[maker-devel] fasta_merge ARRAY error

[USFS Ion PGM]

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
>> 
>> 
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> 
>