Thread: [Transdecoder-users] Transdecoder died with ret 6400 at line 498
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From: Brown, M. <mw...@ms...> - 2014-06-07 14:22:54
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Dear Brian,
My transdecoder install seems to work up until an error that I can not overcome during the best candidate selection. Do you have any suggestions?
Error, no gene obj retrieved based on identifier a2;23981|m.1 at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/../PerlLib/Gene_obj_indexer.pm line 61, <$fh> line 1.
Gene_obj_indexer::get_gene('Gene_obj_indexer=HASH(0x1df59a0)', 'a2;23981|m.1') called at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl line 29
Error, cmd: /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl transdecoder.tmp.25824/longest_orfs.cds.scores.selected transdecoder.tmp.25824/longest_orfs.gff3.inx > transdecoder.tmp.25824/longest_orfs.cds.best_candidates.gff3 died with ret 6400 at /home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/TransDecoder line 498.
Thank you in advance!
Matt
Matthew W. Brown, Ph.D.
Assistant Professor
Biological Sciences
Mississippi State University
008 Harned Hall
Mississippi State, MS 39762
662-325-2406
http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/>
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From: Brian H. <bh...@br...> - 2014-06-07 14:27:09
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Hi Matt, Can you try pulling our latest dev code: svn checkout svn://svn.code.sf.net/p/transdecoder/code-0/trunk transdecoder-code-0 and see if it still errors out? If so, we'll take it from there. best, ~brian On Sat, Jun 7, 2014 at 10:08 AM, Brown, Matthew <mw...@ms...> wrote: > Dear Brian, > > My transdecoder install seems to work up until an error that I can not > overcome during the best candidate selection. Do you have any suggestions? > > Error, no gene obj retrieved based on identifier a2;23981|m.1 at > /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/../PerlLib/Gene_obj_indexer.pm > line 61, <$fh> line 1. > Gene_obj_indexer::get_gene('Gene_obj_indexer=HASH(0x1df59a0)', > 'a2;23981|m.1') called at > /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/ > gene_list_to_gff.pl line 29 > Error, cmd: /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/ > gene_list_to_gff.pl > transdecoder.tmp.25824/longest_orfs.cds.scores.selected > transdecoder.tmp.25824/longest_orfs.gff3.inx > > transdecoder.tmp.25824/longest_orfs.cds.best_candidates.gff3 died with ret > 6400 at /home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/TransDecoder line > 498. > > Thank you in advance! > Matt > > Matthew W. Brown, Ph.D. > Assistant Professor > Biological Sciences > Mississippi State University > 008 Harned Hall > Mississippi State, MS 39762 > 662-325-2406 > http://mwb250.biology.msstate.edu > > > > ------------------------------------------------------------------------------ > Learn Graph Databases - Download FREE O'Reilly Book > "Graph Databases" is the definitive new guide to graph databases and their > applications. Written by three acclaimed leaders in the field, > this first edition is now available. Download your free book today! > http://p.sf.net/sfu/NeoTech > _______________________________________________ > Transdecoder-users mailing list > Tra...@li... > https://lists.sourceforge.net/lists/listinfo/transdecoder-users > > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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From: Brown, M. <mw...@ms...> - 2014-06-07 17:23:14
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Hi Brian,
I pulled off the trunk and recompiled. Same issue though:
Error, no gene obj retrieved based on identifier a2;23981|m.1 at /misc/home/mbrown/SOFTWARE/transdecoder_rel7JUN2014/util/../PerlLib/Gene_obj_indexer.pm line 61, <$fh> line 1.
Gene_obj_indexer::get_gene('Gene_obj_indexer=HASH(0xf499e0)', 'a2;23981|m.1') called at /misc/home/mbrown/SOFTWARE/transdecoder_rel7JUN2014/util/gene_list_to_gff.pl line 29
Error, cmd: /misc/home/mbrown/SOFTWARE/transdecoder_rel7JUN2014/util/gene_list_to_gff.pl transdecoder.tmp.49169/longest_orfs.cds.scores.selected transdecoder.tmp.49169/longest_orfs.gff3.inx > transdecoder.tmp.49169/longest_orfs.cds.best_candidates.gff3 died with ret 6400 at /misc/home/mbrown/SOFTWARE/transdecoder_rel7JUN2014/TransDecoder line 505.
