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Latest Release: 1/17/19
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UI/bucket job status inconsistencies?

esalinasesalinas BroadMember, Broadie ✭✭✭

In the UI, a submission seems to be in an error state.

The attached PDF from the UI shows that one of 5 tasks (conttest) is still running and that there is a red "Done!" status button.

In seeming contrast with that the UI shows, inspection of the bucket contents suggests that all tasks ended with success status zero (see below).

This is confusing....

Inspection of the bucket shows that the output directory for ContEst exists and has a 0 in its status. In addition, the 4 output files that the WDL expects are also present!

output {
    File contamDataFile="contamination_validation.array_free.txt"
    File contestAFFile="contamination.af.txt"
    File contestBaseReport="contamination.base_report.txt"
    File validationOutput="contest_validation.output.tsv"
    }

-eddie

wm8b1-75c:WDLs esalinas$ gsutil ls gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/|ggrep -Pi '3ca2d12e'|ggrep -Pi '6b13a4bb'|ggrep -Pi 'job.rc'
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/job.rc.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-CrossCheckLaneFingerprints/job.rc.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-QC_Task/job.rc.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-normalMM/job.rc.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-tumorMM/job.rc.txt
wm8b1-75c:WDLs esalinas$ gsutil ls gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/
|ggrep -Pi '3ca2d12e'|ggrep -Pi '6b13a4bb'|ggrep -Pi 'job.rc'|xargs -tI {} gsutil cat {}
gsutil cat gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/job.rc.txt
0
gsutil cat gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-CrossCheckLaneFingerprints/job.rc.txt
0
gsutil cat gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-QC_Task/job.rc.txt
0
gsutil cat gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-normalMM/job.rc.txt
0
gsutil cat gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-tumorMM/job.rc.txt
0
wm8b1-75c:WDLs esalinas$
wm8b1-75c:WDLs esalinas$ gsutil ls gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/contamination.af.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/contamination.base_report.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/contamination_validation.array_free.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/contest_validation.output.tsv
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/exec.sh
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/jes-stderr.log
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/jes-stdout.log
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/jes.log
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/job.rc.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/job.stderr.txt
gs://fc-1a98eb1a-d615-4264-bf33-ad148c20dcf9/3ca2d12e-a871-4aa5-8265-f05d931b2677/QC_Workflow/6b13a4bb-c64e-4a90-b50b-fbfc8ff19fbd/call-ContESTTask/job.stdout.txt
wm8b1-75c:WDLs esalinas$

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