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SURPI
chiulab.ucsf.edu/surpi
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"Can not open the database file" for Comprehensive runs against NR database #7

Closed damurdock closed 10 years ago

damurdock commented 10 years ago

When running SURPI in Comprehensive mode against the NR database, RAPSearch produces the following output:

Thu Jun 19 15:23:45 PDT 2014    SURPI.sh    #################### RAPSearch to NR ###########
Thu Jun 19 15:23:46 PDT 2014    SURPI.sh    ############# RAPSearch to NR #################
Thu Jun 19 15:23:46 PDT 2014    SURPI.sh    Starting: RAPSearch to NR Test.Contigs.NT.snap.unmatched.uniq.fl.fasta
Thu Jun 19 15:23:46 PDT 2014    SURPI.sh    Parameters:rapsearch -q Test.Contigs.NT.snap.unmatched.uniq.fl.fasta -d  -o Test.Contigs.and.NTunmatched.NR.RAPSearch.e0  -z 16 -e 0 -v 1 -b 1 -t N -a T
QueryFileName Test.Contigs.NT.snap.unmatched.uniq.fl.fasta
Queries are nucleotide sequences
Can not open the database file
Please check the file name
>>>Main END
Time used: 9 min (0.2 hours)
Thu Jun 19 15:33:38 PDT 2014    SURPI.sh    rapsearch  to nr done

(Test.fastq being the input file)

This is because in the NR RAPSearch portion of SURPI.sh, the variable $RAPSearchDB_NR is used, but never set. Changing this to $RAPSearch_NR_db allows RAPSearch to run.

My pull request https://github.com/chiulab/surpi/pull/6 fixes this in the second commit. I meant to send a separate pull request for this issue, but I misunderstood the process and both issues are in the same request.

sfederman commented 10 years ago

RAPSearch NR should now function properly. Closing this issue.