Defining multiple outputs

shbriefshbrief New YorkMember
edited March 13 in Ask the FireCloud Team

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/[email protected]:dd9b36d719ef00b7c821c5245e997e6ec7d8a71b2bcfeb5ba8132793a604e18f"
2019/03/13 17:45:09 I: Pulled image "bioconductor/[email protected]: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/[email protected]: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

Best Answers

  • shbriefshbrief New York
    Accepted Answer

    Hi @AdelaideR

    Thanks for your comment. After some additional trials, here is my updated script works the way I want. Let me know if you see any part that can be written better. :)

    workflow coverage {
        call Coverage 
    }
    
    task Coverage {
        File bam
        File bai
        File intervals
        String BAM_pre = basename(bam, ".bam")
        String outdir   # .
        String pcn_extdata
    
        # Runtime parameters
        String bioc_docker  # "bioconductor/devel_core2"
        Int? machine_mem_gb
        Int? disk_space_gb
        Int disk_size = ceil(size(bam, "GB")) + 20
    
    
        command <<<
            R -e "BiocManager::install('PureCN'); \
            BiocManager::install('optparse'); \
            library('PureCN');"
    
            mkdir ${outdir}
    
            Rscript ${pcn_extdata}/Coverage.R \
            --outdir ${outdir} \
            --bam ${bam} \
            --intervals ${intervals}
        >>>
    
        runtime {
            docker: bioc_docker
            cpu : 2
            memory: "32 GB"
            disks: "local-disk " + select_first([disk_space_gb, disk_size]) + " SSD"
        }
        output {
            File png = "${outdir}/${BAM_pre}_coverage_loess.png"
            File qc = "${outdir}/${BAM_pre}_coverage_loess_qc.txt"
            File loess = "${outdir}/${BAM_pre}_coverage_loess.txt"
            File cov = "${outdir}/${BAM_pre}_coverage.txt"
        }
    } 
    

Answers

  • AdelaideRAdelaideR Member admin

    Oh, I see that you answered the question that I already asked in the other forum.

    @shbrief I need some time to take a look, but in the future it would be helpful if you kept the discussion on the same page so we have all of the information.

  • shbriefshbrief New YorkMember
    edited March 14

    @AdelaideR
    Thanks! I thought those are two different questions (creating new directory vs. defining multiple outputs), but I guess they are not...

    In case it helps, here is my WDL script for this run.

    workflow coverage {
        call Coverage 
    }
    
    task Coverage {
        File bam
        File bai
        File intervals
        String BAM_pre = basename(bam, ".bam")
        String outdir
        String pcn_extdata
        String bioc_docker  # "bioconductor/devel_core2"
    
    
        command <<<
            R -e "BiocManager::install('PureCN'); \
            BiocManager::install('optparse'); \
            library('PureCN');"
    
            mkdir ${outdir}
    
            Rscript ${pcn_extdata}/Coverage.R \
            --outdir ${outdir} \
            --bam ${bam} \
            --intervals ${intervals}
        >>>
    
        runtime {
            docker: bioc_docker
            disks: "local-disk 100 SSD" 
            cpu : 4
            memory: "32 GB"
        }
        output {
            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"
        }
    }
    
  • shbriefshbrief New YorkMember
    Accepted Answer

    Hi @AdelaideR

    Thanks for your comment. After some additional trials, here is my updated script works the way I want. Let me know if you see any part that can be written better. :)

    workflow coverage {
        call Coverage 
    }
    
    task Coverage {
        File bam
        File bai
        File intervals
        String BAM_pre = basename(bam, ".bam")
        String outdir   # .
        String pcn_extdata
    
        # Runtime parameters
        String bioc_docker  # "bioconductor/devel_core2"
        Int? machine_mem_gb
        Int? disk_space_gb
        Int disk_size = ceil(size(bam, "GB")) + 20
    
    
        command <<<
            R -e "BiocManager::install('PureCN'); \
            BiocManager::install('optparse'); \
            library('PureCN');"
    
            mkdir ${outdir}
    
            Rscript ${pcn_extdata}/Coverage.R \
            --outdir ${outdir} \
            --bam ${bam} \
            --intervals ${intervals}
        >>>
    
        runtime {
            docker: bioc_docker
            cpu : 2
            memory: "32 GB"
            disks: "local-disk " + select_first([disk_space_gb, disk_size]) + " SSD"
        }
        output {
            File png = "${outdir}/${BAM_pre}_coverage_loess.png"
            File qc = "${outdir}/${BAM_pre}_coverage_loess_qc.txt"
            File loess = "${outdir}/${BAM_pre}_coverage_loess.txt"
            File cov = "${outdir}/${BAM_pre}_coverage.txt"
        }
    } 
    
  • AdelaideRAdelaideR Member admin

    @shbrief -

    I think this is pretty clear. Let me know if it stops working. I think being more specific about the outputs was the correct fix.

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