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Sun, 19 May 2019 04:10:23 +0000 Subject: [maker-devel] Maker errors In-Reply-To: References: <3345C6C6-07A5-41A1-8486-37C3005915E5@genetics.utah.edu> Message-ID: On May 18, 2019, at 10:10 PM, Carson Hinton Holt > wrote: Hi Samia, I?ve CC?d my reply to the devel list as well. MAKER can annotate gene positions on prokaryotes although it?s best suited for eukaryotic genomes. It does only support canonical codon usage though (so would not be usful if the prakaryote you are interested has any other codon table). You need to train a predictor like genemark first, although the protein2genome prediction option works relatively well in prokaryotes. Output is in fasta and GFF3 format. If you need GeneBank format (what you have below) you will need to convert. There are tools out there like GAG that can help convert MAKER output for GenBank submission. ?Carson On May 17, 2019, at 2:30 AM, djerroud samia > wrote: Hello, thank you for your answer, I suscribed to the mailing list, but seems that it will take a little time. My question is quite urgent. IF you can answer to my answers from here it would be cool. Well, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia Le jeu. 16 mai 2019 ? 14:25, Carson Hinton Holt > a ?crit : You can post error to the MAKER devel mailing list ?> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org You can search for previous posts to the devel list here (FYI, the google group used is an archive, you must still post original questions to the list above) ?> http://groups.google.com/group/maker-devel Also general info is at wiki here ?> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page ?Carson On May 16, 2019, at 7:13 AM, djerroud samia > wrote: Hello, I am very new in using maker, I get some errors. can you tell me who is the person who deals with the technical problems of maker Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 21 05:25:33 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 21 May 2019 11:25:33 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> , Message-ID: Hi Xavier I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. By the way, I would like to show you my training steps with augustus, in order to know if they are correct: zff2augustus_gbk.pl export.ann export.dna > final_genes.gb randomSplit.pl final_genes.gb 500 new_species.pl --species=Demo etraining --species=Demo final_genes.gb optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test etraining --species=Demo final_genes.gb I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. Thank you in advance Pedro Seoane ________________________________ De: Xabier V?zquez-Campos Enviado: jueves, 16 de mayo de 2019 4:42 Para: p sz Cc: maker-devel at yandell-lab.org Asunto: Re: [maker-devel] RV: Problem training agustus Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz > wrote: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Xabier V?zquez-Campos, PhD Research Associate NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Tue May 21 06:11:18 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Tue, 21 May 2019 08:11:18 -0400 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... My problem is I don't know the pipeline I should follow to get all this informaitions thank you, Samia Le mar. 21 mai 2019 ? 07:25, p sz a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 xvazquezc at gmail.com Tue May 21 17:56:31 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 22 May 2019 09:56:31 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, this is what I did the last time I run it. I had RNAseq, the genome is soft-masked and the training set is the one from zff2augustus_gbk.pl. You only need one step with autoAug.pl, it should be included with your installation of AUGUSTUS AUG_TRAIN= #workingdir MYSP= #name used for the gene model in the augustus config folder RNA_SEQ= #assembled RNAseq data GENOME= #soft-masked genome TRAIN=${BASE}/snap1/pugra.train1.gb mkdir -p ${AUG_TRAIN} cd ${AUG_TRAIN} autoAug.pl --noninteractive -v -v -v \ --cpus=${PBS_NUM_PPN} \ --maxIntronLen=3000 \ --species=${MYSP} \ --genome=${GENOME} \ --cdna=${RNA_SEQ} \ --trainingset=${TRAIN} \ --optrounds=5 \ --workingdir=${AUG_TRAIN} On Tue, 21 May 2019 at 21:25, p sz wrote: > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From liqing850104 at gmail.com Wed May 22 10:18:06 2019 From: liqing850104 at gmail.com (=?UTF-8?B?5p2O6Z2SIExpLCBRaW5n?=) Date: Wed, 22 May 2019 10:18:06 -0600 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila wrote: > Dear Maker group > My name is Nazila, I am a Ph.D. student at Miami University. I'm working > on *Phrynosoma platyrhinos *genome annotation and I'm trying to use > MAKER. So as a requirement I'm trying to use tRNAscan. First I used the > latest version (2.0) and I got the first -q file but I faced a warning like > this: > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > And I tried overwrite and append but it just froze and didn't work anymore. > So I tried to use an older version (1.3.1) but this one is hard to make it > work too. I'm getting an error: > > Can't locate object method "new" via package "tRNAscanSE::Constants" > (perhaps you forgot to load "tRNAscanSE::Constants"?) at > /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. > > Would you please help me with it? Which version should I use? And how > could I solve the problem for that version? > Looking forward for your reply; > Thanks, > Nazila > -------------- next part -------------- An HTML attachment was scrubbed... URL: From atalgarni at gmail.com Wed May 22 05:51:29 2019 From: atalgarni at gmail.com (Abdulmalek Algarni) Date: Wed, 22 May 2019 14:51:29 +0300 Subject: [maker-devel] Failed to run maker after install Message-ID: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Hi there, I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h Couldn't find an appropriate DIRECTORY for Inline to use. at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. Compilation failed in require at (eval 27) line 2. ...propagated at /System/Library/Perl/5.18/base.pm line 84. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. Compilation failed in require at ./maker line 62. BEGIN failed--compilation aborted at ./maker line 62. For the other excutables here is an example : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff Usage: cegma2zff This script converts the output GFF file from CEGMA into ZFF format for use in SNAP training. Output files are always genome.ann and genome.dna. Best regards, Abdulmalek -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 23 10:44:11 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 May 2019 10:44:11 -0600 Subject: [maker-devel] Failed to run maker after install In-Reply-To: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> References: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Message-ID: <47C0BDC5-5B9A-4562-B9D6-3BC74A10BCFC@gmail.com> Install live version of BioPerl, then reinsall MAKER against that ?> https://github.com/bioperl/bioperl-live There is a BioPerl related issue with Inline::C that has been fixed. ?Carson > On May 22, 2019, at 5:51 AM, Abdulmalek Algarni wrote: > > Hi there, > > I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : > > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h > Couldn't find an appropriate DIRECTORY for Inline to use. > > at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. > Compilation failed in require at (eval 27) line 2. > ...propagated at /System/Library/Perl/5.18/base.pm line 84. