Re-running LINCS pipeline for: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16

GCP

Job Status

Created: 2021-04-19 05:46:24
Modified: 2021-04-19 07:30:49
Email: vsharma@uw.edu
Status: COMPLETE
Info:
Description: Re-running LINCS pipeline for: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
File Path: /data/labkey/files/LINCS/GCP/@files/LincsPSP_rerun_LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_2021-04-19_05-46-23.log
Files: LincsPSP_rerun_LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_2021-04-19_05-46-23.log

Log File


19 Apr 2021 05:46:23,999 INFO : Re-running LINCS pipeline for: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 05:46:24,000 INFO : =======================================
19 Apr 2021 05:48:29,279 INFO : Starting to run task 'org.labkey.lincs.cromwell.CromwellGctTask' at location 'webserver-high-priority'
19 Apr 2021 05:48:29,279 INFO : Starting task to create L2 GCT for LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.sky.zip
19 Apr 2021 05:48:29,284 INFO : Submitting job to http://m002.grid.gs.washington.edu:8000/api/workflows/v1
19 Apr 2021 05:48:29,305 INFO : Checking status of job at http://m002.grid.gs.washington.edu:8000/api/workflows/v1/7d7de77e-abb6-41b7-ad20-5d6f765a69f1/status
19 Apr 2021 05:48:49,329 INFO : Cromwell job status: Submitted
19 Apr 2021 05:49:09,345 INFO : Cromwell job status: Running
19 Apr 2021 05:49:49,377 INFO : Cromwell job status: Succeeded
19 Apr 2021 05:49:49,377 INFO : Cromwell job completed successfully
19 Apr 2021 05:49:49,378 INFO : Successfully completed task 'org.labkey.lincs.cromwell.CromwellGctTask'
19 Apr 2021 06:19:56,940 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 06:19:56,941 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 06:19:56,942 INFO : Resubmitting job for runId: 31563, name: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 06:19:56,942 INFO : Old job details:
19 Apr 2021 06:19:56,942 INFO : Id: 68
19 Apr 2021 06:19:56,942 INFO : Pipeline job Id: 68193
19 Apr 2021 06:19:56,942 INFO : Run Id: 31563
19 Apr 2021 06:19:56,942 INFO : PSP Job Id: 5cfd4eda344c151e38c98d7c
19 Apr 2021 06:19:56,942 INFO : PSP Job name: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 06:19:56,943 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 06:19:56,943 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T18:24:26.419Z","name":"LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16","id":"5cfd4eda344c151e38c98d7c","last_modified":"2019-06-09T18:24:52.146Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=31563&remote=true&reportName=GCT%20File%20GCP"}},"status":"POUR : succeeded in uploading all GCTs to Panorama","level 3":{"s3":{"url":"s3://proteomics.clue.io/psp/level3/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct"}}}
19 Apr 2021 06:19:56,943 INFO : Resubmitting...
19 Apr 2021 06:19:56,945 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 06:19:57,285 INFO : Job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16exists.
19 Apr 2021 06:19:57,286 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_2
19 Apr 2021 06:19:57,426 INFO : Job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_2exists.
19 Apr 2021 06:19:57,426 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_3
19 Apr 2021 06:19:57,565 INFO : Job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_3exists.
19 Apr 2021 06:19:57,565 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_4
19 Apr 2021 06:19:57,700 INFO : PSP job name: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_4
19 Apr 2021 06:19:57,701 INFO : Sending JSON:
19 Apr 2021 06:19:57,701 INFO : { "level 4": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct" }}, "assay": "GCP", "name": "LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_4", "config": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg" }}, "level 2": {"panorama": { "method": "GET", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.gct" }}, "level 3": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct" }} }
19 Apr 2021 06:19:57,701 INFO : Sending POST request to https://api.clue.io/api/psp
19 Apr 2021 06:19:57,907 INFO : Response code - 200
19 Apr 2021 06:19:57,907 INFO : Response from server: {"name":"LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_4","assay":"GCP","status":"Waiting_To_Download","id":"607d837d198678001151186f","created":"2021-04-19T13:19:57.779Z","last_modified":"2021-04-19T13:19:57.779Z","level 2":{"panorama":{"method":"GET","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.gct"}},"level 3":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct"}},"level 4":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct"}},"config":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg"}}}
19 Apr 2021 06:19:57,908 INFO : Sent POST request to https://api.clue.io/api/psp
19 Apr 2021 06:19:57,910 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:19:58,051 INFO : Status: Waiting_To_Download
19 Apr 2021 06:20:18,053 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:20:18,342 INFO : Status: created LVL2 GCT
19 Apr 2021 06:20:38,344 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:20:38,637 INFO : Status: created LVL2 GCT
19 Apr 2021 06:20:58,639 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:20:58,932 INFO : Status: created LVL2 GCT
19 Apr 2021 06:21:18,935 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:21:19,316 INFO : Status: created LVL2 GCT
