19 Apr 2021 05:47:18,575 INFO : Re-running LINCS pipeline for: LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 05:47:18,576 INFO : =======================================
19 Apr 2021 05:58:09,819 INFO : Starting to run task 'org.labkey.lincs.cromwell.CromwellGctTask' at location 'webserver-high-priority'
19 Apr 2021 05:58:09,819 INFO : Starting task to create L2 GCT for LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.sky.zip
19 Apr 2021 05:58:09,829 INFO : Submitting job to http://m002.grid.gs.washington.edu:8000/api/workflows/v1
19 Apr 2021 05:58:09,865 INFO : Checking status of job at http://m002.grid.gs.washington.edu:8000/api/workflows/v1/10f1810d-1a97-4c88-8b61-c990bd0bba5d/status
19 Apr 2021 05:58:29,892 INFO : Cromwell job status: Submitted
19 Apr 2021 05:58:49,914 INFO : Cromwell job status: Running
19 Apr 2021 05:59:29,956 INFO : Cromwell job status: Succeeded
19 Apr 2021 05:59:29,957 INFO : Cromwell job completed successfully
19 Apr 2021 05:59:29,958 INFO : Successfully completed task 'org.labkey.lincs.cromwell.CromwellGctTask'
19 Apr 2021 06:47:37,557 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 06:47:37,559 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 06:47:37,560 INFO : Resubmitting job for runId: 30548, name: LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 06:47:37,560 INFO : Old job details:
19 Apr 2021 06:47:37,560 INFO : Id: 104
19 Apr 2021 06:47:37,560 INFO : Pipeline job Id: 68229
19 Apr 2021 06:47:37,560 INFO : Run Id: 30548
19 Apr 2021 06:47:37,560 INFO : PSP Job Id: 5cfd5773344c151e38c98da4
19 Apr 2021 06:47:37,560 INFO : PSP Job name: LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 06:47:37,560 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 06:47:37,560 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T19:01:07.057Z","name":"LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35","id":"5cfd5773344c151e38c98da4","last_modified":"2019-06-09T19:01:34.196Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=30548&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_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL3.gct"}}}
19 Apr 2021 06:47:37,560 INFO : Resubmitting...
19 Apr 2021 06:47:37,562 INFO : Looking for existing job with name LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 06:47:37,799 INFO : Failed to complete task 'org.labkey.lincs.psp.LincsPspTask'
19 Apr 2021 06:47:37,802 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_Plate62_annotated_minimized_2018-04-20_14-38-35. URL: https://api.clue.io/api/psp?filter=%7B%22where%22%3A%7B%22name%22%3A%22LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35%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_Plate62_annotated_minimized_2018-04-20_14-38-35%22%7D%7D
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:64)
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_Plate62_annotated_minimized_2018-04-20_14-38-35%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 08:03:28,169 INFO : Retrying job.
19 Apr 2021 08:03:28,170 DEBUG: Database indicates active task ID is org.labkey.lincs.psp.LincsPspTask
19 Apr 2021 08:03:28,170 DEBUG: Retry details: Old Job ID: 1bf6e420-833b-1039-a447-fea6ddf5a122
19 Apr 2021 08:03:28,194 INFO : Starting to run task 'org.labkey.lincs.psp.LincsPspTask' at location 'webserver-high-priority'
19 Apr 2021 08:03:28,194 INFO : Running LINCS PSP pipeline for LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 08:03:28,195 INFO : Resubmitting job for runId: 30548, name: LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 08:03:28,195 INFO : Old job details:
19 Apr 2021 08:03:28,195 INFO : Id: 104
19 Apr 2021 08:03:28,195 INFO : Pipeline job Id: 68229
19 Apr 2021 08:03:28,195 INFO : Run Id: 30548
19 Apr 2021 08:03:28,195 INFO : PSP Job Id: 5cfd5773344c151e38c98da4
19 Apr 2021 08:03:28,195 INFO : PSP Job name: LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 08:03:28,195 INFO : PSP Job status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 08:03:28,195 INFO : JSON: {"level 4":{"s3":{"url":"s3://proteomics.clue.io/psp/level4/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL4.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL4.gct"}},"assay":"GCP","created":"2019-06-09T19:01:07.057Z","name":"LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35","id":"5cfd5773344c151e38c98da4","last_modified":"2019-06-09T19:01:34.196Z","config":{"s3":{"url":"s3://proteomics.clue.io/psp/config/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.cfg"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.cfg"}},"level 2":{"s3":{"url":"s3://proteomics.clue.io/psp/level2/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL2.gct"},"panorama":{"method":"GET","url":"https://panoramaweb.org/lincs/LINCS/GCP/runGCTReportApi.view?runId=30548&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_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL3.gct"},"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL3.gct"}}}
