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[ERROR] token_pon_size_update

cbaocbao Member, Broadie ✭✭

I ran “token_pon_size_update” two times to build a PoN using hundreds of TCGA blood samples. But, each of them finally failed because of a file transfer issue. Should I try to run the tasks separately? Like, step 1, token_make for each bam file; step 2, aggregateTokensAndMakePon … Thanks a lot!

• message: Task token_wf.token_make:192:2 failed. JES error code 5. Message: 9: Failed to localize files: failed to copy the following files: "gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/GBM/DNA/WGS/BI/ILLUMINA/G49538.TCGA-06-0190-10B-01D-A32W-08.1.bam -> /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/GBM/DNA/WGS/BI/ILLUMINA/G49538.TCGA-06-0190-10B-01D-A32W-08.1.bam (cp failed: gsutil -q -m cp gs://5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/GBM/DNA/WGS/BI/ILLUMINA/G49538.TCGA-06-0190-10B-01D-A32W-08.1.bam /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/GBM/DNA/WGS/BI/ILLUMINA/G49538.TCGA-06-0190-10B-01D-A32W-08.1.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%2FGBM%2FDNA%2FWGS%2FBI%2FILLUMINA%2FG49538.TCGA-06-0190-10B-01D-A32W-08.1.bam?generation=1459406764694000&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 155369054208-181424770066/181424770067', 'etag': 'CPCzq+6p6ssCEAM=', 'x-goog-generation': '1459406764694000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Fri, 22 Sep 2017 12:13:01 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UpGsqruJ_dkn5TtnT9bnKVwhWfTa89VyClt2oc3zG3FVYPEvXA-zeHS4aKhPjYG012SxcO8YryS4SXs89v2SGdMHKHueDsXFIKdD1W1e889IkW2qmo', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>) for download of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/GBM/DNA/WGS/BI/ILLUMINA/G49538.TCGA-06-0190-10B-01D-A32W-08.1.bam component 3.\nResumableDownloadException: Transfer failed after 23 retries. Final exception: HttpError accessing <https://www.googleapis.com/download/storage/v1/b/5aa919de-0aa0-43ec-9ec3-288481102b6d/o/tcga%2FGBM%2FDNA%2FWGS%2FBI%2FILLUMINA%2FG49538.TCGA-06-0190-10B-01D-A32W-08.1.bam?generation=1459406764694000&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 155369054208-181424770066/181424770067', 'etag': 'CPCzq+6p6ssCEAM=', 'x-goog-generation': '1459406764694000', 'pragma': 'no-cache', 'cache-control': 'no-cache, no-store, max-age=0, must-revalidate', 'date': 'Fri, 22 Sep 2017 12:13:01 GMT', 'content-type': 'text/plain; charset=utf-8', 'x-guploader-uploadid': 'AEnB2UpGsqruJ_dkn5TtnT9bnKVwhWfTa89VyClt2oc3zG3FVYPEvXA-zeHS4aKhPjYG012SxcO8YryS4SXs89v2SGdMHKHueDsXFIKdD1W1e889IkW2qmo', 'x-goog-storage-class': 'DURABLE_REDUCED_AVAILABILITY'}>, content <Service Unavailable>\nCommandException: Some components of /mnt/local-disk/5aa919de-0aa0-43ec-9ec3-288481102b6d/tcga/GBM/DNA/WGS/BI/ILLUMINA/G49538.TCGA-06-0190-10B-01D-A32W-08.1.bam were not downloaded successfully. Please retry this download.\nCommandException: 1 file/object could not be transferred.\n)"

Best,
Chunyang

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