19 Apr 2021 06:21:39,319 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:21:39,607 INFO : Status: created LVL2 GCT
19 Apr 2021 06:21:59,610 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:21:59,904 INFO : Status: created LVL2 GCT
19 Apr 2021 06:22:19,907 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:22:20,203 INFO : Status: created LVL2 GCT
19 Apr 2021 06:22:40,206 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:22:40,496 INFO : Status: created LVL2 GCT
19 Apr 2021 06:23:00,504 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:23:00,794 INFO : Status: created LVL2 GCT
19 Apr 2021 06:23:20,796 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:23:21,094 INFO : Status: created LVL2 GCT
19 Apr 2021 06:23:41,096 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:23:41,388 INFO : Status: created LVL2 GCT
19 Apr 2021 06:24:01,391 INFO : Checking status of job 607d837d198678001151186f
19 Apr 2021 06:24:01,709 INFO : Failed to complete task 'org.labkey.lincs.psp.LincsPspTask'
19 Apr 2021 07:29:47,207 INFO : Retrying job.
19 Apr 2021 07:29:47,232 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 07:29:47,233 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 07:29:47,233 INFO : Resubmitting job for runId: 31563, name: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 07:29:47,233 INFO : Old job details:
19 Apr 2021 07:29:47,233 INFO : Id: 68
19 Apr 2021 07:29:47,233 INFO : Pipeline job Id: 68193
19 Apr 2021 07:29:47,233 INFO : Run Id: 31563
19 Apr 2021 07:29:47,234 INFO : PSP Job Id: 5cfd4eda344c151e38c98d7c
19 Apr 2021 07:29:47,234 INFO : PSP Job name: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 07:29:47,234 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 07:29:47,234 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T18:24:26.419Z","name":"LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16","id":"5cfd4eda344c151e38c98d7c","last_modified":"2019-06-09T18:24:52.146Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=31563&remote=true&reportName=GCT%20File%20GCP"}},"status":"POUR : succeeded in uploading all GCTs to Panorama","level 3":{"s3":{"url":"s3://proteomics.clue.io/psp/level3/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct"}}}
19 Apr 2021 07:29:47,234 INFO : Resubmitting...
19 Apr 2021 07:29:47,236 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16
19 Apr 2021 07:29:47,607 INFO : Job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16exists.
19 Apr 2021 07:29:47,608 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_2
19 Apr 2021 07:29:47,745 INFO : Job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_2exists.
19 Apr 2021 07:29:47,745 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_3
19 Apr 2021 07:29:47,879 INFO : Job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_3exists.
19 Apr 2021 07:29:47,879 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_4
19 Apr 2021 07:29:48,014 INFO : Job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_4exists.
19 Apr 2021 07:29:48,014 INFO : Looking for existing job with name LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_5
19 Apr 2021 07:29:48,149 INFO : PSP job name: LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_5
19 Apr 2021 07:29:48,165 INFO : Sending JSON:
19 Apr 2021 07:29:48,165 INFO : { "level 4": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct" }}, "assay": "GCP", "name": "LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_5", "config": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg" }}, "level 2": {"panorama": { "method": "GET", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.gct" }}, "level 3": {"panorama": { "method": "PUT", "url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct" }} }
19 Apr 2021 07:29:48,165 INFO : Sending POST request to https://api.clue.io/api/psp
19 Apr 2021 07:29:48,358 INFO : Response code - 200
19 Apr 2021 07:29:48,358 INFO : Response from server: {"name":"LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_5","assay":"GCP","status":"Waiting_To_Download","id":"607d93dc77d01b0017d7908e","created":"2021-04-19T14:29:48.244Z","last_modified":"2021-04-19T14:29:48.244Z","level 2":{"panorama":{"method":"GET","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.gct"}},"level 3":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL3.gct"}},"level 4":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16_LVL4.gct"}},"config":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate18_annotated_minimized_2018-05-07_14-22-16.cfg"}}}
19 Apr 2021 07:29:48,358 INFO : Sent POST request to https://api.clue.io/api/psp
19 Apr 2021 07:29:48,360 INFO : Checking status of job 607d93dc77d01b0017d7908e
19 Apr 2021 07:29:48,499 INFO : Status: Waiting_To_Download
19 Apr 2021 07:30:08,502 INFO : Checking status of job 607d93dc77d01b0017d7908e
19 Apr 2021 07:30:08,789 INFO : Status: created LVL2 GCT
19 Apr 2021 07:30:28,791 INFO : Checking status of job 607d93dc77d01b0017d7908e
19 Apr 2021 07:30:29,164 INFO : Status: created LVL 4 GCT
19 Apr 2021 07:30:49,165 INFO : Checking status of job 607d93dc77d01b0017d7908e
19 Apr 2021 07:30:49,451 INFO : Status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 07:30:49,451 INFO : PSP job completed with status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 07:30:49,451 INFO : Finished running LINCS PSP pipeline.
19 Apr 2021 07:30:49,451 INFO : Successfully completed task 'org.labkey.lincs.psp.LincsPspTask'