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. > Compilation failed in require at ./maker line 62. > BEGIN failed--compilation aborted at ./maker line 62. > > > For the other excutables here is an example : > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff > > Usage: > cegma2zff > > This script converts the output GFF file from CEGMA into ZFF format > for use in SNAP training. Output files are always genome.ann and > genome.dna. > > > > Best regards, > > Abdulmalek > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Thu May 23 20:12:22 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Fri, 24 May 2019 02:12:22 +0000 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: <6700FDE9-0114-4774-A578-8F30DEB8BE3B@genetics.utah.edu> Use version 1.3.1 (last stable version for 1.X series), we haven?t updated maker to handle tRNAscan version 2 options and output yet. All version here ?> http://trna.ucsc.edu/software/ ?Carson On May 22, 2019, at 10:18 AM, ?? Li, Qing > wrote: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila > wrote: Dear Maker group My name is Nazila, I am a Ph.D. student at Miami University. I'm working on Phrynosoma platyrhinos genome annotation and I'm trying to use MAKER. So as a requirement I'm trying to use tRNAscan. First I used the latest version (2.0) and I got the first -q file but I faced a warning like this: WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? And I tried overwrite and append but it just froze and didn't work anymore. So I tried to use an older version (1.3.1) but this one is hard to make it work too. I'm getting an error: Can't locate object method "new" via package "tRNAscanSE::Constants" (perhaps you forgot to load "tRNAscanSE::Constants"?) at /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. Would you please help me with it? Which version should I use? And how could I solve the problem for that version? Looking forward for your reply; Thanks, Nazila -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 30 12:09:20 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 30 May 2019 12:09:20 -0600 Subject: [maker-devel] Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <3180F4FE-30B1-4A32-B367-850B9219E456@gmail.com> If you are looking to submit to Genebank, tools like GAL are good (https://github.com/The-Sequence-Ontology/GAL ). Things like accession which you listed below only exist inside of GeneBank (i.e. after you submit). They are not produced by pipelines or format converters. ?Carson > On May 21, 2019, at 6:11 AM, djerroud samia wrote: > > Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations > > cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... > My problem is I don't know the pipeline I should follow to get all this informaitions > > thank you, Samia > > Le mar. 21 mai 2019 ? 07:25, p sz > a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > De: Xabier V?zquez-Campos > > Enviado: jueves, 16 de mayo de 2019 4:42 > Para: p sz > Cc: maker-devel at yandell-lab.org > Asunto: Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl . I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz > wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- > Xabier V?zquez-Campos, PhD > Research Associate > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 eduardoconrados at gmail.com Fri May 31 13:27:14 2019 From: eduardoconrados at gmail.com (Eduardo Conrado Souza Queiroz Nascimento) Date: Fri, 31 May 2019 19:27:14 -0000 Subject: [maker-devel] Problems with ipr_update_gff Message-ID: Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Wed May 1 04:25:09 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Wed, 1 May 2019 10:25:09 +0000 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? Message-ID: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Hi Carson and Maker dev team, Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 I cite: "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " I am wondering: 1) Where did you find these statistics ? 2) Do you have new statistics for 2019 ? 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? Thanks. Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon May 6 10:26:18 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 6 May 2019 10:26:18 -0600 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? In-Reply-To: <92f0dde60f734f259c92feb1a085d31b@unil.ch> References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <0C9F80D5-E0DB-4024-9E34-C510E7033034@gmail.com> Those numbers came from https://gold.jgi.doe.gov You can download their tables and filter the data on different attributes. ?Carson > On May 1, 2019, at 4:25 AM, Patrick Tran Van wrote: > > Hi Carson and Maker dev team, > > Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 > > I cite: > > "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " > > "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " > > I am wondering: > > 1) Where did you find these statistics ? > > 2) Do you have new statistics for 2019 ? > > 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? > > Thanks. > > > Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.ence at ufl.edu Mon May 13 07:12:13 2019 From: d.ence at ufl.edu (Ence,daniel) Date: Mon, 13 May 2019 13:12:13 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: References: Message-ID: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Mon May 13 07:50:26 2019 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 13 May 2019 13:50:26 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> References: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Message-ID: <181B8E01-422F-4685-AEEC-A66DEB7B88ED@umail.utah.edu> Hey Dan, How?s life? What are you up to these days? --mark From: maker-devel on behalf of "Ence,daniel" Date: Monday, May 13, 2019 at 7:21 AM To: Christian Ayala Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Running out of time in MAKER Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 14 02:12:09 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 14 May 2019 08:12:09 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch>, Message-ID: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed May 15 09:49:43 2019 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 15 May 2019 09:49:43 -0600 Subject: [maker-devel] Redundant FASTA headers In-Reply-To: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> References: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> Message-ID: <59A2492E-2568-4326-9EC3-BE19D0EE79CC@gmail.com> Headers are used to pull individual sequences out for exonerate polishing. So non-unique headers could result in the wrong sequence being pulled out (it makes the fasta index ambiguous). ?Carson > On Apr 24, 2019, at 1:42 AM, Bastian Schiffthaler wrote: > > Hi, > > I'm running the MPI version of MAKER and I'm supplying seven different trinity assemblies (different experiments) as evidence. Now trinity will not generate unique FASTA headers >across< files, so I'm wondering if there could be an issue with ID collision? What does MAKER use the headers for? Could it create race conditions in temp files? > > Thanks in advance, > Bastian > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Wed May 15 22:42:20 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Thu, 16 May 2019 14:42:20 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Fri May 17 08:30:27 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Fri, 17 May 2019 10:30:27 -0400 Subject: [maker-devel] genome annnotation by maker Message-ID: Hello, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Sat May 18 22:10:23 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Sun, 19 May 2019 04:10:23 +0000 Subject: [maker-devel] Maker errors In-Reply-To: References: <3345C6C6-07A5-41A1-8486-37C3005915E5@genetics.utah.edu> Message-ID: On May 18, 2019, at 10:10 PM, Carson Hinton Holt > wrote: Hi Samia, I?ve CC?d my reply to the devel list as well. MAKER can annotate gene positions on prokaryotes although it?s best suited for eukaryotic genomes. It does only support canonical codon usage though (so would not be usful if the prakaryote you are interested has any other codon table). You need to train a predictor like genemark first, although the protein2genome prediction option works relatively well in prokaryotes. Output is in fasta and GFF3 format. If you need GeneBank format (what you have below) you will need to convert. There are tools out there like GAG that can help convert MAKER output for GenBank submission. ?Carson On May 17, 2019, at 2:30 AM, djerroud samia > wrote: Hello, thank you for your answer, I suscribed to the mailing list, but seems that it will take a little time. My question is quite urgent. IF you can answer to my answers from here it would be cool. Well, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia Le jeu. 16 mai 2019 ? 14:25, Carson Hinton Holt > a ?crit : You can post error to the MAKER devel mailing list ?> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org You can search for previous posts to the devel list here (FYI, the google group used is an archive, you must still post original questions to the list above) ?> http://groups.google.com/group/maker-devel Also general info is at wiki here ?> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page ?Carson On May 16, 2019, at 7:13 AM, djerroud samia > wrote: Hello, I am very new in using maker, I get some errors. can you tell me who is the person who deals with the technical problems of maker Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 21 05:25:33 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 21 May 2019 11:25:33 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> , Message-ID: Hi Xavier I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. By the way, I would like to show you my training steps with augustus, in order to know if they are correct: zff2augustus_gbk.pl export.ann export.dna > final_genes.gb randomSplit.pl final_genes.gb 500 new_species.pl --species=Demo etraining --species=Demo final_genes.gb optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test etraining --species=Demo final_genes.gb I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. Thank you in advance Pedro Seoane ________________________________ De: Xabier V?zquez-Campos Enviado: jueves, 16 de mayo de 2019 4:42 Para: p sz Cc: maker-devel at yandell-lab.org Asunto: Re: [maker-devel] RV: Problem training agustus Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz > wrote: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Xabier V?zquez-Campos, PhD Research Associate NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Tue May 21 06:11:18 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Tue, 21 May 2019 08:11:18 -0400 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... My problem is I don't know the pipeline I should follow to get all this informaitions thank you, Samia Le mar. 21 mai 2019 ? 07:25, p sz a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 xvazquezc at gmail.com Tue May 21 17:56:31 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 22 May 2019 09:56:31 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, this is what I did the last time I run it. I had RNAseq, the genome is soft-masked and the training set is the one from zff2augustus_gbk.pl. You only need one step with autoAug.pl, it should be included with your installation of AUGUSTUS AUG_TRAIN= #workingdir MYSP= #name used for the gene model in the augustus config folder RNA_SEQ= #assembled RNAseq data GENOME= #soft-masked genome TRAIN=${BASE}/snap1/pugra.train1.gb mkdir -p ${AUG_TRAIN} cd ${AUG_TRAIN} autoAug.pl --noninteractive -v -v -v \ --cpus=${PBS_NUM_PPN} \ --maxIntronLen=3000 \ --species=${MYSP} \ --genome=${GENOME} \ --cdna=${RNA_SEQ} \ --trainingset=${TRAIN} \ --optrounds=5 \ --workingdir=${AUG_TRAIN} On Tue, 21 May 2019 at 21:25, p sz wrote: > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From liqing850104 at gmail.com Wed May 22 10:18:06 2019 From: liqing850104 at gmail.com (=?UTF-8?B?5p2O6Z2SIExpLCBRaW5n?=) Date: Wed, 22 May 2019 10:18:06 -0600 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila wrote: > Dear Maker group > My name is Nazila, I am a Ph.D. student at Miami University. I'm working > on *Phrynosoma platyrhinos *genome annotation and I'm trying to use > MAKER. So as a requirement I'm trying to use tRNAscan. First I used the > latest version (2.0) and I got the first -q file but I faced a warning like > this: > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > And I tried overwrite and append but it just froze and didn't work anymore. > So I tried to use an older version (1.3.1) but this one is hard to make it > work too. I'm getting an error: > > Can't locate object method "new" via package "tRNAscanSE::Constants" > (perhaps you forgot to load "tRNAscanSE::Constants"?) at > /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. > > Would you please help me with it? Which version should I use? And how > could I solve the problem for that version? > Looking forward for your reply; > Thanks, > Nazila > -------------- next part -------------- An HTML attachment was scrubbed... URL: From atalgarni at gmail.com Wed May 22 05:51:29 2019 From: atalgarni at gmail.com (Abdulmalek Algarni) Date: Wed, 22 May 2019 14:51:29 +0300 Subject: [maker-devel] Failed to run maker after install Message-ID: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Hi there, I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h Couldn't find an appropriate DIRECTORY for Inline to use. at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. Compilation failed in require at (eval 27) line 2. ...propagated at /System/Library/Perl/5.18/base.pm line 84. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. Compilation failed in require at ./maker line 62. BEGIN failed--compilation aborted at ./maker line 62. For the other excutables here is an example : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff Usage: cegma2zff This script converts the output GFF file from CEGMA into ZFF format for use in SNAP training. Output files are always genome.ann and genome.dna. Best regards, Abdulmalek -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 23 10:44:11 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 May 2019 10:44:11 -0600 Subject: [maker-devel] Failed to run maker after install In-Reply-To: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> References: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Message-ID: <47C0BDC5-5B9A-4562-B9D6-3BC74A10BCFC@gmail.com> Install live version of BioPerl, then reinsall MAKER against that ?