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icgc-argo / ega-file-transfer

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Investigate failed THCA-SA job #8

Closed hknahal closed 3 years ago

hknahal commented 3 years ago

Investigate failed job during EGA->Collab transfer:

The normal sample transferred successfully, but the tumour sample failed: Related to https://github.com/icgc-argo/ega-file-transfer/issues/4

Details: VM: 10.0.0.13 Queue ID: 8206ba60-1811-4444-b1bc-7d7f3aad6988

Failed job: https://github.com/icgc-argo/ega-file-transfer/blob/master/ega_transfer_jobs/failed-jobs/job.EGAZ00001386952.THCA-SA.669C-new.EGAN00001905587.json failed on generate_bai task Job ID: 706a316a-9e9a-417b-a265-db388134ae7a

hknahal commented 3 years ago

Re-ran job on 10.1.0.6 Queue ID: 2edce987-61c7-479e-b257-0eaa02a4d4aa Job ID: d94a906a-2f80-41f5-8853-019da6ea5b70

Failed on generate_bai task: ~/jthome/account.af1309f7-6dd0-4dce-95d7-7e66f989c1a3/node/workflow.6c0b551e-153c-4a18-a144-cd35bdafba7e/0.8.47/queue.2edce987-61c7-479e-b257-0eaa02a4d4aa/executor.f2abc32f-7204-4b6b-9559-3f709e0e56bb/job.d94a906a-2f80-41f5-8853-019da6ea5b70/task.generate_bai

It appears the file is corrupted, so we won't be able to transfer this file

Error:

[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error 4 after 212 of 600 bytes
hknahal commented 3 years ago

EGA re-staged this file, so re-download was attempted but same error:

2021-04-15 19:44:20,818 [INFO] Task failed, task: generate_bai, job: 80bb84a5-b5f4-448b-ac63-771d8c0c08e2
2021-04-15 19:44:20,819 [INFO] [W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::bgzf_read] Read block operation failed with error -1 after 212 of 600 bytes
samtools index: failed to create index for "/home/ubuntu/jthome/account.af1309f7-6dd0-4dce-95d7-7e66f989c1a3/node/workflow.6c0b551e-153c-4a18-a144-cd35bdafba7e/0.8.47/queue.0642f3a4-aad2-44b0-b608-5f6c42703a94/executor.7bfb19ef-ffc8-40c8-a621-66b2a0d21563/job.80bb84a5-b5f4-448b-ac63-771d8c0c08e2/task.download/3ba6aeb0331449d34ecaa63418a453f9.PTC-0669FC.recalibrated.bam": No such file or directory

File is corrupt.

hknahal commented 3 years ago

Closing this ticket. Corrupt file at EGA preventing download.