[maker-devel] gff3_merge error: FINISHED.gff does not exist

[Carson Holt]

Your datastore log is munged.  Sometimes happen with an IO collision.  Delete it and run maker on a single CPU using the -dsindex option.  All it will do is rebuild the datastore log.  Takes less than 5 minutes.

—Carson



> On Jul 1, 2015, at 8:42 AM, Arun Seetharam <arnstrm at gmail.com> wrote:
> 
> Hi all,
> 
> I am unable to generate the GFF file from the maker output. I originally ran maker with several processors (using mpi) as follows:
> 
> /usr/lib64/mpich/bin/mpiexec -machinefile $PBS_NODEFILE -n 160 maker -base maker_R1 -fix_nucleotides
> 
> Once completed, I tried to create GFF file with the gff3_merge script:
> 
> $ gff3_merge  -d maker_R1.maker.output/maker_R1_master_datastore_index.log
> ERROR: The file 'maker_R1.maker.output/./FINISHED/FINISHED.gff' does not exist
> 
> I searched online to find this thread  <http://gmod.827538.n3.nabble.com/FINISHED-FINISHED-gff-td4032857.html>which asked to build the index again if you ran mpi enalbled maker. so I ran it as,
> 
> $ maker -base maker_R1 -dsindex
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> STATUS: Setting up database for any GFF3 input...
> A data structure will be created for you at:
> /data003/TIL/maker_R1.maker.output/maker_R1_datastore
> 
> To access files for individual sequences use the datastore index:
> /data003/TIL/maker_R1.maker.output/maker_R1_master_datastore_index.log
> 
> When I tried again to run the gff3_merge:
> 
> $ gff3_merge  -d maker_R1.maker.output/maker_R1_master_datastore_index.log
> ERROR: The file 'maker_R1.maker.output/./FINISHED/FINISHED.gff' does not exist
> 
> I still get the same error. Please tell me what am I doing wrong. My worst fear is that If I have to re-run it again, I will take another week or so. Both my genomes have the same issue.
> 
> Any help will greatly be appreciated.
> 
> Thanks,
> 
> -- 
> Arun Seetharam
> 
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