IgBlast error

[isnapkov]

Hi! I constantly receive the following error irrespective of I run my analysis locally or on a server.

Error in rule igdiscover_igblast: jobid: 37 output: iteration-01/assigned.tab.gz, iteration-01/stats/assigned.json shell: time igdiscover igblast --sequence-type=Ig --threads=1 --stats=iteration-01/stats/assigned.json iteration-01/database reads/sequences.fasta.gz | pigz > iteration-01/assigned.tab.gz (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[marcelm]

Hi, sorry for the late reply – I was on vacation.

I don’t see an actual error message in the log that you posted, so I cannot diagnose the problem. Can you copy a little bit more of the log output? You can run igdiscover run in the same directory, and IgDiscover will try to re-run the last failed command. You could just copy the entire output from that command.

Alternatively, you could manually run the IgBLAST command like so:

igdiscover igblast --sequence-type=Ig --threads=1 --stats=iteration-01/stats/assigned.json iteration-01/database reads/sequences.fasta.gz > /dev/null

That should directly give you the relevant error message.