I've been trying to run 50 Strelka jobs on TCGA THCA WGS data in workspace rebc-oct16/rebc_template, I've been running into a brick wall of jobs that are unable to localize the bams with JES log messages like below. According to gsutil ls, the bams are in the source bucket.
ResumableDownloadException: Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%2FTHCA%2FDNA%2FWGS%2FBI%2FILLUMINA%2FG49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 1732247552-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Thu, 22 Jun 2017 22:26:07 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2Uqc5_-cg8U0yhLPjlbPgGxxBwbSPe3OtQhknRW06gj6Qr-HLmNx_Ece4HxKidU_NAErgxkQlaaQCy1VAU2YEuekkSBlcg', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>
CommandException: Some components of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam were not downloaded successfully. Please retry this download.
CommandException: 1 file/object could not be transferred.
(exit status 1)
2017/06/22 22:50:16 W: cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam, command failed: Caught ResumableDownloadException (Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%!F(MISSING)THCA%!F(MISSING)DNA%!F(MISSING)WGS%!F(MISSING)BI%!F(MISSING)ILLUMINA%!F(MISSING)G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 1732247552-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Thu, 22 Jun 2017 22:26:07 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2Uqc5_-cg8U0yhLPjlbPgGxxBwbSPe3OtQhknRW06gj6Qr-HLmNx_Ece4HxKidU_NAErgxkQlaaQCy1VAU2YEuekkSBlcg', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>) for download of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam component 0.
ResumableDownloadException: Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%!F(MISSING)THCA%!F(MISSING)DNA%!F(MISSING)WGS%!F(MISSING)BI%!F(MISSING)ILLUMINA%!F(MISSING)G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 1732247552-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Thu, 22 Jun 2017 22:26:07 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2Uqc5_-cg8U0yhLPjlbPgGxxBwbSPe3OtQhknRW06gj6Qr-HLmNx_Ece4HxKidU_NAErgxkQlaaQCy1VAU2YEuekkSBlcg', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>
CommandException: Some components of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam were not downloaded successfully. Please retry this download.
CommandException: 1 file/object could not be transferred.
2017/06/22 22:50:17 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam
2017/06/22 23:45:21 E: command failed: Caught ResumableDownloadException (Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%2FTHCA%2FDNA%2FWGS%2FBI%2FILLUMINA%2FG49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Thu, 22 Jun 2017 23:45:01 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UoRWHrWBfzAC7yYR18dVeDagSKY6n_ocZ00UDWTQbwb4MjrgGk76THhHYvseg-NaGp_MpA0bEBws2YnXrKIeB_c8UHBIfs57z-lt9dHWSUyk2HRNag', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>) for download of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam component 0.
ResumableDownloadException: Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%2FTHCA%2FDNA%2FWGS%2FBI%2FILLUMINA%2FG49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Thu, 22 Jun 2017 23:45:01 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UoRWHrWBfzAC7yYR18dVeDagSKY6n_ocZ00UDWTQbwb4MjrgGk76THhHYvseg-NaGp_MpA0bEBws2YnXrKIeB_c8UHBIfs57z-lt9dHWSUyk2HRNag', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>
CommandException: Some components of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam were not downloaded successfully. Please retry this download.
CommandException: 1 file/object could not be transferred.
(exit status 1)
2017/06/22 23:45:21 W: cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam, command failed: Caught ResumableDownloadException (Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%!F(MISSING)THCA%!F(MISSING)DNA%!F(MISSING)WGS%!F(MISSING)BI%!F(MISSING)ILLUMINA%!F(MISSING)G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Thu, 22 Jun 2017 23:45:01 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UoRWHrWBfzAC7yYR18dVeDagSKY6n_ocZ00UDWTQbwb4MjrgGk76THhHYvseg-NaGp_MpA0bEBws2YnXrKIeB_c8UHBIfs57z-lt9dHWSUyk2HRNag', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>) for download of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam component 0.
ResumableDownloadException: Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%!F(MISSING)THCA%!F(MISSING)DNA%!F(MISSING)WGS%!F(MISSING)BI%!F(MISSING)ILLUMINA%!F(MISSING)G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Thu, 22 Jun 2017 23:45:01 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UoRWHrWBfzAC7yYR18dVeDagSKY6n_ocZ00UDWTQbwb4MjrgGk76THhHYvseg-NaGp_MpA0bEBws2YnXrKIeB_c8UHBIfs57z-lt9dHWSUyk2HRNag', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>
CommandException: Some components of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam were not downloaded successfully. Please retry this download.
