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Mutect2 Oncotator failed to delocalize files
I tried to run Mutect2 with Oncotator in FireCloud and it seems like Cromwell is having trouble copying files, though I don't know what that means. I got the following error message.
Task Mutect2.oncotate_m2:NA:1 failed. Job exit code 1. Check gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a/e343f02f-89f4-42e4-8041-d92d91be3077/Mutect2/69442194-e6a1-4922-9419-7de4905bbce6/call-oncotate_m2/oncotate_m2-stderr.log for more information. PAPI error code 5. Message: 10: Failed to delocalize files: failed to copy the following files: "/mnt/local-disk/A1_t.maf.annotated -> gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a/e343f02f-89f4-42e4-8041-d92d91be3077/Mutect2/69442194-e6a1-4922-9419-7de4905bbce6/call-oncotate_m2/A1_t.maf.annotated (cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/A1_t.maf.annotated gs://fc-9eebc834-cb07-4ed3-8dda-a3638ae1722a/e343f02f-89f4-42e4-8041-d92d91be3077/Mutect2/69442194-e6a1-4922-9419-7de4905bbce6/call-oncotate_m2/A1_t.maf.annotated, command failed: CommandException: No URLs matched: /mnt/local-disk/A1_t.maf.annotated\nCommandException: 1 file/object could not be transferred.\n)"``
I looked at the "oncotate_m2-stderr.log" and it ended with:
/cromwell_root/exec.sh: line 43: 12 Segmentation fault (core dumped) wget ftp://[email protected]/bundle/oncotator/oncotator_v1_ds_April052016.tar.gz'
Any idea what's going on and how I can fix it? Thanks!