I keep receiving this error when attempting to run my WDL script. I have run the WDL locally without error using the same docker image. I have permission to the files in the google bucket. I believe it may be something with the docker image and trying to run it on FireCloud. It is an image I created that is currently on dockerhub at kdgosik/demuxlet. Would there be permission issues that can arise by using certain docker images?
There is no stdout or stderr messages written, even though there should be a message to stdout for the task being called. I have tried using the same docker image and just writing an echo message to stdout, without calling any additional commands, and it still gives me a similar error of failed to copy the following files: ...
Any help would be greatly appreciated!
Full error message:
Task DemuxletScatter.demuxlet:0:1 failed. The job was stopped before the command finished. PAPI error code 5. Message: 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.sing2 -> gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.sing2 (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.sing2 gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.sing2, command failed: CommandException: No URLs matched: /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.sing2\nCommandException: 1 file/object could not be transferred.\n); /mnt/local-disk/demuxlet-0-rc.txt -> gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/demuxlet-0-rc.txt (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/demuxlet-0-rc.txt gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/demuxlet-0-rc.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/demuxlet-0-rc.txt\nCommandException: 1 file/object could not be transferred.\n); /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.best -> gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.best (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.best gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.best, command failed: CommandException: No URLs matched: /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.best\nCommandException: 1 file/object could not be transferred.\n); /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.single -> gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.single (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.single gs://fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/5e6085a5-f972-453a-9812-83a9b6c8ad9f/DemuxletScatter/ddb5a1a8-f0da-403d-bfb5-e01aebe132de/call-demuxlet/shard-0/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.single, command failed: CommandException: No URLs matched: /mnt/local-disk/fc-6aff27a4-00f0-460b-af6d-db1e0a1f7d40/C11.single\nCommandException: 1 file/object could not be transferred.\n)"