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pre-process failure due to recovery #560

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keiranmraine opened this issue Feb 1, 2022 · 1 comment
Closed

pre-process failure due to recovery #560

keiranmraine opened this issue Feb 1, 2022 · 1 comment

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@keiranmraine
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Hi,

It appears that the pre-process step doesn't cope well if a pervious execution fails (in our case job overrun):

[bam_sort_core] merging from 0 files and 4 in-memory blocks...
[bam_merge] File '/lustre/scratch124/casm/team78pipelines/canpipe/live/data/analysis/2619_2792329/Gridss/gridss_tmp/2792329.bam.gridss.working/2792329.bam.sv.tmp.bam' exists. Please apply '-f' to overwrite. Abort.
Sat Jan 29 13:03:47 GMT 2022: pre-processing failed for /lustre/scratch124/casm/team78pipelines/canpipe/live/data/stage/2619_2792329/2792329.bam

Solution, always remove the anticipated merge destination file if already present.

(@rulixxx)
d-cameron pushed a commit that referenced this issue Feb 1, 2022
#560 removing .sv.tmp.bam prior to merge (if it exists)
14165a3
@d-cameron
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Fixed for assmbly.sv.tmp.bam as well.

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@keiranmraine @d-cameron