Bug #4577
closed
[Crunch] Pipeline instance mysteriously restarts and fails
Description
1) https://workbench.qr1hi.arvadosapi.com/pipeline_instances/qr1hi-d1hrv-qzactq0a5lamky7,
Failed near the end due to a typo in my script. It appears to mysteriously re-run itself (I'd left at this point) as
2) https://workbench.qr1hi.arvadosapi.com/pipeline_instances/qr1hi-d1hrv-5b2my2fy7n02fys
and fails with
"stderr Error: '/tmp/crunch-job/output' exists; use -f to overwrite"
Pipeline 1) started at 7:25 pm, 2) started at 8:03 pm.
Updated by Nancy Ouyang over 11 years ago
The actual command was:
$ arv-run --docker-image nancy/cgatools-wormtable /bin/bash ./makewormtable.sh qr1hi-4zz18-3izq2vjb7skl79k
Updated by Tim Pierce over 11 years ago
- Category set to Crunch
- Target version set to Bug Triage
Updated by Tim Pierce over 11 years ago
- Subject changed from Pipeline instance mysteriously restarts and fails to [Crunch] Pipeline instance mysteriously restarts and fails
Updated by Brett Smith over 11 years ago
Nancy,
The two pipelines you listed are not identical. They use different versions of the makewormtable.sh script. For that to happen, someone would've needed to run arv-run a second time with a modified version of makewormtable.sh. According to the metadata on the pipeline instance, that was you.
Are you sure you didn't run arv-run twice, possibly in rapid succession after fixing the typo?
Updated by Brett Smith over 11 years ago
- Status changed from New to Closed
- Target version deleted (
Bug Triage)
The script for the second pipeline calls vcf2wt with -f (along with some debugging changes). This both confirms that the script changed between runs, and explains why there's such a different in runtimes between the two pipelines: the first one failed more or less immediately, while the second failed due to #4578.
Closing this, since there seems to have been a misunderstanding with the bug as described, and we have #4578 to cover the other issue.