Hello! I'm trying to run a task (designed for samples) on a sample set by doing: "Define expression: this.samples", but the task failed on all 20 samples in the sample set with the following message: (I'm running the task on TCGA controlled access files available on FireCloud - WXS bams)
Failures:
message: Task DepthOfCoverageWorkflow.DepthOfCoverage:NA:1 failed. JES error code 5. Message: 9: Failed to localize files: failed to copy the following files: "gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam -> /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam (cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam, command failed: CommandException: No URLs matched: gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam\nCommandException: 1 file/object could not be transferred.\n)"
stderr.log is an empty file.
stdout.log shows:
]0;root@308754f4622d: /root@308754f4622d:/# ln -snf /usr/local/share/google-genomics/bin/python2.7 /usr/bin/python
]0;root@308754f4622d: /root@308754f4622d:/# [Kln -snf /usr/local/share/google-genomics/lib/python2.7 /usr/lib/python2.7
]0;root@308754f4622d: /root@308754f4622d:/# [Kln -snf /usr/local/share/google/google-cloud-sdk/bin/gcloud /usr/local/bin/gcloud
]0;root@308754f4622d: /root@308754f4622d:/# [Kln -snf /usr/local/share/google/google-cloud-sdk/bin/gsutil /usr/local/bin/gsutil
]0;root@308754f4622d: /root@308754f4622d:/# [Kln -snf /usr/local/share/google/google-cloud-sdk/bin/gsutil /usr/local/bin/gsutilcloud /usr/local/bin/gcloud[8P-genomics/lib/python2.7 /usr/lib/python2.7l[1@l[1@o[1@c[1@al[1@l[1@/[1@D[1@D[1P[1P/l[1@l[1@o[1@c[1@al[1@l[1@/
]0;root@308754f4622d: /root@308754f4622d:/# [Kgsutil version -l
gsutil version: 4.13
checksum: 141a3e09b42e1b0b6033108aa24c2286 (OK)
boto version: 2.38.0
python version: 2.7.3 (default, Mar 13 2014, 11:03:55) [GCC 4.7.2]
OS: Linux 3.16.0-0.bpo.4-amd64
multiprocessing available: True
using cloud sdk: True
config path: no config found
gsutil path: /usr/local/share/google/google-cloud-sdk/platform/gsutil/gsutil
compiled crcmod: True
installed via package manager: False
editable install: False
]0;root@308754f4622d: /root@308754f4622d:/#
]0;root@308754f4622d: /root@308754f4622d:/# exit
.log file shows:
2017/06/07 16:52:30 I: Switching to status: pulling-image
2017/06/07 16:52:30 I: Calling SetOperationStatus(pulling-image)
2017/06/07 16:52:30 I: SetOperationStatus(pulling-image) succeeded
2017/06/07 16:52:30 I: Writing new Docker configuration file
2017/06/07 16:52:30 I: Pulling image "broadinstitute/genomes-in-the-cloud@sha256:14b722539410c5f5dcda8d0d5a1d75915d38bfa71467b724535dee5e353270a5"
2017/06/07 16:53:29 I: Pulled image "broadinstitute/genomes-in-the-cloud@sha256:14b722539410c5f5dcda8d0d5a1d75915d38bfa71467b724535dee5e353270a5" successfully.
2017/06/07 16:53:29 I: Switching to status: localizing-files
2017/06/07 16:53:29 I: Calling SetOperationStatus(localizing-files)
2017/06/07 16:53:29 I: SetOperationStatus(localizing-files) succeeded
2017/06/07 16:53:29 I: Docker file /cromwell_root/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam.bai maps to host location /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam.bai.
2017/06/07 16:53:29 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam.bai /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam.bai
2017/06/07 16:53:32 I: Docker file /cromwell_root/firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict maps to host location /mnt/local-disk/firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict.
2017/06/07 16:53:32 I: Running command: sudo gsutil -q -m cp gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict /mnt/local-disk/firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict
...
2017/06/07 16:54:09 I: Docker file /cromwell_root/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam maps to host location /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam.
2017/06/07 16:54:09 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
2017/06/07 16:54:10 E: command failed: CommandException: No URLs matched: gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
CommandException: 1 file/object could not be transferred.
(exit status 1)
2017/06/07 16:54:10 W: cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam, command failed: CommandException: No URLs matched: gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
CommandException: 1 file/object could not be transferred.
2017/06/07 16:54:12 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
2017/06/07 16:54:13 E: command failed: CommandException: No URLs matched: gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
CommandException: 1 file/object could not be transferred.
(exit status 1)
2017/06/07 16:54:13 W: cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam, command failed: CommandException: No URLs matched: gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
CommandException: 1 file/object could not be transferred.
2017/06/07 16:54:15 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
2017/06/07 16:54:16 E: command failed: CommandException: No URLs matched: gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
CommandException: 1 file/object could not be transferred.
(exit status 1)
2017/06/07 16:54:16 W: cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam, command failed: CommandException: No URLs matched: gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/COAD/WGA_RepliG/WXS/BI/ILLUMINA/TCGA_MC3.TCGA-AA-3955-10A-01W-0995-10.bam
CommandException: 1 file/object could not be transferred.
2017/06/07 16:54:18 I: Docker file /cromwell_root/exec.sh maps to host location /mnt/local-disk/exec.sh.
2017/06/07 16:54:18 I: Running command: sudo gsutil -q -m cp gs://fc-f3a3e6b7-da75-4a43-9bea-7b1aebcfbe65/4656bfc4-8719-42b0-9c71-0359f7f1bbf7/DepthOfCoverageWorkflow/956f51d5-8d44-478d-981c-8ba185c14c19/call-DepthOfCoverage/exec.sh /mnt/local-disk/exec.sh
When I run on the same task on any of the samples in the sample set by itself, it runs successfully without any issues. Any pointers would be great! Thanks!