Hi! My command creates multiple output files and I'm not sure how to properly define them in output section of my WDL script.
Here is the script:
Rscript ${pcn_extdata}/Coverage.R \
--outdir ${outdir} \
--bam ${bam} \
--intervals ${intervals}
and my outputs will be:
File png = "${BAM_pre}_coverage_loess.png"
File qc = "${BAM_pre}_coverage_loess_qc.txt"
File loess = "${BAM_pre}_coverage_loess.txt"
File cov = "${BAM_pre}_coverage.txt"
Also, here is the log file.
2019/03/13 17:42:44 I: Switching to status: pulling-image
2019/03/13 17:42:44 I: Calling SetOperationStatus(pulling-image)
2019/03/13 17:42:44 I: SetOperationStatus(pulling-image) succeeded
2019/03/13 17:42:44 I: Writing new Docker configuration file
2019/03/13 17:42:44 I: Pulling image "bioconductor/devel_core2@sha256:dd9b36d719ef00b7c821c5245e997e6ec7d8a71b2bcfeb5ba8132793a604e18f"
2019/03/13 17:45:09 I: Pulled image "bioconductor/devel_core2@sha256:dd9b36d719ef00b7c821c5245e997e6ec7d8a71b2bcfeb5ba8132793a604e18f" successfully.
2019/03/13 17:45:09 I: Switching to status: localizing-files
2019/03/13 17:45:09 I: Calling SetOperationStatus(localizing-files)
2019/03/13 17:45:09 I: SetOperationStatus(localizing-files) succeeded
2019/03/13 17:45:09 I: Docker file /cromwell_root/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam maps to host location /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam.
2019/03/13 17:45:09 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam
2019/03/13 17:56:34 I: Docker file /cromwell_root/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam.bai maps to host location /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam.bai.
2019/03/13 17:56:34 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam.bai /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam.bai
2019/03/13 17:56:35 I: Docker file /cromwell_root/fc-secure-0893eb66-fffa-4cc2-a919-5c803249c3b9/Test/whole_exome_agilent_1.1_hg19_gcgene.txt maps to host location /mnt/local-disk/fc-secure-0893eb66-fffa-4cc2-a919-5c803249c3b9/Test/whole_exome_agilent_1.1_hg19_gcgene.txt.
2019/03/13 17:56:35 I: Running command: sudo gsutil -q -m cp gs://fc-secure-0893eb66-fffa-4cc2-a919-5c803249c3b9/Test/whole_exome_agilent_1.1_hg19_gcgene.txt /mnt/local-disk/fc-secure-0893eb66-fffa-4cc2-a919-5c803249c3b9/Test/whole_exome_agilent_1.1_hg19_gcgene.txt
2019/03/13 17:56:37 I: Docker file /cromwell_root/script maps to host location /mnt/local-disk/script.
2019/03/13 17:56:37 I: Running command: sudo gsutil -q -m cp gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/script /mnt/local-disk/script
2019/03/13 17:56:39 I: Done copying files.
2019/03/13 17:56:39 I: Switching to status: running-docker
2019/03/13 17:56:39 I: Calling SetOperationStatus(running-docker)
2019/03/13 17:56:39 I: SetOperationStatus(running-docker) succeeded
2019/03/13 17:56:39 I: Setting these data volumes on the docker container: [-v /tmp/ggp-199678580:/tmp/ggp-199678580 -v /mnt/local-disk:/cromwell_root]
2019/03/13 17:56:39 I: Running command: docker run -v /tmp/ggp-199678580:/tmp/ggp-199678580 -v /mnt/local-disk:/cromwell_root -e __extra_config_gcs_path=gs://cromwell-auth-fccredits-thorium-corn-3153/db196b97-e2ce-4c6a-b27e-ca337096522f_auth.json -e C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt=/cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt -e exec=/cromwell_root/script -e C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt=/cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt -e coverage.Coverage.intervals-0=/cromwell_root/fc-secure-0893eb66-fffa-4cc2-a919-5c803249c3b9/Test/whole_exome_agilent_1.1_hg19_gcgene.txt -e coverage.Coverage.bai-0=/cromwell_root/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam.bai -e stderr=/cromwell_root/stderr -e C239.TCGA-09-0365-10A-01W.6_coverage_loess.png=/cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png -e C239.TCGA-09-0365-10A-01W.6_coverage.txt=/cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage.txt -e stdout=/cromwell_root/stdout -e coverage.Coverage.bam-0=/cromwell_root/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/OV/WGA_RepliG/WXS/BI/ILLUMINA/C239.TCGA-09-0365-10A-01W.6.bam -e rc=/cromwell_root/rc bioconductor/devel_core2@sha256:dd9b36d719ef00b7c821c5245e997e6ec7d8a71b2bcfeb5ba8132793a604e18f /tmp/ggp-199678580
2019/03/13 18:46:53 I: Switching to status: delocalizing-files
2019/03/13 18:46:53 I: Calling SetOperationStatus(delocalizing-files)
2019/03/13 18:46:53 I: SetOperationStatus(delocalizing-files) succeeded
2019/03/13 18:46:53 I: Docker file /cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage.txt maps to host location /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt.
