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Bug #4577

closed

[Crunch] Pipeline instance mysteriously restarts and fails

Added by Nancy Ouyang over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Assigned To:
-
Category:
Crunch
Target version:
-
Story points:
-

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.

Actions #1

Updated by Nancy Ouyang over 9 years ago

The actual command was:
$ arv-run --docker-image nancy/cgatools-wormtable /bin/bash ./makewormtable.sh qr1hi-4zz18-3izq2vjb7skl79k

Actions #2

Updated by Tim Pierce over 9 years ago

  • Category set to Crunch
  • Target version set to Bug Triage
Actions #3

Updated by Tim Pierce over 9 years ago

  • Subject changed from Pipeline instance mysteriously restarts and fails to [Crunch] Pipeline instance mysteriously restarts and fails
Actions #4

Updated by Brett Smith over 9 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?

Actions #5

Updated by Brett Smith over 9 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.

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