19 Apr 2021 05:48:50,711 INFO : Re-running LINCS pipeline for: LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 05:48:50,713 INFO : =======================================
19 Apr 2021 06:11:56,079 INFO : Starting to run task 'org.labkey.lincs.cromwell.CromwellGctTask' at location 'webserver-high-priority'
19 Apr 2021 06:11:56,081 INFO : Starting task to create L2 GCT for LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.sky.zip
19 Apr 2021 06:11:56,087 INFO : Submitting job to http://m002.grid.gs.washington.edu:8000/api/workflows/v1
19 Apr 2021 06:11:56,113 INFO : Checking status of job at http://m002.grid.gs.washington.edu:8000/api/workflows/v1/e1306112-5b09-4f67-ad31-029ca1b7c2b0/status
19 Apr 2021 06:12:16,131 INFO : Cromwell job status: Running
19 Apr 2021 06:13:16,178 INFO : Cromwell job status: Succeeded
19 Apr 2021 06:13:16,179 INFO : Cromwell job completed successfully
19 Apr 2021 06:13:16,180 INFO : Successfully completed task 'org.labkey.lincs.cromwell.CromwellGctTask'
19 Apr 2021 06:47:40,224 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 06:47:40,226 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 06:47:40,226 INFO : Resubmitting job for runId: 20406, name: LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 06:47:40,226 INFO : Old job details:
19 Apr 2021 06:47:40,226 INFO : Id: 97
19 Apr 2021 06:47:40,226 INFO : Pipeline job Id: 68222
19 Apr 2021 06:47:40,226 INFO : Run Id: 20406
19 Apr 2021 06:47:40,227 INFO : PSP Job Id: 5cfd5651344c151e38c98d9d
19 Apr 2021 06:47:40,227 INFO : PSP Job name: LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 06:47:40,227 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 06:47:40,227 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T18:56:17.456Z","name":"LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44","id":"5cfd5651344c151e38c98d9d","last_modified":"2019-06-09T18:56:44.768Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=20406&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_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL3.gct"}}}
19 Apr 2021 06:47:40,227 INFO : Resubmitting...
19 Apr 2021 06:47:40,229 INFO : Looking for existing job with name LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 06:47:40,512 INFO : Job with name LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44exists.
19 Apr 2021 06:47:40,512 INFO : Looking for existing job with name LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2
19 Apr 2021 06:47:40,585 INFO : Failed to complete task 'org.labkey.lincs.psp.LincsPspTask'
19 Apr 2021 06:47:40,590 ERROR: Error submitting PSP job
org.labkey.api.pipeline.PipelineJobException: Error submitting PSP job
at org.labkey.lincs.psp.LincsPspTask.postToPsp(LincsPspTask.java:96)
at org.labkey.lincs.psp.LincsPspTask.run(LincsPspTask.java:36)
at org.labkey.api.pipeline.PipelineJob.runActiveTask(PipelineJob.java:818)
at org.labkey.api.pipeline.PipelineJob.run(PipelineJob.java:1055)
at org.labkey.pipeline.mule.PipelineJobRunner.run(PipelineJobRunner.java:40)
at jdk.internal.reflect.GeneratedMethodAccessor1683.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invokeMethod(DynamicEntryPoint.java:312)
at org.mule.impl.model.resolvers.DynamicEntryPoint.invoke(DynamicEntryPoint.java:259)
at org.mule.impl.DefaultLifecycleAdapter.intercept(DefaultLifecycleAdapter.java:193)
at org.mule.impl.InterceptorsInvoker.execute(InterceptorsInvoker.java:47)
at org.mule.impl.model.DefaultMuleProxy.run(DefaultMuleProxy.java:470)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$CallerRunsPolicy.rejectedExecution(ThreadPoolExecutor.java:1486)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.reject(ThreadPoolExecutor.java:391)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor.execute(ThreadPoolExecutor.java:865)
at org.mule.impl.work.ScheduleWorkExecutor.doExecute(ScheduleWorkExecutor.java:39)
at org.mule.impl.work.MuleWorkManager.executeWork(MuleWorkManager.java:277)
at org.mule.impl.work.MuleWorkManager.scheduleWork(MuleWorkManager.java:244)
at org.mule.impl.model.seda.SedaComponent.run(SedaComponent.java:483)
at org.mule.impl.work.WorkerContext.run(WorkerContext.java:310)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:650)
at edu.emory.mathcs.backport.java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:675)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: org.labkey.lincs.psp.LincsPspException: Error looking for job with name LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2. URL: https://api.clue.io/api/psp?filter=%7B%22where%22%3A%7B%22name%22%3A%22LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2%22%7D%7D
at org.labkey.lincs.psp.LincsPspUtil.jobExists(LincsPspUtil.java:251)
at org.labkey.lincs.psp.LincsPspUtil.getJobName(LincsPspUtil.java:201)
at org.labkey.lincs.psp.LincsPspTask.postToPsp(LincsPspTask.java:89)
... 24 more
Caused by: java.io.IOException: Server returned HTTP response code: 502 for URL: https://api.clue.io/api/psp?filter=%7B%22where%22%3A%7B%22name%22%3A%22LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2%22%7D%7D
at java.base/jdk.internal.reflect.GeneratedConstructorAccessor1563.newInstance(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:500)
at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:481)
at java.base/sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1982)
at java.base/sun.net.www.protocol.http.HttpURLConnection$10.run(HttpURLConnection.java:1977)
at java.base/java.security.AccessController.doPrivileged(AccessController.java:554)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getChainedException(HttpURLConnection.java:1976)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1544)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1528)
at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getInputStream(HttpsURLConnectionImpl.java:224)
at org.labkey.lincs.psp.LincsPspUtil.jobExists(LincsPspUtil.java:229)
... 26 more
Caused by: java.io.IOException: Server returned HTTP response code: 502 for URL: https://api.clue.io/api/psp?filter=%7B%22where%22%3A%7B%22name%22%3A%22LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2%22%7D%7D
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1932)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1528)
at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:527)
at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:308)
at org.labkey.lincs.psp.LincsPspUtil.jobExists(LincsPspUtil.java:227)
