[maker-devel] fasta_merge ARRAY error

[Daniel Ence]

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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