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

[Arun Seetharam]

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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