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Added a comment: another example of git-annex-fsck reporting dead keys as errors

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Ilya_Shlyakhter 2020-02-27 21:39:57 +00:00 committed by admin
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[[!comment format=mdwn
username="Ilya_Shlyakhter"
avatar="http://cdn.libravatar.org/avatar/1647044369aa7747829c38b9dcc84df0"
subject="another example of git-annex-fsck reporting dead keys as errors"
date="2020-02-27T21:39:57Z"
content="""
[[!format sh \"\"\"
(master_env_v174_py36) 16:36 [viral-ngs-benchmarks] $ git annex fsck wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-f\
ix-gatk-mindepth_sha256_20bbb1d96cf58235d325a4ea2def8c3d840d9c2ab5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl
fsck wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-fix-gatk-mindepth_sha256_20bbb1d96cf58235d325a4ea2def8c3d840d9c2ab\
5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl
** Required content wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-fix-gatk-mindepth_sha256_20bbb1d96cf58235d325a4ea\
2def8c3d840d9c2ab5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl is missing from these repositories:
449efa47-a0e1-4376-a17f-42c7a1f509d1 -- Benchmarks for viral-ngs, stored on Amazon S3 [viral-ngs-benchmarks-s3]
** No known copies exist of wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-fix-gatk-mindepth_sha256_20bbb1d96cf58235\
d325a4ea2def8c3d840d9c2ab5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl
These dead repositories used to have copies
461e3f01-1ff4-43d6-8dfa-71b839a25881 -- crogit runner crogrun_200207_174047__8035____git_9cb32e7230b
failed
(recording state in git...)
git-annex: fsck: 1 failed
(master_env_v174_py36) 16:36 [viral-ngs-benchmarks] $ git annex dead --key `git annex lookupkey wdl/quay.io-broadinstitute-viral-ngs-\
dev_1.25.0-11-g6fe46aa-is-fix-gatk-mindepth_sha256_20bbb1d96cf58235d325a4ea2def8c3d840d9c2ab5dddf573f9471c57f7414f1/assemble_denovo/ta\
sks_assembly.wdl`
dead MD5E-s15002--4f40b2c4a2ba81128db649e6096b5fec.wdl ok
(master_env_v174_py36) 16:37 [viral-ngs-benchmarks] $ git annex fsck wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-f\
ix-gatk-mindepth_sha256_20bbb1d96cf58235d325a4ea2def8c3d840d9c2ab5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl
fsck wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-fix-gatk-mindepth_sha256_20bbb1d96cf58235d325a4ea2def8c3d840d9c2ab\
5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl
** Required content wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-fix-gatk-mindepth_sha256_20bbb1d96cf58235d325a4ea\
2def8c3d840d9c2ab5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl is missing from these repositories:
449efa47-a0e1-4376-a17f-42c7a1f509d1 -- Benchmarks for viral-ngs, stored on Amazon S3 [viral-ngs-benchmarks-s3]
** No known copies exist of wdl/quay.io-broadinstitute-viral-ngs-dev_1.25.0-11-g6fe46aa-is-fix-gatk-mindepth_sha256_20bbb1d96cf58235\
d325a4ea2def8c3d840d9c2ab5dddf573f9471c57f7414f1/assemble_denovo/tasks_assembly.wdl
These dead repositories used to have copies
461e3f01-1ff4-43d6-8dfa-71b839a25881 -- crogit runner crogrun_200207_174047__8035____git_9cb32e7230b
failed
(recording state in git...)
git-annex: fsck: 1 failed
\"\"\"]]
"""]]