[maker-devel] maker output- transcripts.fasta and proteins.fasta files missing

[dhivya arasappan]

Hello,

I've been running maker with different assembly files, reference files  
etc  and I check the output by:

1. concatenating the gff files
2. concatenating the *transcripts.fasta files
3. concatenating the *proteins.fasta files

I'm noticing that when I ran maker twice with same parameters, the  
second time around, many of the output subdirectories  do not have a  
*transcripts.fasta or *proteins.fasta file in it.
There are 251 subdirectories and only 97 of them have all 3 output  
files.  Maker log looks ok to me, but I've attached it here as well.

What could be the reason for this?

Thanks
dhivya

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