2019/03/13 18:46:53 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt
2019/03/13 18:46:54 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:46:54 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:46:55 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt
2019/03/13 18:46:56 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:46:56 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:46:58 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt
2019/03/13 18:46:59 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:46:59 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:02 I: Switching to status: copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt"
2019/03/13 18:47:02 I: Calling SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt")
2019/03/13 18:47:02 I: SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage.txt") succeeded
2019/03/13 18:47:02 I: Docker file /cromwell_root/stdout maps to host location /mnt/local-disk/stdout.
2019/03/13 18:47:02 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/stdout gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stdout
2019/03/13 18:47:03 I: Deleting log file
2019/03/13 18:47:03 I: Running command: sudo rm -f /var/log/google-genomics/out.log
2019/03/13 18:47:03 I: Switching to status: copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stdout"
2019/03/13 18:47:03 I: Calling SetOperationStatus(copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stdout")
2019/03/13 18:47:03 I: SetOperationStatus(copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stdout") succeeded
2019/03/13 18:47:03 I: Docker file /cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png maps to host location /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png.
2019/03/13 18:47:03 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
2019/03/13 18:47:04 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:04 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:06 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
2019/03/13 18:47:07 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:07 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:09 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
2019/03/13 18:47:10 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:10 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:12 I: Switching to status: copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png"
2019/03/13 18:47:12 I: Calling SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png")
2019/03/13 18:47:12 I: SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.png") succeeded
2019/03/13 18:47:12 I: Docker file /cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt maps to host location /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt.
2019/03/13 18:47:12 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
2019/03/13 18:47:13 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:13 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:14 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
2019/03/13 18:47:15 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:15 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:17 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
2019/03/13 18:47:18 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:18 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:21 I: Switching to status: copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt"
2019/03/13 18:47:21 I: Calling SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt")
2019/03/13 18:47:21 I: SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess_qc.txt") succeeded
2019/03/13 18:47:21 I: Docker file /cromwell_root/stderr maps to host location /mnt/local-disk/stderr.
2019/03/13 18:47:21 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/stderr gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stderr
2019/03/13 18:47:22 I: Deleting log file
2019/03/13 18:47:22 I: Running command: sudo rm -f /var/log/google-genomics/out.log
2019/03/13 18:47:22 I: Switching to status: copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stderr"
2019/03/13 18:47:22 I: Calling SetOperationStatus(copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stderr")
2019/03/13 18:47:22 I: SetOperationStatus(copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/stderr") succeeded
2019/03/13 18:47:22 I: Docker file /cromwell_root/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt maps to host location /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt.
2019/03/13 18:47:22 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
2019/03/13 18:47:23 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:23 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:25 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
2019/03/13 18:47:26 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:26 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:27 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
2019/03/13 18:47:28 E: command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
CommandException: 1 file/object could not be transferred.
(exit status 1)
2019/03/13 18:47:28 W: cp failed: gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt, command failed: CommandException: No URLs matched: /mnt/local-disk/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt
CommandException: 1 file/object could not be transferred.
2019/03/13 18:47:31 I: Switching to status: copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt"
2019/03/13 18:47:31 I: Calling SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt")
2019/03/13 18:47:31 I: SetOperationStatus(copied 0 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/C239.TCGA-09-0365-10A-01W.6_coverage_loess.txt") succeeded
2019/03/13 18:47:31 I: Docker file /cromwell_root/rc maps to host location /mnt/local-disk/rc.
2019/03/13 18:47:31 I: Running command: sudo gsutil -q -m cp -L /var/log/google-genomics/out.log /mnt/local-disk/rc gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/rc
2019/03/13 18:47:32 I: Deleting log file
2019/03/13 18:47:32 I: Running command: sudo rm -f /var/log/google-genomics/out.log
2019/03/13 18:47:32 I: Switching to status: copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/rc"
2019/03/13 18:47:32 I: Calling SetOperationStatus(copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/rc")
2019/03/13 18:47:33 I: SetOperationStatus(copied 1 file(s) to "gs://fc-secure-7796a61e-c9f1-415c-81eb-174b72d40092/ff6c1564-c389-47e3-87ce-b96c4daa1096/coverage/db196b97-e2ce-4c6a-b27e-ca337096522f/call-Coverage/rc") succeeded