Matthew W. Brown, Ph.D.
Assistant Professor
Biological Sciences
Mississippi State University
008 Harned Hall
Mississippi State, MS 39762
662-325-2406
http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/>
________________________________
From: Brian Haas <bh...@br...>
Sent: Saturday, June 7, 2014 9:27 AM
To: Brown, Matthew
Cc: tra...@li...
Subject: Re: [Transdecoder-users] Transdecoder died with ret 6400 at line 498
Hi Matt,
Can you try pulling our latest dev code:
svn checkout svn://svn.code.sf.net/p/transdecoder/code-0/trunk<http://svn.code.sf.net/p/transdecoder/code-0/trunk> transdecoder-code-0
and see if it still errors out? If so, we'll take it from there.
best,
~brian
On Sat, Jun 7, 2014 at 10:08 AM, Brown, Matthew <mw...@ms...<mailto:mw...@ms...>> wrote:
Dear Brian,
My transdecoder install seems to work up until an error that I can not overcome during the best candidate selection. Do you have any suggestions?
Error, no gene obj retrieved based on identifier a2;23981|m.1 at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/../PerlLib/Gene_obj_indexer.pm line 61, <$fh> line 1.
Gene_obj_indexer::get_gene('Gene_obj_indexer=HASH(0x1df59a0)', 'a2;23981|m.1') called at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl<http://gene_list_to_gff.pl> line 29
Error, cmd: /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl<http://gene_list_to_gff.pl> transdecoder.tmp.25824/longest_orfs.cds.scores.selected transdecoder.tmp.25824/longest_orfs.gff3.inx > transdecoder.tmp.25824/longest_orfs.cds.best_candidates.gff3 died with ret 6400 at /home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/TransDecoder line 498.
Thank you in advance!
Matt
Matthew W. Brown, Ph.D.
Assistant Professor
Biological Sciences
Mississippi State University
008 Harned Hall
Mississippi State, MS 39762
662-325-2406<tel:662-325-2406>
http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/>
------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Transdecoder-users mailing list
Tra...@li...<mailto:Tra...@li...>
https://lists.sourceforge.net/lists/listinfo/transdecoder-users
--
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas
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From: Brown, M. <mw...@ms...> - 2014-06-07 17:49:41
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Hi Brian, It turns out to be the headers. I was using an inchworm output header that seems to be the problem. I scripted a header change to simplify the headers. I am not sure at the moment what the problem is, be it whitespace or non-alphanumeric characters (i.e., ";" or ":"). I will do some tests and report back. Best, Matt Matthew W. Brown, Ph.D. Assistant Professor Biological Sciences Mississippi State University 008 Harned Hall Mississippi State, MS 39762 662-325-2406 http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/> ________________________________ From: Brian Haas <bh...@br...> Sent: Saturday, June 7, 2014 9:27 AM To: Brown, Matthew Cc: tra...@li... Subject: Re: [Transdecoder-users] Transdecoder died with ret 6400 at line 498 Hi Matt, Can you try pulling our latest dev code: svn checkout svn://svn.code.sf.net/p/transdecoder/code-0/trunk<http://svn.code.sf.net/p/transdecoder/code-0/trunk> transdecoder-code-0 and see if it still errors out? If so, we'll take it from there. best, ~brian On Sat, Jun 7, 2014 at 10:08 AM, Brown, Matthew <mw...@ms...<mailto:mw...@ms...>> wrote: Dear Brian, My transdecoder install seems to work up until an error that I can not overcome during the best candidate selection. Do you have any suggestions? Error, no gene obj retrieved based on identifier a2;23981|m.1 at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/../PerlLib/Gene_obj_indexer.pm line 61, <$fh> line 1. Gene_obj_indexer::get_gene('Gene_obj_indexer=HASH(0x1df59a0)', 'a2;23981|m.1') called at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl<http://gene_list_to_gff.pl> line 29 Error, cmd: /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl<http://gene_list_to_gff.pl> transdecoder.tmp.25824/longest_orfs.cds.scores.selected transdecoder.tmp.25824/longest_orfs.gff3.inx > transdecoder.tmp.25824/longest_orfs.cds.best_candidates.gff3 died with ret 6400 at /home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/TransDecoder line 498. Thank you in advance! Matt Matthew W. Brown, Ph.D. Assistant Professor Biological Sciences Mississippi State University 008 Harned Hall Mississippi State, MS 39762 662-325-2406<tel:662-325-2406> http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/> ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Transdecoder-users mailing list Tra...@li...<mailto:Tra...@li...> https://lists.sourceforge.net/lists/listinfo/transdecoder-users -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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From: Brown, M. <mw...@ms...> - 2014-06-07 17:59:44
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Hi Brian, It is the occurrence of ";" in the headers. Everything seems to be working fine now. I just added a script to handle the replacement of ";" to ":" in my fasta inputs. Best, Matt Matthew W. Brown, Ph.D. Assistant Professor Biological Sciences Mississippi State University 008 Harned Hall Mississippi State, MS 39762 662-325-2406 http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/> ________________________________ From: Brown, Matthew Sent: Saturday, June 7, 2014 12:49 PM To: Brian Haas Cc: tra...@li... Subject: RE: [Transdecoder-users] Transdecoder died with ret 6400 at line 498 Hi Brian, It turns out to be the headers. I was using an inchworm output header that seems to be the problem. I scripted a header change to simplify the headers. I am not sure at the moment what the problem is, be it whitespace or non-alphanumeric characters (i.e., ";" or ":"). I will do some tests and report back. Best, Matt Matthew W. Brown, Ph.D. Assistant Professor Biological Sciences Mississippi State University 008 Harned Hall Mississippi State, MS 39762 662-325-2406 http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/> ________________________________ From: Brian Haas <bh...@br...> Sent: Saturday, June 7, 2014 9:27 AM To: Brown, Matthew Cc: tra...@li... Subject: Re: [Transdecoder-users] Transdecoder died with ret 6400 at line 498 Hi Matt, Can you try pulling our latest dev code: svn checkout svn://svn.code.sf.net/p/transdecoder/code-0/trunk<http://svn.code.sf.net/p/transdecoder/code-0/trunk> transdecoder-code-0 and see if it still errors out? If so, we'll take it from there. best, ~brian On Sat, Jun 7, 2014 at 10:08 AM, Brown, Matthew <mw...@ms...<mailto:mw...@ms...>> wrote: Dear Brian, My transdecoder install seems to work up until an error that I can not overcome during the best candidate selection. Do you have any suggestions? Error, no gene obj retrieved based on identifier a2;23981|m.1 at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/../PerlLib/Gene_obj_indexer.pm line 61, <$fh> line 1. Gene_obj_indexer::get_gene('Gene_obj_indexer=HASH(0x1df59a0)', 'a2;23981|m.1') called at /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl<http://gene_list_to_gff.pl> line 29 Error, cmd: /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/gene_list_to_gff.pl<http://gene_list_to_gff.pl> transdecoder.tmp.25824/longest_orfs.cds.scores.selected transdecoder.tmp.25824/longest_orfs.gff3.inx > transdecoder.tmp.25824/longest_orfs.cds.best_candidates.gff3 died with ret 6400 at /home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/TransDecoder line 498. Thank you in advance! Matt Matthew W. Brown, Ph.D. Assistant Professor Biological Sciences Mississippi State University 008 Harned Hall Mississippi State, MS 39762 662-325-2406<tel:662-325-2406> http://mwb250.biology.msstate.edu<http://mwb250.biology.msstate.edu/> ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ Transdecoder-users mailing list Tra...@li...<mailto:Tra...@li...> https://lists.sourceforge.net/lists/listinfo/transdecoder-users -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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From: Brian H. <bh...@br...> - 2014-06-07 18:53:29