CommandException: 1 file/object could not be transferred.
2017/06/22 23:45:24 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam
2017/06/23 00:33:04 E: command failed: Caught ResumableDownloadException (Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%2FTHCA%2FDNA%2FWGS%2FBI%2FILLUMINA%2FG49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Fri, 23 Jun 2017 00:32:44 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UqDPbkyOw7e3Kdv95hGpbxK4Q19922MtQJs1oX7Bj1s9KmB9k3VUaZ-X-DLiJopdN_esXVfRL6gF4CE1CyAfnz5Ta_eyw', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>) for download of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam component 0.
ResumableDownloadException: Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%2FTHCA%2FDNA%2FWGS%2FBI%2FILLUMINA%2FG49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Fri, 23 Jun 2017 00:32:44 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UqDPbkyOw7e3Kdv95hGpbxK4Q19922MtQJs1oX7Bj1s9KmB9k3VUaZ-X-DLiJopdN_esXVfRL6gF4CE1CyAfnz5Ta_eyw', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>
CommandException: Some components of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam were not downloaded successfully. Please retry this download.
CommandException: 1 file/object could not be transferred.
(exit status 1)
2017/06/23 00:33:04 W: cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam, command failed: Caught ResumableDownloadException (Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%!F(MISSING)THCA%!F(MISSING)DNA%!F(MISSING)WGS%!F(MISSING)BI%!F(MISSING)ILLUMINA%!F(MISSING)G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Fri, 23 Jun 2017 00:32:44 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UqDPbkyOw7e3Kdv95hGpbxK4Q19922MtQJs1oX7Bj1s9KmB9k3VUaZ-X-DLiJopdN_esXVfRL6gF4CE1CyAfnz5Ta_eyw', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>) for download of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam component 0.
ResumableDownloadException: Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%!F(MISSING)THCA%!F(MISSING)DNA%!F(MISSING)WGS%!F(MISSING)BI%!F(MISSING)ILLUMINA%!F(MISSING)G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam?generation=1459401050139000&alt=media>: response: <{'status': '503', 'x-goog-metageneration': '3', 'content-disposition': 'attachment', 'content-language': 'en', 'expires': 'Mon, 01 Jan 1990 00:00:00 GMT', 'vary': 'Origin, X-Origin', 'content-length': '19', 'server': 'UploadServer', 'content-range': 'bytes 58527318016-78208179025/312832716103', 'etag': 'CPjStsmU6ssCEAM=', 'x-goog-generation': '1459401050139000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Fri, 23 Jun 2017 00:32:44 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UqDPbkyOw7e3Kdv95hGpbxK4Q19922MtQJs1oX7Bj1s9KmB9k3VUaZ-X-DLiJopdN_esXVfRL6gF4CE1CyAfnz5Ta_eyw', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>
CommandException: Some components of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam were not downloaded successfully. Please retry this download.
CommandException: 1 file/object could not be transferred.
2017/06/23 00:33:07 I: Docker file /cromwell_root/fc-4520e968-446a-4f9f-85e2-8fcc901269dc/strelka_config_bwa_cga_wgs.ini maps to host location /mnt/local-disk/fc-4520e968-446a-4f9f-85e2-8fcc901269dc/strelka_config_bwa_cga_wgs.ini.
2017/06/23 00:33:07 I: Running command: sudo gsutil -q -m cp gs://fc-4520e968-446a-4f9f-85e2-8fcc901269dc/strelka_config_bwa_cga_wgs.ini /mnt/local-disk/fc-4520e968-446a-4f9f-85e2-8fcc901269dc/strelka_config_bwa_cga_wgs.ini
2017/06/23 00:33:08 I: Docker file /cromwell_root/firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta maps to host location /mnt/local-disk/firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.
2017/06/23 00:33:08 I: Running command: sudo gsutil -q -m cp gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta /mnt/local-disk/firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta
2017/06/23 00:33:39 I: Docker file /cromwell_root/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam.bai maps to host location /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam.bai.
2017/06/23 00:33:39 I: Running command: sudo gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam.bai /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/THCA/DNA/WGS/BI/ILLUMINA/G49537.TCGA-BJ-A0Z2-01A-11D-A10S-08.2.bam.bai_