Error executing

[ucassee]

Hi,
I run orthomcl-pipeline with the following error. Could you help me solve it? Thanks

=Stage 9: Parse Blast Results=
cat /home/software/orthomcl-pipeline/testout/blast_results/blast_results.* > /home/software/orthomcl-pipeline/testout/blast_load/all.fasta
/home/software/orthomclSoftware-v2.0.9/bin/orthomclBlastParser "/home/software/orthomcl-pipeline/testout/blast_load/all.fasta" "/home/software/orthomcl-pipeline/testout/compliant_fasta" 1>/home/software/orthomcl-pipeline/testout/blast_load/similarSequences.txt 2>/home/software/orthomcl-pipeline/testout/log/9.parseBlast.log
Error executing command: /home/software/orthomclSoftware-v2.0.9/bin/orthomclBlastParser "/home/software/orthomcl-pipeline/testout/blast_load/all.fasta" "/home/software/orthomcl-pipeline/testout/compliant_fasta" 1>/home/software/orthomcl-pipeline/testout/blast_load/similarSequences.txt 2>/home/software/orthomcl-pipeline/testout/log/9.parseBlast.log. See logs /home/software/orthomcl-pipeline/testout/blast_load/similarSequences.txt and /home/software/orthomcl-pipeline/testout/log/9.parseBlast.log

[ucassee]

Hi @apetkau ,
I solved it by changing the pathway of mysql database.
I want to know how can I set the identity and coverage for filtration in orthomcl-pipeline.
Hope to your reply.

[apetkau]

That's great @ucassee . For setting certain parameters, you can modify them in etc/orthomcl-pipeline.conf. See this file for an example https://github.com/apetkau/orthomcl-pipeline/blob/master/etc/orthomcl-pipeline.conf.default.