19 Apr 2021 05:49:14,283 INFO : Re-running LINCS pipeline for: LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 05:49:14,284 INFO : =======================================
19 Apr 2021 06:14:36,365 INFO : Starting to run task 'org.labkey.lincs.cromwell.CromwellGctTask' at location 'webserver-high-priority'
19 Apr 2021 06:14:36,366 INFO : Starting task to create L2 GCT for LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.sky.zip
19 Apr 2021 06:14:36,372 INFO : Submitting job to http://m002.grid.gs.washington.edu:8000/api/workflows/v1
19 Apr 2021 06:14:36,395 INFO : Checking status of job at http://m002.grid.gs.washington.edu:8000/api/workflows/v1/03430a75-fed9-4cea-9db4-c67fbc9caf35/status
19 Apr 2021 06:14:56,414 INFO : Cromwell job status: Running
19 Apr 2021 06:15:56,478 INFO : Cromwell job status: Succeeded
19 Apr 2021 06:15:56,480 INFO : Cromwell job completed successfully
19 Apr 2021 06:15:56,481 INFO : Successfully completed task 'org.labkey.lincs.cromwell.CromwellGctTask'
19 Apr 2021 06:47:41,022 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 06:47:41,024 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 06:47:41,024 INFO : Resubmitting job for runId: 16052, name: LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 06:47:41,024 INFO : Old job details:
19 Apr 2021 06:47:41,024 INFO : Id: 94
19 Apr 2021 06:47:41,024 INFO : Pipeline job Id: 68219
19 Apr 2021 06:47:41,024 INFO : Run Id: 16052
19 Apr 2021 06:47:41,024 INFO : PSP Job Id: 5cfd55d5344c151e38c98d9a
19 Apr 2021 06:47:41,024 INFO : PSP Job name: LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 06:47:41,024 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 06:47:41,025 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T18:54:13.331Z","name":"LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57","id":"5cfd55d5344c151e38c98d9a","last_modified":"2019-06-09T18:54:41.576Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=16052&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_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL3.gct"}}}
19 Apr 2021 06:47:41,025 INFO : Resubmitting...
19 Apr 2021 06:47:41,026 INFO : Looking for existing job with name LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 06:47:41,317 INFO : Job with name LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57exists.
19 Apr 2021 06:47:41,318 INFO : Looking for existing job with name LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_2
19 Apr 2021 06:47:41,392 INFO : Failed to complete task 'org.labkey.lincs.psp.LincsPspTask'
19 Apr 2021 06:47:41,396 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_Plate47_annotated_minimized_2017-04-18_16-55-57_2. URL: https://api.clue.io/api/psp?filter=%7B%22where%22%3A%7B%22name%22%3A%22LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_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_Plate47_annotated_minimized_2017-04-18_16-55-57_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_Plate47_annotated_minimized_2017-04-18_16-55-57_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 14:07:27,990 INFO : Retrying job.
19 Apr 2021 14:07:27,992 DEBUG: Database indicates active task ID is org.labkey.lincs.psp.LincsPspTask
19 Apr 2021 14:07:27,992 DEBUG: Retry details: Old Job ID: 1bf6ec73-833b-1039-a447-fea6ddf5a122
19 Apr 2021 14:07:28,015 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 14:07:28,016 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 14:07:28,016 INFO : Resubmitting job for runId: 16052, name: LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 14:07:28,016 INFO : Old job details:
19 Apr 2021 14:07:28,016 INFO : Id: 94
19 Apr 2021 14:07:28,016 INFO : Pipeline job Id: 68219
19 Apr 2021 14:07:28,017 INFO : Run Id: 16052
19 Apr 2021 14:07:28,017 INFO : PSP Job Id: 5cfd55d5344c151e38c98d9a
19 Apr 2021 14:07:28,017 INFO : PSP Job name: LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 14:07:28,017 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 14:07:28,017 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T18:54:13.331Z","name":"LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57","id":"5cfd55d5344c151e38c98d9a","last_modified":"2019-06-09T18:54:41.576Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=16052&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_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL3.gct"}}}
19 Apr 2021 14:07:28,017 INFO : Resubmitting...
19 Apr 2021 14:07:28,019 INFO : Looking for existing job with name LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57
19 Apr 2021 14:07:28,498 INFO : Job with name LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57exists.
19 Apr 2021 14:07:28,498 INFO : Looking for existing job with name LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_2
19 Apr 2021 14:07:28,633 INFO : PSP job name: LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_2
19 Apr 2021 14:07:28,634 INFO : Sending JSON:
19 Apr 2021 14:07:28,634 INFO : {
"level 4": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL4.gct"
}},
"assay": "GCP",
"name": "LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_2",
"config": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.cfg"
}},
"level 2": {"panorama": {
"method": "GET",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.gct"
}},
"level 3": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL3.gct"
}}
}
19 Apr 2021 14:07:28,643 INFO : Sending POST request to https://api.clue.io/api/psp
19 Apr 2021 14:07:28,945 INFO : Response code - 200
19 Apr 2021 14:07:28,945 INFO : Response from server: {"name":"LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_2","assay":"GCP","status":"Waiting_To_Download","id":"607df11077d01b0017d790ff","created":"2021-04-19T21:07:28.723Z","last_modified":"2021-04-19T21:07:28.724Z","level 2":{"panorama":{"method":"GET","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.gct"}},"level 3":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL3.gct"}},"level 4":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57_LVL4.gct"}},"config":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate47_annotated_minimized_2017-04-18_16-55-57.cfg"}}}
19 Apr 2021 14:07:28,946 INFO : Sent POST request to https://api.clue.io/api/psp
19 Apr 2021 14:07:28,948 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:07:29,083 INFO : Status: Waiting_To_Download
19 Apr 2021 14:07:49,085 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:07:49,374 INFO : Status: created LVL2 GCT
19 Apr 2021 14:08:09,377 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:08:09,667 INFO : Status: created LVL2 GCT
19 Apr 2021 14:08:29,669 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:08:29,956 INFO : Status: created LVL2 GCT
19 Apr 2021 14:08:49,959 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:08:50,332 INFO : Status: created LVL2 GCT
19 Apr 2021 14:09:10,334 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:09:10,623 INFO : Status: created LVL2 GCT
19 Apr 2021 14:09:30,625 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:09:30,915 INFO : Status: created LVL2 GCT
19 Apr 2021 14:09:50,918 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:09:51,210 INFO : Status: created LVL2 GCT
19 Apr 2021 14:10:11,212 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:10:11,588 INFO : Status: created LVL2 GCT
19 Apr 2021 14:10:31,589 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:10:31,884 INFO : Status: created LVL2 GCT
19 Apr 2021 14:10:51,886 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:10:52,177 INFO : Status: created LVL2 GCT
19 Apr 2021 14:11:12,179 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:11:12,467 INFO : Status: created LVL2 GCT
19 Apr 2021 14:11:32,470 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:11:32,833 INFO : Status: created LVL 4 GCT
19 Apr 2021 14:11:52,836 INFO : Checking status of job 607df11077d01b0017d790ff
19 Apr 2021 14:11:53,126 INFO : Status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 14:11:53,126 INFO : PSP job completed with status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 14:11:53,126 INFO : Finished running LINCS PSP pipeline.
19 Apr 2021 14:11:53,126 INFO : Successfully completed task 'org.labkey.lincs.psp.LincsPspTask'