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Bug #10710

closed

Task not in slurm queue

Added by Bryan Cosca over 9 years ago. Updated over 9 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Lucas Di Pentima
Category:
-
Target version:
-
Story points:
-

Description

This job should complete, but gets lost somewhere along the line.

https://collections.qr1hi.arvadosapi.com/c=c0815de927f4fb27f59e88fde99b7491-89/_/qr1hi-8i9sb-j9sp1evpseq11ks.log.txt

job https://cloud.curoverse.com/jobs/qr1hi-8i9sb-j9sp1evpseq11ks#Log

pipeline instance: https://cloud.curoverse.com/pipeline_instances/qr1hi-d1hrv-n60whtn8d02aj1l

2016-12-09_22:55:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr 7871  -7.349629e+01  -1.693066239     1   347       Colombia             <NA>
2016-12-09_22:55:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr 7872  -7.352525e+01  -1.638867259     1   348       Colombia             <NA>
2016-12-09_22:55:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr 7873  -7.349434e+01  -1.536621332     1   349       Colombia             <NA>
2016-12-09_22:55:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr 7874  -7.352139e+01  -1.449707031     1   350       Colombia             <NA>
2016-12-09_22:55:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr 7875  -7.357549e+01  -1.401367068     1   351       Colombia             <NA>
2016-12-09_22:55:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr 7876  -7.361025e+01  -1.316406012     1   352       Colombia             <NA>
2016-12-09_22:55:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr 7877  -7.366431e+01  -1.248827934     1   353       Colombia             <NA>
2016-12-09_22:55:18 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 notice: task is not in slurm queue but srun process 35885 has not exited
2016-12-09_22:55:48 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 killing orphaned srun process 35885 (task not in slurm queue, no stderr received in last 53s)
2016-12-09_22:55:48 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 sending 2x signal 2 to pid 35885
2016-12-09_22:56:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 killing orphaned srun process 35885 (task not in slurm queue, no stderr received in last 68s)
2016-12-09_22:56:03 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 sending 2x signal 15 to pid 35885
2016-12-09_22:56:18 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 killing orphaned srun process 35885 (task not in slurm queue, no stderr received in last 83s)
2016-12-09_22:56:18 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 sending 2x signal 9 to pid 35885
2016-12-09_22:56:18 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 child 35885 on compute1.1 exit 0 with signal 9 success=false
2016-12-09_22:56:18 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 failure (#1, permanent) after 6004 seconds
2016-12-09_22:56:18 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 task output (343 bytes): .

Files

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qr1hi-8i9sb-zzmvakdfxormlh1.txt (1.26 KB) qr1hi-8i9sb-zzmvakdfxormlh1.txt Bryan Cosca, 12/12/2016 03:12 PM
qr1hi-8i9sb-zzmvakdfxormlh1.html (81.2 KB) qr1hi-8i9sb-zzmvakdfxormlh1.html Bryan Cosca, 12/12/2016 03:12 PM
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 #2

Updated by Lucas Di Pentima over 9 years ago

  • Status changed from New to In Progress
  • Assigned To set to Lucas Di Pentima
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 #3

Updated by Lucas Di Pentima over 9 years ago

  • Status changed from In Progress to Resolved

This was part of the (very long) log file, was somewhat difficult to see because it was mixed with lots of job output lines.

2016-12-09_22:53:58 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr   File "finalCut.py", line 9, in <module>
2016-12-09_22:53:58 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr     f = open(inFile, "r")
2016-12-09_22:53:58 qr1hi-8i9sb-j9sp1evpseq11ks 29278 0 stderr IOError: [Errno 2] No such file or directory: 'VG160407_S1_S1_R1_001.vcf+_summary'
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