Re: [Transdecoder-users] Transdecoder died with ret 6400 at line 498

[Brown, M. <mw...@ms...>]

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/>


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Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas