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"File not found" errors when using call caching

I've enabled call-caching as shown below. However, when I remove a cromwell-execution folder, I expected the cache to be invalidated, and the whole analysis to be run again. However, cromwell crashes with a bunch of 'File not found' errors since it cannot find the cached files.

Now, I can't even re-run my analysis, since cromwell keeps crashing due to the missing cache files. Is this the expected behaviour?

Cromwell config:

// Optional call-caching configuration.                                                                
call-caching {                                                                                         
  # Allows re-use of existing results for jobs you've already run                                      
  # (default: false)                                                                                   
  enabled = true                                                                                       

  # Whether to invalidate a cache result forever if we cannot reuse them. Disable this if you expect some cache copies
  # to fail for external reasons which should not invalidate the cache (e.g. auth differences between users):
  # (default: true)                                                                                    
  invalidate-bad-cache-results = true                                                                  

File not found errors:

Could not localize /home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-trim/shard-0/execution/lane_21_1.trimmed.gz -> /home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-abyssPE/shard-0/inputs/home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-trim/shard-0/execution/lane_21_1.trimmed.gz:
    /home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-trim/shard-0/execution/lane_21_1.trimmed.gz doesn't exists
    File not found /home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-abyssPE/shard-0/inputs/home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-trim/shard-0/execution/lane_21_1.trimmed.gz -> /home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-trim/shard-0/execution/lane_21_1.trimmed.gz
    File not found /home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-trim/shard-0/execution/lane_21_1.trimmed.gz
    File not found /home/redmar/devel/wdl/cromwell-executions/resfinder/c381d730-1b3d-424f-ad64-6fa29634ac03/call-trim/shard-0/execution/lane_21_1.trimmed.gz

Issue · Github
by Geraldine_VdAuwera

Issue Number
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