[maker-devel] problem with dsindex

[kdelmore at zoology.ubc.ca]

I am having some trouble with the dsindex tool. I used the fasta_tool to
split my original multifasta file and ran maker with the –base and –g
flags. I then used the dsindex tool to summarize results from each fasta.
The tool finished without an error message and pointed me to where the
files should be but when I went to that directory there was no datastore
and the index.log said that it had started on each of the fastas but not
finished. I got around this problem using gff3_merge by using the –o
option and providing paths to the gff files but this is not working with
the fasta_merge tool. I don’t want to just cat the files together because
I want to be sure the merged gff and protein.fasta files are the same for
downstream annotation steps. I’ve included examples of the commands I used
below and the output from dsindex. Note that the individual fastas
finished without errors and produced datastores.

I would really appreciate any input you might have with this problem and
THANK YOU for developing such a user friendly pipeline.

/maker/bin/fasta_tool --split placed.fasta

mpiexec -n 4 /maker/bin/maker -base 1 -g 1.fasta -fix_nucleotides

maker/bin/maker -dsindex -fix_nucleotides
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:
/placed.maker.output/placed_datastore ##this directory was not generated
To access files for individual sequences use the datastore index:
/placed.maker.output/placed_master_datastore_index.log

/maker/bin/gff3_merge -o placed.gff *

/maker/bin/fasta_merge –o placed.all 1.maker.proteins.fasta
2.maker.proteins.fasta ##this did not work