CODEWITHSUNDEEP
javaperlcronpicard
sirisha sunkara
sirisha sunkara

Reputation: 21

An interesting cron, bash, perl and java problem

Essentially, I have a perl workflow that runs a suite of java tools via the system command (picard in GATK4 for those of you who are familiar with Broad Institute's software). These gatk4 commands return code 0 if successful. When I kick off the perl workflow manually (RHE7.6), it all seems to flow through fine.

However, the Gatk4 processes that return a 0 upon success, fail when the same workflow is run as part of a cron-job like so:

0,15,30 * * * * /usr/bin/flock -n /tmp/QAQC.lock -c "/seq/QAQC/bin/launch_QAQC.pl 1>>launch_QAQC.log 2>>launch_QAQC.err"

I suspect that something about running flock with the –c option is causing those jobs (and therefore the perl pipeline) to abort.

Any insights that you can provide would be very much appreciated.

Thanks

EDIT: Figured out the solution, in that the problem is not with flock. Cron wasn't seeing the same env variables as the interactive shell.

Upvotes: 1

Views: 85

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