> https://github.com/bioperl/bioperl-live There is a BioPerl related issue with Inline::C that has been fixed. ?Carson > On May 22, 2019, at 5:51 AM, Abdulmalek Algarni wrote: > > Hi there, > > I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : > > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h > Couldn't find an appropriate DIRECTORY for Inline to use. > > at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. > Compilation failed in require at (eval 27) line 2. > ...propagated at /System/Library/Perl/5.18/base.pm line 84. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. > Compilation failed in require at ./maker line 62. > BEGIN failed--compilation aborted at ./maker line 62. > > > For the other excutables here is an example : > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff > > Usage: > cegma2zff > > This script converts the output GFF file from CEGMA into ZFF format > for use in SNAP training. Output files are always genome.ann and > genome.dna. > > > > Best regards, > > Abdulmalek > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Thu May 23 20:12:22 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Fri, 24 May 2019 02:12:22 +0000 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: <6700FDE9-0114-4774-A578-8F30DEB8BE3B@genetics.utah.edu> Use version 1.3.1 (last stable version for 1.X series), we haven?t updated maker to handle tRNAscan version 2 options and output yet. All version here ?> http://trna.ucsc.edu/software/ ?Carson On May 22, 2019, at 10:18 AM, ?? Li, Qing > wrote: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila > wrote: Dear Maker group My name is Nazila, I am a Ph.D. student at Miami University. I'm working on Phrynosoma platyrhinos genome annotation and I'm trying to use MAKER. So as a requirement I'm trying to use tRNAscan. First I used the latest version (2.0) and I got the first -q file but I faced a warning like this: WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? And I tried overwrite and append but it just froze and didn't work anymore. So I tried to use an older version (1.3.1) but this one is hard to make it work too. I'm getting an error: Can't locate object method "new" via package "tRNAscanSE::Constants" (perhaps you forgot to load "tRNAscanSE::Constants"?) at /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. Would you please help me with it? Which version should I use? And how could I solve the problem for that version? Looking forward for your reply; Thanks, Nazila -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 30 12:09:20 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 30 May 2019 12:09:20 -0600 Subject: [maker-devel] Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <3180F4FE-30B1-4A32-B367-850B9219E456@gmail.com> If you are looking to submit to Genebank, tools like GAL are good (https://github.com/The-Sequence-Ontology/GAL ). Things like accession which you listed below only exist inside of GeneBank (i.e. after you submit). They are not produced by pipelines or format converters. ?Carson > On May 21, 2019, at 6:11 AM, djerroud samia wrote: > > Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations > > cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... > My problem is I don't know the pipeline I should follow to get all this informaitions > > thank you, Samia > > Le mar. 21 mai 2019 ? 07:25, p sz > a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > De: Xabier V?zquez-Campos > > Enviado: jueves, 16 de mayo de 2019 4:42 > Para: p sz > Cc: maker-devel at yandell-lab.org > Asunto: Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl . I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz > wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- > Xabier V?zquez-Campos, PhD > Research Associate > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 eduardoconrados at gmail.com Fri May 31 13:27:14 2019 From: eduardoconrados at gmail.com (Eduardo Conrado Souza Queiroz Nascimento) Date: Fri, 31 May 2019 19:27:14 -0000 Subject: [maker-devel] Problems with ipr_update_gff Message-ID: Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. -------------- next part -------------- An HTML attachment was scrubbed... URL: From patrick.tranvan at unil.ch Wed May 1 04:25:09 2019 From: patrick.tranvan at unil.ch (Patrick Tran Van) Date: Wed, 1 May 2019 10:25:09 +0000 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? Message-ID: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Hi Carson and Maker dev team, Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 I cite: "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " I am wondering: 1) Where did you find these statistics ? 2) Do you have new statistics for 2019 ? 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? Thanks. Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Mon May 6 10:26:18 2019 From: carsonhh at gmail.com (Carson Holt) Date: Mon, 6 May 2019 10:26:18 -0600 Subject: [maker-devel] Statistics about genomes and annotation in 2019 ? In-Reply-To: <92f0dde60f734f259c92feb1a085d31b@unil.ch> References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <0C9F80D5-E0DB-4024-9E34-C510E7033034@gmail.com> Those numbers came from https://gold.jgi.doe.gov You can download their tables and filter the data on different attributes. ?Carson > On May 1, 2019, at 4:25 AM, Patrick Tran Van wrote: > > Hi Carson and Maker dev team, > > Based on that website: http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018 > > I cite: > > "As of January 2018, 8,955 Eukaryotic genome projects were at various stages of completion (4,683 were still being sequenced and 4,272 had at least a draft assembly, but not necessarily gene annotations). " > > "There are an additional 82,859 prokaryotic genome projects with various stages of completion with hundred of millions of additional potential gene annotations. " > > I am wondering: > > 1) Where did you find these statistics ? > > 2) Do you have new statistics for 2019 ? > > 3) I am interesed especially for genomes that have been assembled and annotated "independently" ( so NOT by Ensembl or NCBI), do you have any number or documentations about it ? > > Thanks. > > > Patrick T -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.ence at ufl.edu Mon May 13 07:12:13 2019 From: d.ence at ufl.edu (Ence,daniel) Date: Mon, 13 May 2019 13:12:13 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: References: Message-ID: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From myandell at genetics.utah.edu Mon May 13 07:50:26 2019 From: myandell at genetics.utah.edu (Mark Yandell) Date: Mon, 13 May 2019 13:50:26 +0000 Subject: [maker-devel] Running out of time in MAKER In-Reply-To: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> References: <94D6B826-D29F-4D95-B318-71E519CBAA4C@ufl.edu> Message-ID: <181B8E01-422F-4685-AEEC-A66DEB7B88ED@umail.utah.edu> Hey Dan, How?s life? What are you up to these days? --mark From: maker-devel on behalf of "Ence,daniel" Date: Monday, May 13, 2019 at 7:21 AM To: Christian Ayala Cc: "maker-devel at yandell-lab.org" Subject: Re: [maker-devel] Running out of time in MAKER Hi Christian, If you restart maker on the same output directory, maker will start from where it left off and continue. You can also speed up your maker run by