19 Apr 2021 08:03:28,195 INFO : Resubmitting...
19 Apr 2021 08:03:28,197 INFO : Looking for existing job with name LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35
19 Apr 2021 08:03:28,731 INFO : Job with name LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35exists.
19 Apr 2021 08:03:28,731 INFO : Looking for existing job with name LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_2
19 Apr 2021 08:03:28,867 INFO : Job with name LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_2exists.
19 Apr 2021 08:03:28,867 INFO : Looking for existing job with name LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_3
19 Apr 2021 08:03:29,000 INFO : PSP job name: LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_3
19 Apr 2021 08:03:29,000 INFO : Sending JSON:
19 Apr 2021 08:03:29,000 INFO : {
"level 4": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL4.gct"
}},
"assay": "GCP",
"name": "LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_3",
"config": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.cfg"
}},
"level 2": {"panorama": {
"method": "GET",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.gct"
}},
"level 3": {"panorama": {
"method": "PUT",
"url": "https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL3.gct"
}}
}
19 Apr 2021 08:03:29,012 INFO : Sending POST request to https://api.clue.io/api/psp
19 Apr 2021 08:03:29,221 INFO : Response code - 200
19 Apr 2021 08:03:29,221 INFO : Response from server: {"name":"LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_3","assay":"GCP","status":"Waiting_To_Download","id":"607d9bc1e1c96f0017d8b78f","created":"2021-04-19T15:03:29.091Z","last_modified":"2021-04-19T15:03:29.091Z","level 2":{"panorama":{"method":"GET","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.gct"}},"level 3":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL3.gct"}},"level 4":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35_LVL4.gct"}},"config":{"panorama":{"method":"PUT","url":"https://panoramaweb.org/_webdav/LINCS/GCP/%40files/GCT/LINCS_GCP_Plate62_annotated_minimized_2018-04-20_14-38-35.cfg"}}}
19 Apr 2021 08:03:29,221 INFO : Sent POST request to https://api.clue.io/api/psp
19 Apr 2021 08:03:29,223 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:03:29,358 INFO : Status: Waiting_To_Download
19 Apr 2021 08:03:49,362 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:03:49,653 INFO : Status: created LVL2 GCT
19 Apr 2021 08:04:09,654 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:04:09,941 INFO : Status: created LVL2 GCT
19 Apr 2021 08:04:29,942 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:04:30,240 INFO : Status: created LVL2 GCT
19 Apr 2021 08:04:50,243 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:04:50,605 INFO : Status: created LVL2 GCT
19 Apr 2021 08:05:10,607 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:05:10,896 INFO : Status: created LVL2 GCT
19 Apr 2021 08:05:30,898 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:05:31,185 INFO : Status: created LVL2 GCT
19 Apr 2021 08:05:51,187 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:05:51,472 INFO : Status: created LVL2 GCT
19 Apr 2021 08:06:11,473 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:06:11,846 INFO : Status: created LVL2 GCT
19 Apr 2021 08:06:31,850 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:06:32,133 INFO : Status: created LVL2 GCT
19 Apr 2021 08:06:52,135 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:06:52,427 INFO : Status: created LVL2 GCT
19 Apr 2021 08:07:12,429 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:07:12,716 INFO : Status: created LVL2 GCT
19 Apr 2021 08:07:32,723 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:07:33,091 INFO : Status: created LVL 3 GCT
19 Apr 2021 08:07:53,094 INFO : Checking status of job 607d9bc1e1c96f0017d8b78f
19 Apr 2021 08:07:53,381 INFO : Status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 08:07:53,381 INFO : PSP job completed with status: POUR : succeeded in uploading all GCTs to Panorama
19 Apr 2021 08:07:53,381 INFO : Finished running LINCS PSP pipeline.
19 Apr 2021 08:07:53,382 INFO : Successfully completed task 'org.labkey.lincs.psp.LincsPspTask'