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geneontology / pipeline

Declarative pipeline for the Gene Ontology.
https://build.geneontology.org/job/geneontology/job/pipeline/
BSD 3-Clause "New" or "Revised" License
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Pipeline fails due to "Argument list too long" #360

Closed kltm closed 5 months ago

kltm commented 5 months ago

Pipeline fails with:

06:26:36  /var/lib/jenkins/workspace/eontology_pipeline_snapshot-OLCOSBORX7TUJKUSVDZQNZDGXCRFSUQLNESYCP3R63U6FLW5DJ2A/noctua-models@tmp/durable-d13d4bd8/script.sh: 1: /var/lib/jenkins/workspace/eontology_pipeline_snapshot-OLCOSBORX7TUJKUSVDZQNZDGXCRFSUQLNESYCP3R63U6FLW5DJ2A/noctua-models@tmp/durable-d13d4bd8/script.sh: perl: Argument list too long

Originating from:

perl ./collate-gpads.pl legacy/gpad/0000000300000001.gpad legacy/gpad/531a636500000001.gpad legacy/gpad/5323da1800000002.gpad legacy/gpad/5362b2ed00000016.gpad legacy/gpad/536d71c500000004.gpad legacy/gpad/539a033300000004.gpad legacy/gpad/5408ded300000003.gpad legacy/gpad/542732ad00000005.gpad legacy/gpad/542732ad00000010.gpad legacy/gpad/5437882f00000001.gpad legacy/gpad/5437882f00000010.gpad legacy/gpad/5437882f00000021.gpad legacy/gpad/5437882f00000024.gpad legacy/gpad/5437882f00000034.gpad [...]
kltm commented 5 months ago

Likely something like: https://unix.stackexchange.com/questions/179641/bash-usr-bin-perl-argument-list-too-long

kltm commented 5 months ago

Testing now on snapshot.

kltm commented 5 months ago

I believe we've gotten farther in the pipeline now and this can be cleared as an issue.