using it's MPI parallelization capabilities or by running multiple maker instances on the same output directory. Hopefully this is helps, Daniel Ence Daniel Ence Postdoctoral Associate School of Forest Resources and Conservation University of Florida On Apr 30, 2019, at 2:42 PM, Christian Ayala > wrote: Good afternoon, I am trying to annotate some insect genomes using MAKER. MAKER is running in a system that uses a PBS scheduler and has a walltime of 120 hours. So , my jobs are running out of time and are killed before MAKER finishes the annotation. Is there a way to resume a killed MAKER run? Thanks for your help. Best regards, Christian Ayala-Ortiz _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com https://urldefense.proofpoint.com/v2/url?u=http-3A__box290.bluehost.com_mailman_listinfo_maker-2Ddevel-5Fyandell-2Dlab.org&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=SEXKDKpdOPS3f7lTbi9ULp36zhWcE30DCUfP3txgY4I&m=Hj-EmkEU1CUoanurMvuwBOKLHp6iiKBxuv3y1JcIh-8&s=66il2ByeMbl3HRuB-XkVxVfM7ntNSs9Q9A6ejXJWbCU&e= -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 14 02:12:09 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 14 May 2019 08:12:09 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch>, Message-ID: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Wed May 15 09:49:43 2019 From: carsonhh at gmail.com (Carson Holt) Date: Wed, 15 May 2019 09:49:43 -0600 Subject: [maker-devel] Redundant FASTA headers In-Reply-To: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> References: <251d38f5-c15a-6070-fcd9-d6144744885e@umu.se> Message-ID: <59A2492E-2568-4326-9EC3-BE19D0EE79CC@gmail.com> Headers are used to pull individual sequences out for exonerate polishing. So non-unique headers could result in the wrong sequence being pulled out (it makes the fasta index ambiguous). ?Carson > On Apr 24, 2019, at 1:42 AM, Bastian Schiffthaler wrote: > > Hi, > > I'm running the MPI version of MAKER and I'm supplying seven different trinity assemblies (different experiments) as evidence. Now trinity will not generate unique FASTA headers >across< files, so I'm wondering if there could be an issue with ID collision? What does MAKER use the headers for? Could it create race conditions in temp files? > > Thanks in advance, > Bastian > > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org From xvazquezc at gmail.com Wed May 15 22:42:20 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Thu, 16 May 2019 14:42:20 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Fri May 17 08:30:27 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Fri, 17 May 2019 10:30:27 -0400 Subject: [maker-devel] genome annnotation by maker Message-ID: Hello, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Sat May 18 22:10:23 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Sun, 19 May 2019 04:10:23 +0000 Subject: [maker-devel] Maker errors In-Reply-To: References: <3345C6C6-07A5-41A1-8486-37C3005915E5@genetics.utah.edu> Message-ID: On May 18, 2019, at 10:10 PM, Carson Hinton Holt > wrote: Hi Samia, I?ve CC?d my reply to the devel list as well. MAKER can annotate gene positions on prokaryotes although it?s best suited for eukaryotic genomes. It does only support canonical codon usage though (so would not be usful if the prakaryote you are interested has any other codon table). You need to train a predictor like genemark first, although the protein2genome prediction option works relatively well in prokaryotes. Output is in fasta and GFF3 format. If you need GeneBank format (what you have below) you will need to convert. There are tools out there like GAG that can help convert MAKER output for GenBank submission. ?Carson On May 17, 2019, at 2:30 AM, djerroud samia > wrote: Hello, thank you for your answer, I suscribed to the mailing list, but seems that it will take a little time. My question is quite urgent. IF you can answer to my answers from here it would be cool. Well, I am trying to do the structural annotation of procaryotic genomes and metagenomes. I want to get the positions with the sequence of cds and the gaps. Something like that: gene 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" CDS 478..1299 /locus_tag="DU99_RS00005" /old_locus_tag="DU99_00005" /function="miscellaneous; hypothetical/global homology" /inference="COORDINATES: similar to AA sequence:RefSeq:NP_384107.1" /note="Derived by automated computational analysis using gene prediction method: Protein Homology." /codon_start=1 /transl_table=11 /product="phosphoenolpyruvate synthase regulatory protein" /protein_id="WP_010968285.1" /translation="MENRKNYFHLHLISDSTGETLIAAGRAAAAQFQSSHALEHVYPL IRNRKQLMQVMDAVDGAPGIVLYTIVDRELAGLIDQRCREIGVPCVSVLDPIIELFQS YLGSPSRRRSGAQHVMDAEYFARIEALNFTMDHDDGQVPSDFNEADVVLVGVSRTSKT PTSIYLANRGIKTANIPIVPGVPLPDALLKATKPLIVGLIASAERLSQVRQHRVLGTT QSFHGEDYTDRAAIAEELKYARSLCARNNWPLIDVTRRSIEETAAAIVALRPRLR" Do you think that maker can help me to do that ?? IF so what is the part of maker that can do that ?? I will really appreciate if you help me :) Thank you, Samia Le jeu. 16 mai 2019 ? 14:25, Carson Hinton Holt > a ?crit : You can post error to the MAKER devel mailing list ?> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org You can search for previous posts to the devel list here (FYI, the google group used is an archive, you must still post original questions to the list above) ?> http://groups.google.com/group/maker-devel Also general info is at wiki here ?> http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page ?Carson On May 16, 2019, at 7:13 AM, djerroud samia > wrote: Hello, I am very new in using maker, I get some errors. can you tell me who is the person who deals with the technical problems of maker Thank you, Samia -------------- next part -------------- An HTML attachment was scrubbed... URL: From seoanezonjic at hotmail.com Tue May 21 05:25:33 2019 From: seoanezonjic at hotmail.com (p sz) Date: Tue, 21 May 2019 11:25:33 +0000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> , Message-ID: Hi Xavier I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. By the way, I would like to show you my training steps with augustus, in order to know if they are correct: zff2augustus_gbk.pl export.ann export.dna > final_genes.gb randomSplit.pl final_genes.gb 500 new_species.pl --species=Demo etraining --species=Demo final_genes.gb optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test etraining --species=Demo final_genes.gb I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. Thank you in advance Pedro Seoane ________________________________ De: Xabier V?zquez-Campos Enviado: jueves, 16 de mayo de 2019 4:42 Para: p sz Cc: maker-devel at yandell-lab.org Asunto: Re: [maker-devel] RV: Problem training agustus Hi Pedro, I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl Cheers, Xabi On Tue, 14 May 2019 at 18:12, p sz > wrote: Hi Maker author I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: zff2genbank.pl export.ann export.dna > final_genes.gb train_augustus.pl final_genes.gb MyOrg For each of my gene models the error is the following: Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. Encountered error after reading 0 annotations. The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: (export.ann file) >MODEL236 Eterm 23624 23647 MODEL236 Exon 23354 23549 MODEL236 Exon 23004 23249 MODEL236 Exon 20923 21067 MODEL236 Exon 20389 