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

[Brian H. <bh...@br...>]

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



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