2019-04-30 08:34:02,612[INFO]: Logfile: ./log/extract/extract.2019_04_30.log
2019-04-30 08:34:04,504[INFO]: Retrieving packages from broad-firecloud-cptac: awg_cptac3-luad__2019_04_17
2019-04-30 08:34:04,504[INFO]: Start time: 2019-04-30 08:34:04.504505
2019-04-30 08:34:04,505[INFO]: Downloading in parallel using 8 threads
2019-04-30 08:34:05,307[DEBUG]: Converted retries value: 3 -> Retry(total=3, connect=None, read=None, redirect=None, status=None)
2019-04-30 08:34:05,345[DEBUG]: Starting new HTTPS connection (1): oauth2.googleapis.com:443
2019-04-30 08:34:05,534[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:05,539[DEBUG]: Starting new HTTPS connection (1): api.firecloud.org:443
2019-04-30 08:34:05,612[DEBUG]: https://api.firecloud.org:443 "GET /health HTTP/1.1" 200 2
2019-04-30 08:34:05,616[DEBUG]: Starting new HTTPS connection (1): www.googleapis.com:443
2019-04-30 08:34:05,770[DEBUG]: https://www.googleapis.com:443 "GET /oauth2/v1/certs HTTP/1.1" 200 1558
2019-04-30 08:34:06,512[DEBUG]: https://api.firecloud.org:443 "GET /api/workspaces/broad-firecloud-cptac/awg_cptac3-luad__2019_04_17/entityQuery/sample_set?sortDirection=asc&page=1&pageSize=1000 HTTP/1.1" 200 None
2019-04-30 08:34:08,079[DEBUG]: https://api.firecloud.org:443 "GET /api/workspaces/broad-firecloud-cptac/awg_cptac3-luad__2019_04_17 HTTP/1.1" 200 None
2019-04-30 08:34:08,340[DEBUG]: https://api.firecloud.org:443 "GET /api/workspaces/broad-firecloud-cptac/awg_cptac3-luad__2019_04_17/methodconfigs?allRepos=False HTTP/1.1" 200 None
2019-04-30 08:34:08,590[DEBUG]: https://api.firecloud.org:443 "GET /api/workspaces/broad-firecloud-cptac/awg_cptac3-luad__2019_04_17/entities/sample_set/CPTAC3-LUAD-TP HTTP/1.1" 200 None
2019-04-30 08:34:08,618[DEBUG]: Converted retries value: 3 -> Retry(total=3, connect=None, read=None, redirect=None, status=None)
2019-04-30 08:34:08,621[DEBUG]: Converted retries value: 3 -> Retry(total=3, connect=None, read=None, redirect=None, status=None)
2019-04-30 08:34:08,619[DEBUG]: Converted retries value: 3 -> Retry(total=3, connect=None, read=None, redirect=None, status=None)
2019-04-30 08:34:08,620[DEBUG]: Converted retries value: 3 -> Retry(total=3, connect=None, read=None, redirect=None, status=None)
2019-04-30 08:34:08,680[DEBUG]: Starting new HTTPS connection (1): oauth2.googleapis.com:443
2019-04-30 08:34:08,685[DEBUG]: Starting new HTTPS connection (1): oauth2.googleapis.com:443
2019-04-30 08:34:08,689[DEBUG]: Starting new HTTPS connection (1): oauth2.googleapis.com:443
2019-04-30 08:34:08,691[DEBUG]: Starting new HTTPS connection (2): oauth2.googleapis.com:443
2019-04-30 08:34:08,692[DEBUG]: Starting new HTTPS connection (2): oauth2.googleapis.com:443
2019-04-30 08:34:08,699[DEBUG]: Starting new HTTPS connection (1): oauth2.googleapis.com:443
2019-04-30 08:34:08,700[DEBUG]: Starting new HTTPS connection (3): oauth2.googleapis.com:443
2019-04-30 08:34:08,705[DEBUG]: Starting new HTTPS connection (3): oauth2.googleapis.com:443
2019-04-30 08:34:08,843[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:08,855[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:08,910[DEBUG]: Starting new HTTPS connection (1): www.googleapis.com:443
2019-04-30 08:34:08,912[DEBUG]: Starting new HTTPS connection (1): www.googleapis.com:443
2019-04-30 08:34:08,938[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:08,942[DEBUG]: Starting new HTTPS connection (1): www.googleapis.com:443
2019-04-30 08:34:08,961[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:08,962[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:08,962[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:08,964[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:08,988[DEBUG]: https://oauth2.googleapis.com:443 "POST /token HTTP/1.1" 200 None
2019-04-30 08:34:09,052[DEBUG]: Starting new HTTPS connection (1): www.googleapis.com:443
2019-04-30 08:34:09,054[DEBUG]: Starting new HTTPS connection (2): www.googleapis.com:443
2019-04-30 08:34:09,058[DEBUG]: Starting new HTTPS connection (2): www.googleapis.com:443
2019-04-30 08:34:09,060[DEBUG]: Starting new HTTPS connection (3): www.googleapis.com:443
2019-04-30 08:34:09,062[DEBUG]: Starting new HTTPS connection (3): www.googleapis.com:443
2019-04-30 08:34:09,079[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,085[DEBUG]: Starting new HTTPS connection (2): www.googleapis.com:443
2019-04-30 08:34:09,119[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,120[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,176[DEBUG]: Starting new HTTPS connection (3): www.googleapis.com:443
2019-04-30 08:34:09,314[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,316[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/a5576ec1-417d-4f38-91ab-8144cba9b161%2Fcorrelate_genomic_events%2F2b20f37d-184b-4f47-8170-73e898ad05ea%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events.zip HTTP/1.1" 200 1489
2019-04-30 08:34:09,323[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,325[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,346[DEBUG]: Starting new HTTPS connection (4): www.googleapis.com:443
2019-04-30 08:34:09,349[DEBUG]: Starting new HTTPS connection (5): www.googleapis.com:443
2019-04-30 08:34:09,350[DEBUG]: Starting new HTTPS connection (6): www.googleapis.com:443
2019-04-30 08:34:09,352[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/69dd18b3-97fe-4143-b0f4-32e5d55e929d%2Faggregate_clusters_workflow%2Fd44c315a-761b-4b72-be1f-cb969be36102%2Fcall-aggregate_clusters%2Faggregate_clusters.zip HTTP/1.1" 200 1391
2019-04-30 08:34:09,367[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,381[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,382[DEBUG]: Starting new HTTPS connection (7): www.googleapis.com:443
2019-04-30 08:34:09,390[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/a7374c5f-932d-4c15-b5d9-50740e58a2b0%2Ftool_gistic2_postprocess_workflow%2Ffd5af1f4-76dc-4f37-a0cc-fbddba539710%2Fcall-tool_gistic2_postprocess%2Ftool_gistic2_postprocess.zip HTTP/1.1" 200 1463
2019-04-30 08:34:09,471[DEBUG]: Starting new HTTPS connection (8): www.googleapis.com:443
2019-04-30 08:34:09,502[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/39eab10a-1791-41cf-866c-13e6472ce02e%2Fnormalize_clinical_cptac%2Fdf4eac3a-77b6-4ce7-961f-e1027c1ad609%2Fcall-normalize_clinical_cptac_task_1%2Fnormalize_clinical_cptac.zip HTTP/1.1" 200 1455
2019-04-30 08:34:09,570[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/069a11b4-7b1a-48bc-8231-942ea7a19e7c%2Fcorrelate_genomic_events_all%2Fabf2ca5c-bd5f-4d49-8b37-7914065d06a1%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events_all.zip HTTP/1.1" 200 1523
2019-04-30 08:34:09,571[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/5f3cf94d-1fd8-4096-b606-bcdd9599f833%2Fcorrelate_genomic_events_all%2F3441da4a-c848-4650-95a4-60c86ad83a57%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events_all.zip HTTP/1.1" 200 1522
2019-04-30 08:34:09,599[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/ba1a026a-1f61-4edb-af03-265ba4ac43e5%2Fcopy_number_gistic2%2Fe341778e-2a5c-4d9c-b17a-bd3126ba4440%2Fcall-report_gistic2%2Fcopy_number_gistic2.zip HTTP/1.1" 200 1351
2019-04-30 08:34:09,601[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/2b02efbb-57f3-49fd-9ff5-757853aef38c%2Faggregate_feature_table_workflow%2F22f8b2c7-1b28-47f4-8030-b3832e841bec%2Fcall-aggregate_feature_table%2Faggregate_feature_table.zip HTTP/1.1" 200 1453
2019-04-30 08:34:09,672[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/69dd18b3-97fe-4143-b0f4-32e5d55e929d%2Faggregate_clusters_workflow%2Fd44c315a-761b-4b72-be1f-cb969be36102%2Fcall-aggregate_clusters%2Faggregate_clusters.zip?generation=1556577089958637&alt=media HTTP/1.1" 200 2841
2019-04-30 08:34:09,683[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.Aggregate_Molecular_Subtype_Clusters.20190417.0.zip
2019-04-30 08:34:09,697[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/a7374c5f-932d-4c15-b5d9-50740e58a2b0%2Ftool_gistic2_postprocess_workflow%2Ffd5af1f4-76dc-4f37-a0cc-fbddba539710%2Fcall-tool_gistic2_postprocess%2Ftool_gistic2_postprocess.zip?generation=1556573839155253&alt=media HTTP/1.1" 200 2412
2019-04-30 08:34:09,702[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.CopyNumber_Gistic2_Postprocess_Focal.20190417.0.zip
2019-04-30 08:34:09,707[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/a5576ec1-417d-4f38-91ab-8144cba9b161%2Fcorrelate_genomic_events%2F2b20f37d-184b-4f47-8170-73e898ad05ea%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events.zip?generation=1556577507288028&alt=media HTTP/1.1" 200 964941
2019-04-30 08:34:09,767[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.Correlate_Clinical_vs_Molecular_Subtypes.20190417.0.zip
2019-04-30 08:34:09,769[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,792[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,816[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/39eab10a-1791-41cf-866c-13e6472ce02e%2Fnormalize_clinical_cptac%2Fdf4eac3a-77b6-4ce7-961f-e1027c1ad609%2Fcall-normalize_clinical_cptac_task_1%2Fnormalize_clinical_cptac.zip?generation=1556569935470962&alt=media HTTP/1.1" 200 3838
2019-04-30 08:34:09,823[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.Clinical_Pick_Tier1.20190417.0.zip
2019-04-30 08:34:09,859[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,875[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/7e5c0b4f-e849-41ec-a1f1-6255d4b3b676%2Fcorrelate_clinical_vs_expression%2Feef2971f-420b-4233-9785-5a33253582e7%2Fcall-report_correlate_expression_clinical%2Fcorrelate_clinical_vs_expression.zip HTTP/1.1" 200 1541
2019-04-30 08:34:09,899[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/f466592e-c6e5-4ee3-a314-14eeeca1d630%2Fcorrelate_genomic_events_all%2F0d3ab625-b3a9-4a3c-86b8-2befa86be129%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events_all.zip HTTP/1.1" 200 1522
2019-04-30 08:34:09,914[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:09,924[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/5f3cf94d-1fd8-4096-b606-bcdd9599f833%2Fcorrelate_genomic_events_all%2F3441da4a-c848-4650-95a4-60c86ad83a57%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events_all.zip?generation=1556574223267138&alt=media HTTP/1.1" 200 7534034
2019-04-30 08:34:09,954[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/069a11b4-7b1a-48bc-8231-942ea7a19e7c%2Fcorrelate_genomic_events_all%2Fabf2ca5c-bd5f-4d49-8b37-7914065d06a1%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events_all.zip?generation=1556574308723242&alt=media HTTP/1.1" 200 11590017
2019-04-30 08:34:09,975[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/ba1a026a-1f61-4edb-af03-265ba4ac43e5%2Fcopy_number_gistic2%2Fe341778e-2a5c-4d9c-b17a-bd3126ba4440%2Fcall-report_gistic2%2Fcopy_number_gistic2.zip?generation=1556573682024349&alt=media HTTP/1.1" 200 26160054
2019-04-30 08:34:09,978[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/2b02efbb-57f3-49fd-9ff5-757853aef38c%2Faggregate_feature_table_workflow%2F22f8b2c7-1b28-47f4-8030-b3832e841bec%2Fcall-aggregate_feature_table%2Faggregate_feature_table.zip?generation=1556577383098899&alt=media HTTP/1.1" 200 626055
2019-04-30 08:34:09,991[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/4f266055-3350-4131-baac-9594721b5488%2Fcorrelate_clinical_vs_expression%2F4f214c4b-4adc-4efb-9bad-39703636aae2%2Fcall-report_correlate_expression_clinical%2Fcorrelate_clinical_vs_expression.zip HTTP/1.1" 200 1540
2019-04-30 08:34:10,006[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/273826fb-812f-4d11-843d-1bbc9108c8bc%2Fcorrelate_genomic_events%2F6fcfed0f-ca9a-4138-baf3-d7fc2e43a396%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events.zip HTTP/1.1" 200 1489
2019-04-30 08:34:10,151[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.Aggregate_Analysis_Features.20190417.0.zip
2019-04-30 08:34:10,219[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/f466592e-c6e5-4ee3-a314-14eeeca1d630%2Fcorrelate_genomic_events_all%2F0d3ab625-b3a9-4a3c-86b8-2befa86be129%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events_all.zip?generation=1556576274162968&alt=media HTTP/1.1" 200 1996324
2019-04-30 08:34:10,273[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/7e5c0b4f-e849-41ec-a1f1-6255d4b3b676%2Fcorrelate_clinical_vs_expression%2Feef2971f-420b-4233-9785-5a33253582e7%2Fcall-report_correlate_expression_clinical%2Fcorrelate_clinical_vs_expression.zip?generation=1556576106043871&alt=media HTTP/1.1" 200 146598
2019-04-30 08:34:10,331[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/4f266055-3350-4131-baac-9594721b5488%2Fcorrelate_clinical_vs_expression%2F4f214c4b-4adc-4efb-9bad-39703636aae2%2Fcall-report_correlate_expression_clinical%2Fcorrelate_clinical_vs_expression.zip?generation=1556577209082627&alt=media HTTP/1.1" 200 18642
2019-04-30 08:34:10,345[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.Correlate_Clinical_vs_MutationRate.20190417.0.zip
2019-04-30 08:34:10,346[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.Correlate_Clinical_vs_Mutation_APOBEC_Continuous.20190417.0.zip
2019-04-30 08:34:10,357[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
2019-04-30 08:34:10,423[DEBUG]: https://www.googleapis.com:443 "GET /download/storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a/o/273826fb-812f-4d11-843d-1bbc9108c8bc%2Fcorrelate_genomic_events%2F6fcfed0f-ca9a-4138-baf3-d7fc2e43a396%2Fcall-report_correlate_genomic_event_clinical%2Fcorrelate_genomic_events.zip?generation=1556577245516491&alt=media HTTP/1.1" 200 920729
2019-04-30 08:34:10,536[INFO]: Downloaded /xchip/gdac_data/runs/awg_cptac3-luad__2019_04_17/CPTAC3-LUAD-TP.Correlate_Clinical_vs_CopyNumber_Focal.20190417.0.zip
2019-04-30 08:34:10,573[DEBUG]: https://www.googleapis.com:443 "GET /storage/v1/b/fc-e7058367-eaa6-44b5-aab5-1ec08acf146a?projection=noAcl HTTP/1.1" 200 681
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2019-04-30 08:34:12,865[INFO]: Number of Candidate Files:   23
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