20558 MODEL236 Exon 18821 18898 MODEL236 Exon 18471 18637 MODEL236 Exon 14945 14971 MODEL236 Exon 13511 13598 MODEL236 Exon 11920 13315 MODEL236 Exon 10459 10467 MODEL236 Exon 8873 9050 MODEL236 Exon 8628 8775 MODEL236 Exon 8374 8485 MODEL236 Exon 7880 7993 MODEL236 Exon 7689 7791 MODEL236 Exon 1917 2051 MODEL236 Einit 1001 1006 MODEL236 (genbankfile) LOCUS MODEL236 24647 bp dna linear UNK ACCESSION unknown FEATURES Location/Qualifiers source 1..24647 CDS complement(join(1006..1001,2051..1917,7791..7689, 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, 13315..11920,13598..13511,14971..14945,18637..18471, 18898..18821,20558..20389,21067..20923,23249..23004, 23549..23354,23647..23624)) It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? Thank you in advance Pedro Seoane _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -- Xabier V?zquez-Campos, PhD Research Associate NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From djerroudsamia at gmail.com Tue May 21 06:11:18 2019 From: djerroudsamia at gmail.com (djerroud samia) Date: Tue, 21 May 2019 08:11:18 -0400 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... My problem is I don't know the pipeline I should follow to get all this informaitions thank you, Samia Le mar. 21 mai 2019 ? 07:25, p sz a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 xvazquezc at gmail.com Tue May 21 17:56:31 2019 From: xvazquezc at gmail.com (=?UTF-8?Q?Xabier_V=C3=A1zquez=2DCampos?=) Date: Wed, 22 May 2019 09:56:31 +1000 Subject: [maker-devel] RV: Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: Hi Pedro, this is what I did the last time I run it. I had RNAseq, the genome is soft-masked and the training set is the one from zff2augustus_gbk.pl. You only need one step with autoAug.pl, it should be included with your installation of AUGUSTUS AUG_TRAIN= #workingdir MYSP= #name used for the gene model in the augustus config folder RNA_SEQ= #assembled RNAseq data GENOME= #soft-masked genome TRAIN=${BASE}/snap1/pugra.train1.gb mkdir -p ${AUG_TRAIN} cd ${AUG_TRAIN} autoAug.pl --noninteractive -v -v -v \ --cpus=${PBS_NUM_PPN} \ --maxIntronLen=3000 \ --species=${MYSP} \ --genome=${GENOME} \ --cdna=${RNA_SEQ} \ --trainingset=${TRAIN} \ --optrounds=5 \ --workingdir=${AUG_TRAIN} On Tue, 21 May 2019 at 21:25, p sz wrote: > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the > problem is fixed. I used zff2genbank.pl because it is packaged into the > maker suite. I think that MAKER authors should include zff2augustus_gbk.pl > into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in > order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train > final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from > the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > ------------------------------ > *De:* Xabier V?zquez-Campos > *Enviado:* jueves, 16 de mayo de 2019 4:42 > *Para:* p sz > *Cc:* maker-devel at yandell-lab.org > *Asunto:* Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the > inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember > the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: > https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz wrote: > > Hi Maker author > I have been using Maker for long years and recently, I've tried to train > agustus using the snap training files. To do this, I have used the > train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: > 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when > reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference > guides (two maker rounds). The issue seems related with the sense of the > gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene > model in order to read the gb file and perform the training. How could I > fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > > -- > Xabier V?zquez-Campos, *PhD* > *Research Associate* > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > -- Xabier V?zquez-Campos, *PhD* *Research Associate* NSW Systems Biology Initiative School of Biotechnology and Biomolecular Sciences The University of New South Wales Sydney NSW 2052 AUSTRALIA -------------- next part -------------- An HTML attachment was scrubbed... URL: From liqing850104 at gmail.com Wed May 22 10:18:06 2019 From: liqing850104 at gmail.com (=?UTF-8?B?5p2O6Z2SIExpLCBRaW5n?=) Date: Wed, 22 May 2019 10:18:06 -0600 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila wrote: > Dear Maker group > My name is Nazila, I am a Ph.D. student at Miami University. I'm working > on *Phrynosoma platyrhinos *genome annotation and I'm trying to use > MAKER. So as a requirement I'm trying to use tRNAscan. First I used the > latest version (2.0) and I got the first -q file but I faced a warning like > this: > > WARNING: -q exists already. > > (O)verwrite file, (A)ppend to file, or (Q)uit program? > > And I tried overwrite and append but it just froze and didn't work anymore. > So I tried to use an older version (1.3.1) but this one is hard to make it > work too. I'm getting an error: > > Can't locate object method "new" via package "tRNAscanSE::Constants" > (perhaps you forgot to load "tRNAscanSE::Constants"?) at > /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. > > Would you please help me with it? Which version should I use? And how > could I solve the problem for that version? > Looking forward for your reply; > Thanks, > Nazila > -------------- next part -------------- An HTML attachment was scrubbed... URL: From atalgarni at gmail.com Wed May 22 05:51:29 2019 From: atalgarni at gmail.com (Abdulmalek Algarni) Date: Wed, 22 May 2019 14:51:29 +0300 Subject: [maker-devel] Failed to run maker after install Message-ID: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Hi there, I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h Couldn't find an appropriate DIRECTORY for Inline to use. at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. Compilation failed in require at (eval 27) line 2. ...propagated at /System/Library/Perl/5.18/base.pm line 84. BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. Compilation failed in require at ./maker line 62. BEGIN failed--compilation aborted at ./maker line 62. For the other excutables here is an example : Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff Usage: cegma2zff This script converts the output GFF file from CEGMA into ZFF format for use in SNAP training. Output files are always genome.ann and genome.dna. Best regards, Abdulmalek -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 23 10:44:11 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 23 May 2019 10:44:11 -0600 Subject: [maker-devel] Failed to run maker after install In-Reply-To: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> References: <360FF947-5ABD-4C1F-A5CF-3F71188F43AA@gmail.com> Message-ID: <47C0BDC5-5B9A-4562-B9D6-3BC74A10BCFC@gmail.com> Install live version of BioPerl, then reinsall MAKER against that ?> https://github.com/bioperl/bioperl-live There is a BioPerl related issue with Inline::C that has been fixed. ?Carson > On May 22, 2019, at 5:51 AM, Abdulmalek Algarni wrote: > > Hi there, > > I having a problem when running maker after installing it following the installation instructions. All the excutables located at ?/maker/bin works show no error, except for the maker it show an error : > > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./maker -h > Couldn't find an appropriate DIRECTORY for Inline to use. > > at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 251. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/IndexedBase.pm line 282. > Compilation failed in require at (eval 27) line 2. > ...propagated at /System/Library/Perl/5.18/base.pm line 84. > BEGIN failed--compilation aborted at /Library/Perl/5.18/Bio/DB/Fasta.pm line 137. > Compilation failed in require at ./maker line 62. > BEGIN failed--compilation aborted at ./maker line 62. > > > For the other excutables here is an example : > Abdulmaleks-Mac-Pro:bin abdulmalek$ ./cegma2zff > > Usage: > cegma2zff > > This script converts the output GFF file from CEGMA into ZFF format > for use in SNAP training. Output files are always genome.ann and > genome.dna. > > > > Best regards, > > Abdulmalek > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From carson.holt at genetics.utah.edu Thu May 23 20:12:22 2019 From: carson.holt at genetics.utah.edu (Carson Hinton Holt) Date: Fri, 24 May 2019 02:12:22 +0000 Subject: [maker-devel] MAKER and tRNAscan In-Reply-To: References: Message-ID: <6700FDE9-0114-4774-A578-8F30DEB8BE3B@genetics.utah.edu> Use version 1.3.1 (last stable version for 1.X series), we haven?t updated maker to handle tRNAscan version 2 options and output yet. All version here ?> http://trna.ucsc.edu/software/ ?Carson On May 22, 2019, at 10:18 AM, ?? Li, Qing > wrote: Hi Nazila, The right one to contact is Carson and Maker developer group (cced). best, Qing On Wed, May 22, 2019 at 6:39 AM Koochekian, Nazila > wrote: Dear Maker group My name is Nazila, I am a Ph.D. student at Miami University. I'm working on Phrynosoma platyrhinos genome annotation and I'm trying to use MAKER. So as a requirement I'm trying to use tRNAscan. First I used the latest version (2.0) and I got the first -q file but I faced a warning like this: WARNING: -q exists already. (O)verwrite file, (A)ppend to file, or (Q)uit program? And I tried overwrite and append but it just froze and didn't work anymore. So I tried to use an older version (1.3.1) but this one is hard to make it work too. I'm getting an error: Can't locate object method "new" via package "tRNAscanSE::Constants" (perhaps you forgot to load "tRNAscanSE::Constants"?) at /home/koochen/tRNAscan-SE-1.3.1/tRNAscan-SE line 57. Would you please help me with it? Which version should I use? And how could I solve the problem for that version? Looking forward for your reply; Thanks, Nazila -------------- next part -------------- An HTML attachment was scrubbed... URL: From carsonhh at gmail.com Thu May 30 12:09:20 2019 From: carsonhh at gmail.com (Carson Holt) Date: Thu, 30 May 2019 12:09:20 -0600 Subject: [maker-devel] Problem training agustus In-Reply-To: References: <92f0dde60f734f259c92feb1a085d31b@unil.ch> Message-ID: <3180F4FE-30B1-4A32-B367-850B9219E456@gmail.com> If you are looking to submit to Genebank, tools like GAL are good (https://github.com/The-Sequence-Ontology/GAL ). Things like accession which you listed below only exist inside of GeneBank (i.e. after you submit). They are not produced by pipelines or format converters. ?Carson > On May 21, 2019, at 6:11 AM, djerroud samia wrote: > > Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations > > cds: accession, protein product, protein sequence, start, end , locus_tag, gene, ..... > My problem is I don't know the pipeline I should follow to get all this informaitions > > thank you, Samia > > Le mar. 21 mai 2019 ? 07:25, p sz > a ?crit : > Hi Xavier > I've changed from zff2genbank.pl to zff2augustus_gbk.pl and the the problem is fixed. I used zff2genbank.pl because it is packaged into the maker suite. I think that MAKER authors should include zff2augustus_gbk.pl into the main suite, I didn't know about this genome-scripts repository. > By the way, I would like to show you my training steps with augustus, in order to know if they are correct: > > zff2augustus_gbk.pl export.ann export.dna > final_genes.gb > randomSplit.pl final_genes.gb 500 > new_species.pl --species=Demo > etraining --species=Demo final_genes.gb > optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test > etraining --species=Demo final_genes.gb > > I have taken the training parameters (excepting the 500 parameter) from the train_augustus.pl script included in MAKER suite. > Thank you in advance > Pedro Seoane > De: Xabier V?zquez-Campos > > Enviado: jueves, 16 de mayo de 2019 4:42 > Para: p sz > Cc: maker-devel at yandell-lab.org > Asunto: Re: [maker-devel] RV: Problem training agustus > > Hi Pedro, > I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine. > You need to use zff2augustus_gbk.pl not zff2genbank.pl . I don't remember the differences but I know that zff2augustus_gbk.pl works for sure. > > Link: https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl > Cheers, > Xabi > > On Tue, 14 May 2019 at 18:12, p sz > wrote: > Hi Maker author > I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the train_augustus.pl script as follows: > > zff2genbank.pl export.ann export.dna > final_genes.gb > train_augustus.pl final_genes.gb MyOrg > > For each of my gene models the error is the following: > > Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624 > GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format. > Encountered error after reading 0 annotations. > > The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here: > (export.ann file) > >MODEL236 > Eterm 23624 23647 MODEL236 > Exon 23354 23549 MODEL236 > Exon 23004 23249 MODEL236 > Exon 20923 21067 MODEL236 > Exon 20389 20558 MODEL236 > Exon 18821 18898 MODEL236 > Exon 18471 18637 MODEL236 > Exon 14945 14971 MODEL236 > Exon 13511 13598 MODEL236 > Exon 11920 13315 MODEL236 > Exon 10459 10467 MODEL236 > Exon 8873 9050 MODEL236 > Exon 8628 8775 MODEL236 > Exon 8374 8485 MODEL236 > Exon 7880 7993 MODEL236 > Exon 7689 7791 MODEL236 > Exon 1917 2051 MODEL236 > Einit 1001 1006 MODEL236 > > (genbankfile) > LOCUS MODEL236 24647 bp dna linear UNK > ACCESSION unknown > FEATURES Location/Qualifiers > source 1..24647 > CDS complement(join(1006..1001,2051..1917,7791..7689, > 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459, > 13315..11920,13598..13511,14971..14945,18637..18471, > 18898..18821,20558..20389,21067..20923,23249..23004, > 23549..23354,23647..23624)) > > It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem? > Thank you in advance > Pedro Seoane > _______________________________________________ > maker-devel mailing list > maker-devel at box290.bluehost.com > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org > > > -- > Xabier V?zquez-Campos, PhD > Research Associate > NSW Systems Biology Initiative > School of Biotechnology and Biomolecular Sciences > The University of New South Wales > Sydney NSW 2052 AUSTRALIA > _______________________________________________ > 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 eduardoconrados at gmail.com Fri May 31 13:27:14 2019 From: eduardoconrados at gmail.com (Eduardo Conrado Souza Queiroz Nascimento) Date: Fri, 31 May 2019 19:27:14 -0000 Subject: [maker-devel] Problems with ipr_update_gff Message-ID: Hi, I'm a graduate student at the Federal University of Rio de Janeiro in Brazil, I've been running into problems while trying to run the "ipr_update_gff" script. This message keeps showing and I haven't found a way to solve it. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178309. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178310. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178311. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178312. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178313. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178314. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178315. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178316. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178317. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178318. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178319. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178320. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178321. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178322. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178323. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178324. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178325. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178326. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178327. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178328. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178329. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178330. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178331. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178332. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178333. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178334. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178335. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178336. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178337. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178338. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178339. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178340. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178341. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178342. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178343. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178344. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178345. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178346. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178347. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178348. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178349. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178350. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178351. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178352. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178353. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178354. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178355. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178356. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178357. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178358. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178359. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178360. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178361. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178362. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178363. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178364. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178365. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178366. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178367. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178368. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178369. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178370. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178371. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178372. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178373. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178374. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178375. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178376. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178377. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178378. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178379. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178380. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178381. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178382. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178383. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178384. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178385. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178386. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178387. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178388. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178389. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178390. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178391. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178392. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178393. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178394. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178395. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178396. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178397. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178398. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178399. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178400. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178401. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178402. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178403. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178404. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178405. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178406. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178407. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178408. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178409. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178410. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178411. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178412. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178413. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178414. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178415. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178416. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178417. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178418. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178419. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178420. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178421. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 204, <$IN> line 178422. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178423. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178424. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178425. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178426. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 200, <$IN> line 178427. Use of uninitialized value $gene_id in hash element at /usr/bin/maker/bin/ipr_update_gff line 202, <$IN> line 178427. -------------- next part -------------- An HTML attachment was scrubbed... URL: