[maker-devel] fasta_merge ARRAY error

[Carson Holt]

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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