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Gotcha! Thanks for the update. Note - beware of using the inchworm contigs. The inchworm output can be useful, but it's really intended to be an intermediate, that the rest of Trinity fine-tunes in various ways. best, ~brian On Sat, Jun 7, 2014 at 1:59 PM, Brown, Matthew <mw...@ms...> wrote: > Hi Brian, > It is the occurrence of ";" in the headers. Everything seems to be working > fine now. I just added a script to handle the replacement of ";" to ":" in > my fasta inputs. > > Best, > Matt > > > Matthew W. Brown, Ph.D. > Assistant Professor > Biological Sciences > Mississippi State University > 008 Harned Hall > Mississippi State, MS 39762 > 662-325-2406 > http://mwb250.biology.msstate.edu > > ------------------------------ > *From:* Brown, Matthew > *Sent:* Saturday, June 7, 2014 12:49 PM > *To:* Brian Haas > *Cc:* tra...@li... > *Subject:* RE: [Transdecoder-users] Transdecoder died with ret 6400 at > line 498 > > Hi Brian, > > It turns out to be the headers. I was using an inchworm output header > that seems to be the problem. I scripted a header change to simplify the > headers. I am not sure at the moment what the problem is, be it whitespace > or non-alphanumeric characters (i.e., ";" or ":"). I will do some tests and > report back. > > Best, > Matt > > > Matthew W. Brown, Ph.D. > Assistant Professor > Biological Sciences > Mississippi State University > 008 Harned Hall > Mississippi State, MS 39762 > 662-325-2406 > http://mwb250.biology.msstate.edu > > ------------------------------ > *From:* Brian Haas <bh...@br...> > *Sent:* Saturday, June 7, 2014 9:27 AM > *To:* Brown, Matthew > *Cc:* tra...@li... > *Subject:* Re: [Transdecoder-users] Transdecoder died with ret 6400 at > line 498 > > Hi Matt, > > Can you try pulling our latest dev code: > > svn checkout svn://svn.code.sf.net/p/transdecoder/code-0/trunk > transdecoder-code-0 > > and see if it still errors out? If so, we'll take it from there. > > best, > > ~brian > > > > > On Sat, Jun 7, 2014 at 10:08 AM, Brown, Matthew <mw...@ms...> > wrote: > >> Dear Brian, >> >> My transdecoder install seems to work up until an error that I can not >> overcome during the best candidate selection. Do you have any suggestions? >> >> Error, no gene obj retrieved based on identifier a2;23981|m.1 at >> /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/../PerlLib/Gene_obj_indexer.pm >> line 61, <$fh> line 1. >> Gene_obj_indexer::get_gene('Gene_obj_indexer=HASH(0x1df59a0)', >> 'a2;23981|m.1') called at >> /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/ >> gene_list_to_gff.pl line 29 >> Error, cmd: /misc/home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/util/ >> gene_list_to_gff.pl >> transdecoder.tmp.25824/longest_orfs.cds.scores.selected >> transdecoder.tmp.25824/longest_orfs.gff3.inx > >> transdecoder.tmp.25824/longest_orfs.cds.best_candidates.gff3 died with ret >> 6400 at /home/mbrown/SOFTWARE/transdecoder_rel16JAN2014/TransDecoder line >> 498. >> >> Thank you in advance! >> Matt >> >> Matthew W. Brown, Ph.D. >> Assistant Professor >> Biological Sciences >> Mississippi State University >> 008 Harned Hall >> Mississippi State, MS 39762 >> 662-325-2406 >> http://mwb250.biology.msstate.edu >> >> >> >> ------------------------------------------------------------------------------ >> Learn Graph Databases - Download FREE O'Reilly Book >> "Graph Databases" is the definitive new guide to graph databases and their >> applications. Written by three acclaimed leaders in the field, >> this first edition is now available. Download your free book today! >> http://p.sf.net/sfu/NeoTech >> _______________________________________________ >> Transdecoder-users mailing list >> Tra...@li... >> https://lists.sourceforge.net/lists/listinfo/transdecoder-users >> >> > > > -- > -- > Brian J. Haas > The Broad Institute > http://broad.mit.edu/~bhaas > > > -- -- Brian J. Haas The Broad Institute http://broad.mit.edu/~bhaas |
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