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Bug #11917

closed

Error fetching collection (HttpError 422) during call to arvados.util.listdir_recursive

Added by Joshua Randall over 6 years ago. Updated over 5 years ago.

Status:
Resolved
Priority:
Normal
Assigned To:
Category:
API
Target version:
-
Story points:
-

Description

2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr 2017-06-27 16:17:34 arvados.arvados_fuse[45815] ERROR: Error fetching collection 'f23f6b30aa7d658b565af6d4e2
e5368a+9409': Failed to retrieve collection 'f23f6b30aa7d658b565af6d4e2e5368a+9409' from either API server (<HttpError 422 when requesting https://api.arvados.sanger.ac.uk/arvados/v1/collections/f23f6b30aa7d658b565af6d4e2e5368a%2B9409?alt=json returned "#<Errno::ENOENT: No such file or directory @ rb_sysopen - /var/www/arvados-api/current/tmp/cache/94F/070/.permissions_check.70302752543300.5829.180478>">) or Keep (f23f6b30aa7d658b565af6d4e2e5368a+9409 not found:  http://humgen-01-01.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-03-02.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-04-03.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-02-03.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-03-03.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-02-02.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-03-01.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-01-03.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-02-01.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-04-02.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-04-01.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ;  http://humgen-01-02.internal.sanger.ac.uk:25107/ responded with 404 HTTP/1.1 404 Not Found\015
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr ).
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr Traceback (most recent call last):
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr   File "/data/crunch-tmp/crunch-job/src/crunch_scripts/gatk-haplotypecaller-cram.py", line 99, in <module>
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr     main()
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr   File "/data/crunch-tmp/crunch-job/src/crunch_scripts/gatk-haplotypecaller-cram.py", line 54, in main
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr     cram_file = gatk_helper.mount_gatk_cram_input(input_param="input")
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr   File "/data/crunch-tmp/crunch-job/src/crunch_scripts/hgi_arvados/gatk_helper.py", line 81, in mount_gatk_cram_input
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr     for f in arvados.util.listdir_recursive(input_dir):
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr   File "/usr/lib/python2.7/dist-packages/arvados/util.py", line 332, in listdir_recursive
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr     for ent in sorted(os.listdir(dirname)):
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 stderr OSError: [Errno 2] No such file or directory: '/keep/f23f6b30aa7d658b565af6d4e2e5368a+9409'
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 child 29639 on humgen-02-01.16 exit 1 success=
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 ERROR: Task process exited 1, but never updated its task record to indicate success and record its output.
2017-06-27_15:17:34 z8ta6-8i9sb-b6xy0airw233wkt 21286 151 failure (#1, permanent) after 35 seconds


Subtasks 1 (0 open1 closed)

Task #11940: Review 11917-dont-clear-cacheResolvedRadhika Chippada06/29/2017Actions

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Related to Arvados - Bug #11470: [API] container_requests#update alternately responds 422 or 404 for no apparent reasonResolvedNico César04/12/2017Actions
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