... 26 more
19 Apr 2021 13:44:31,976 INFO : Retrying job.
19 Apr 2021 13:44:31,977 DEBUG: Database indicates active task ID is org.labkey.lincs.psp.LincsPspTask
19 Apr 2021 13:44:31,977 DEBUG: Retry details: Old Job ID: 1bf6eafd-833b-1039-a447-fea6ddf5a122
19 Apr 2021 13:44:32,003 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 13:44:32,003 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 13:44:32,003 INFO : Resubmitting job for runId: 20406, name: LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 13:44:32,003 INFO : Old job details:
19 Apr 2021 13:44:32,004 INFO : Id: 97
19 Apr 2021 13:44:32,004 INFO : Pipeline job Id: 68222
19 Apr 2021 13:44:32,004 INFO : Run Id: 20406
19 Apr 2021 13:44:32,004 INFO : PSP Job Id: 5cfd5651344c151e38c98d9d
19 Apr 2021 13:44:32,004 INFO : PSP Job name: LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 13:44:32,004 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 13:44:32,004 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T18:56:17.456Z","name":"LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44","id":"5cfd5651344c151e38c98d9d","last_modified":"2019-06-09T18:56:44.768Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=20406&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_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL3.gct"}}}
19 Apr 2021 13:44:32,004 INFO : Resubmitting...
19 Apr 2021 13:44:32,007 INFO : Looking for existing job with name LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44
19 Apr 2021 13:44:32,462 INFO : Job with name LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44exists.
19 Apr 2021 13:44:32,463 INFO : Looking for existing job with name LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2
19 Apr 2021 13:44:32,598 INFO : PSP job name: LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2
19 Apr 2021 13:44:32,599 INFO : Sending JSON:
19 Apr 2021 13:44:32,599 INFO : {
"level 4": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL4.gct"
}},
"assay": "GCP",
"name": "LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2",
"config": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.cfg"
}},
"level 2": {"panorama": {
"method": "GET",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.gct"
}},
"level 3": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL3.gct"
}}
}
19 Apr 2021 13:44:32,614 INFO : Sending POST request to https://api.clue.io/api/psp
19 Apr 2021 13:44:32,813 INFO : Response code - 200
19 Apr 2021 13:44:32,813 INFO : Response from server: {"name":"LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_2","assay":"GCP","status":"Waiting_To_Download","id":"607debb077d01b0017d790f8","created":"2021-04-19T20:44:32.693Z","last_modified":"2021-04-19T20:44:32.693Z","level 2":{"panorama":{"method":"GET","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.gct"}},"level 3":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL3.gct"}},"level 4":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44_LVL4.gct"}},"config":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate52_annotated_minimized_2017-08-16_14-28-44.cfg"}}}
19 Apr 2021 13:44:32,814 INFO : Sent POST request to https://api.clue.io/api/psp
19 Apr 2021 13:44:32,816 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:44:32,952 INFO : Status: Waiting_To_Download
19 Apr 2021 13:44:52,960 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:44:53,272 INFO : Status: created LVL2 GCT
19 Apr 2021 13:45:13,275 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:45:13,562 INFO : Status: created LVL2 GCT
19 Apr 2021 13:45:33,563 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:45:33,847 INFO : Status: created LVL2 GCT
19 Apr 2021 13:45:53,848 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:45:54,218 INFO : Status: created LVL2 GCT
19 Apr 2021 13:46:14,223 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:46:14,526 INFO : Status: created LVL2 GCT
19 Apr 2021 13:46:34,529 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:46:34,816 INFO : Status: created LVL2 GCT
19 Apr 2021 13:46:54,818 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:46:55,109 INFO : Status: created LVL2 GCT
19 Apr 2021 13:47:15,111 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:47:15,502 INFO : Status: created LVL2 GCT
19 Apr 2021 13:47:35,505 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:47:35,793 INFO : Status: created LVL2 GCT
19 Apr 2021 13:47:55,795 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:47:56,083 INFO : Status: created LVL2 GCT
19 Apr 2021 13:48:16,085 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:48:16,373 INFO : Status: created LVL2 GCT
19 Apr 2021 13:48:36,375 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:48:36,755 INFO : Status: created LVL 3 GCT
19 Apr 2021 13:48:56,757 INFO : Checking status of job 607debb077d01b0017d790f8
19 Apr 2021 13:48:57,054 INFO : Status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 13:48:57,054 INFO : PSP job completed with status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 13:48:57,055 INFO : Finished running LINCS PSP pipeline.
19 Apr 2021 13:48:57,055 INFO : Successfully completed task 'org.labkey.lincs.psp.LincsPspTask'