[maker-devel] fasta_merge ARRAY error

[Carson Holt]

I've attached the fixed version (I see that the patched one is not in
2.31.3, but I'll get that taken care of).

The tRNA genes will be in the maker.trnascan.transcripts.fasta.  The other
files will have only the coding genes.

--Carson



On 4/8/14, 6:56 AM, "USFS Ion PGM" <nextgen.usfs at gmail.com> wrote:

>Hi Carson and Daniel,
>I’m running Maker 2.31.2 and yes I did have tRNAscan turned on - so
>perhaps I should just get fasta_merge from 2.31.3 and give it a shot.
>But first to clarify, fasta_merge -d maker1_master_datastore_index.log -
>returns the appropriate files, however both the maker.all.proteins.fasta
>and maker.all.transcripts.fasta return 7401 with a grep command counting
>‘>’, while the gff3_merge -d maker1_master_datastore_index.log runs
>without failure and a grep command counting ‘gene’ returns 7525 models.
>
>I uploaded the files requested below.  Thanks for the help.
>
>-Jon
>
>
>On Apr 7, 2014, at 9:02 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> What version of MAKER are you using, and did you run with the new
>>trnascan
>> option turned on?  Basically the script is finding a fasta file for
>> transcripts but the file for proteins is missing.  Turning trnascan on
>>can
>> do this (obviously tRNAs can encode transcripts but don't encode
>> proteins).  The version of fasta_merge included in the current MAKER
>> 2.31.3 download should handle this correctly.
>> 
>> --Carson
>> 
>> 
>> 
>> On 4/7/14, 7:23 PM, "Daniel Ence" <dence at genetics.utah.edu> wrote:
>> 
>>> Hi Jon, Will you please send the command that gave you that error?
>>>Also,
>>> will you upload the maker control files you used and the gff3 file to
>>>the
>>> URL below?
>>> 
>>> http://weatherby.genetics.utah.edu/cgi-bin/mwas/bug.cgi?guest_id=360
>>> 
>>> Also, which version of MAKER are you using?
>>> 
>>> Thanks,
>>> Daniel
>>> 
>>> 
>>> Daniel Ence
>>> Graduate Student
>>> Eccles Institute of Human Genetics
>>> University of Utah
>>> 15 North 2030 East, Room 2100
>>> Salt Lake City, UT 84112-5330
>>> ________________________________________
>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of
>>>USFS
>>> Ion PGM [nextgen.usfs at gmail.com]
>>> Sent: Monday, April 07, 2014 4:34 PM
>>> To: maker-devel at yandell-lab.org
>>> Subject: [maker-devel] fasta_merge ARRAY error
>>> 
>>> Hello,
>>> 
>>> I’m getting an error when running fasta_merge as follows:
>>> 
>>> Can't use an undefined value as an ARRAY reference at
>>> /home/ngs/maker/bin/fasta_merge line 116, <IN> line 1942.
>>> 
>>> The result is that the fasta files are somewhat truncated, that is they
>>> do not match the gff3 file created from gff3_merge (which does run
>>> without any errors).  Seems like it is getting stuck somewhere and then
>>> crashes.  Is there another way to easily get the CDS out of the maker
>>> generated GFF file?
>>> 
>>> Thanks,
>>> 
>>> Jon
>>> 
>>> 
>>> _______________________________________________
>>> 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
>> 
>> 
>

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