[maker-devel] fasta_merge ARRAY error

[Jon Palmer]

Thanks Carson, error is gone and is now working.  Thanks for a great 
tool and for the fantastic support!

-Jon

On 04/08/2014 09:54 AM, Carson Holt wrote:
> 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
>>>>
>>>>
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>>>