search

broadinstitute / warp

WDL Analysis Research Pipelines
https://broadinstitute.github.io/warp
BSD 3-Clause "New" or "Revised" License
200 stars 93 forks source link

Keep running into this error when running IlluminaGenotypingArray.wdl (/usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)) #1328

Open seetarajpara opened 1 month ago

seetarajpara commented 1 month ago

Here's my command and the output:

(seeta_env) Seeta@MacBook-Pro-USC Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024 % java -jar /Users/Seeta/homebrew2/Cellar/cromwell/87/libexec/cromwell.jar run IlluminaGenotypingArray.wdl -i input.json
[2024-07-10 12:57:41,96] [info] Running with database db.url = jdbc:hsqldb:mem:9c161498-f5df-4ef3-8f76-62df58769482;shutdown=false;hsqldb.tx=mvcc
[2024-07-10 12:57:46,69] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2024-07-10 12:57:46,72] [info] [RenameWorkflowOptionsInMetadata] 100%
[2024-07-10 12:57:47,10] [info] Running with database db.url = jdbc:hsqldb:mem:15f756b7-e25e-424c-9d1b-d6778060726f;shutdown=false;hsqldb.tx=mvcc
[2024-07-10 12:57:47,89] [info] Slf4jLogger started
[2024-07-10 12:57:48,02] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-7f01eaf",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "failureShutdownDuration" : "5 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2024-07-10 12:57:48,11] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2024-07-10 12:57:48,11] [info] Metadata summary refreshing every 1 second.
[2024-07-10 12:57:48,11] [info] No metadata archiver defined in config
[2024-07-10 12:57:48,11] [info] No metadata deleter defined in config
[2024-07-10 12:57:48,11] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2024-07-10 12:57:48,15] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2024-07-10 12:57:48,38] [info] JobRestartCheckTokenDispenser - Distribution rate: 50 per 1 seconds.
[2024-07-10 12:57:48,40] [info] JobExecutionTokenDispenser - Distribution rate: 20 per 10 seconds.
[2024-07-10 12:57:48,49] [info] SingleWorkflowRunnerActor: Version 87
[2024-07-10 12:57:48,50] [info] SingleWorkflowRunnerActor: Submitting workflow
[2024-07-10 12:57:48,54] [info] Unspecified type (Unspecified version) workflow 5e861e43-3b62-4685-a9f5-6f21c9c1ee5d submitted
[2024-07-10 12:57:48,55] [info] SingleWorkflowRunnerActor: Workflow submitted 5e861e43-3b62-4685-a9f5-6f21c9c1ee5d
[2024-07-10 12:57:48,56] [info] 1 new workflows fetched by cromid-7f01eaf: 5e861e43-3b62-4685-a9f5-6f21c9c1ee5d
[2024-07-10 12:57:48,56] [info] WorkflowManagerActor: Starting workflow 5e861e43-3b62-4685-a9f5-6f21c9c1ee5d
[2024-07-10 12:57:48,57] [info] WorkflowManagerActor: Successfully started WorkflowActor-5e861e43-3b62-4685-a9f5-6f21c9c1ee5d
[2024-07-10 12:57:48,57] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2024-07-10 12:57:48,59] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2024-07-10 12:57:48,65] [info] MaterializeWorkflowDescriptorActor [5e861e43]: Parsing workflow as WDL 1.0
[2024-07-10 12:57:50,05] [info] MaterializeWorkflowDescriptorActor [5e861e43]: Call-to-Backend assignments: IlluminaGenotypingArray.VerifyIDIntensity -> Local, IlluminaGenotypingArray.CollectArraysVariantCallingMetrics -> Local, IlluminaGenotypingArray.MergePedIntoVcf -> Local, IlluminaGenotypingArray.SelectVariantsForGenotypeConcordance -> Local, IlluminaGenotypingArray.GreenIdatMd5Sum -> Local, IlluminaGenotypingArray.CheckFingerprintTask -> Local, IlluminaGenotypingArray.GenotypeConcordance -> Local, IlluminaGenotypingArray.zCall -> Local, IlluminaGenotypingArray.CreateVerifyIDIntensityContaminationMetricsFile -> Local, IlluminaGenotypingArray.AutoCall -> Local, IlluminaGenotypingArray.SubsetArrayVCF -> Local, IlluminaGenotypingArray.RedIdatMd5Sum -> Local, IlluminaGenotypingArray.SubsettedVariantCallingMetrics -> Local, IlluminaGenotypingArray.BpmToNormalizationManifestCsv -> Local, IlluminaGenotypingArray.BafRegress -> Local, IlluminaGenotypingArray.GenderAutocall -> Local, IlluminaGenotypingArray.VcfToAdpc -> Local, IlluminaGenotypingArray.VcfToIntervalList -> Local, IlluminaGenotypingArray.SelectFingerprintVariants -> Local, IlluminaGenotypingArray.VcfMd5Sum -> Local, IlluminaGenotypingArray.GtcToVcf -> Local
[2024-07-10 12:57:50,18] [warn] Local [5e861e43]: Key/s [memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2024-07-10 12:57:52,34] [info] WorkflowExecutionActor-5e861e43-3b62-4685-a9f5-6f21c9c1ee5d [5e861e43]: Starting IlluminaGenotypingArray.GreenIdatMd5Sum, IlluminaGenotypingArray.AutoCall, IlluminaGenotypingArray.RedIdatMd5Sum
[2024-07-10 12:57:53,40] [info] Not triggering log of restart checking token queue status. Effective log interval = None
[2024-07-10 12:57:53,42] [info] Not triggering log of execution token queue status. Effective log interval = None
[2024-07-10 12:57:58,44] [info] Assigned new job execution tokens to the following groups: 5e861e43: 3
[2024-07-10 12:57:59,96] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.GreenIdatMd5Sum:NA:1]: set -e
set -o pipefail
md5sum /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum/inputs/-431968697/208197710050_R01C01_Grn.idat | awk '{ print $1 }' > 208197710050_R01C01_Grn.idat.md5sum
[2024-07-10 12:57:59,97] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.RedIdatMd5Sum:NA:1]: set -e
set -o pipefail
md5sum /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum/inputs/-431968697/208197710050_R01C01_Red.idat | awk '{ print $1 }' > 208197710050_R01C01_Red.idat.md5sum
[2024-07-10 12:57:59,98] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.AutoCall:NA:1]: set -e
rm -rf 208459880001_R01C01
mkdir 208459880001_R01C01
mv /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/inputs/-431968697/208197710050_R01C01_Grn.idat 208459880001_R01C01
mv /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/inputs/-431968697/208197710050_R01C01_Red.idat 208459880001_R01C01
# Make an empty gtc file so that if autocall fails PAPI won't fail on this task (for inability to find the output) and the WF can move on.
touch 208459880001_R01C01.gtc

/usr/gitc/iaap/iaap-cli/iaap-cli \
  gencall \
  /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/inputs/-371031717/GDAConfluence_20032938X375356_A1.bpm \
  /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/inputs/-1361839242/GDA-Confluence_Salhia_Females_240509.egt \
  . \
  -f 208459880001_R01C01 \
  --gender-estimate-call-rate-threshold 0.9 \
  --output-gtc
[2024-07-10 12:58:00,00] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.RedIdatMd5Sum:NA:1]: executing: # make sure there is no preexisting Docker CID file
rm -f /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum/execution/docker_cid
# run as in the original configuration without --rm flag (will remove later)
docker run \
  --cidfile /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum/execution/docker_cid \
  -i \
   \
  --entrypoint /bin/bash \
  -v /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum:/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum:delegated \
  gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum/execution/script

# get the return code (working even if the container was detached)
rc=$(docker wait cat /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum/execution/docker_cid)

# remove the container after waiting
docker rm cat /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-RedIdatMd5Sum/execution/docker_cid

# return exit code
exit $rc
[2024-07-10 12:58:00,00] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.GreenIdatMd5Sum:NA:1]: executing: # make sure there is no preexisting Docker CID file
rm -f /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum/execution/docker_cid
# run as in the original configuration without --rm flag (will remove later)
docker run \
  --cidfile /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum/execution/docker_cid \
  -i \
   \
  --entrypoint /bin/bash \
  -v /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum:/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum:delegated \
  gcr.io/gcp-runtimes/ubuntu_16_0_4@sha256:025124e2f1cf4d29149958f17270596bffe13fc6acca6252977c572dd5ba01bf /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum/execution/script

# get the return code (working even if the container was detached)
rc=$(docker wait cat /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum/execution/docker_cid)

# remove the container after waiting
docker rm cat /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-GreenIdatMd5Sum/execution/docker_cid

# return exit code
exit $rc
[2024-07-10 12:58:00,00] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.AutoCall:NA:1]: executing: # make sure there is no preexisting Docker CID file
rm -f /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/execution/docker_cid
# run as in the original configuration without --rm flag (will remove later)
docker run \
  --cidfile /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/execution/docker_cid \
  -i \
   \
  --entrypoint /bin/bash \
  -v /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall:/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall:delegated \
  us.gcr.io/broad-gotc-prod/illumina-iaap-autocall@sha256:99fc49aab9f68b5ed2397d30e0321c872dbca6cde179d6d19a451dedcf1ee290 /cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/execution/script

# get the return code (working even if the container was detached)
rc=$(docker wait cat /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/execution/docker_cid)

# remove the container after waiting
docker rm cat /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/execution/docker_cid

# return exit code
exit $rc
[2024-07-10 12:58:03,20] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.GreenIdatMd5Sum:NA:1]: job id: 2940
[2024-07-10 12:58:03,20] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.RedIdatMd5Sum:NA:1]: job id: 2941
[2024-07-10 12:58:03,21] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.AutoCall:NA:1]: job id: 2942
[2024-07-10 12:58:03,21] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.RedIdatMd5Sum:NA:1]: Status change from - to Done
[2024-07-10 12:58:03,21] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.AutoCall:NA:1]: Status change from - to WaitingForReturnCode
[2024-07-10 12:58:03,21] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.GreenIdatMd5Sum:NA:1]: Status change from - to Done
[2024-07-10 12:58:05,64] [info] BackgroundConfigAsyncJobExecutionActor [5e861e43IlluminaGenotypingArray.AutoCall:NA:1]: Status change from WaitingForReturnCode to Done
[2024-07-10 12:58:06,69] [info] WorkflowManagerActor: Workflow 5e861e43-3b62-4685-a9f5-6f21c9c1ee5d failed (during ExecutingWorkflowState): Job IlluminaGenotypingArray.AutoCall:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details.
Check the content of stderr for potential additional information: /Users/Seeta/Dropbox/Batch3_Salhia_GDA-Confluence_plates_01-02-June_2024/cromwell-executions/IlluminaGenotypingArray/5e861e43-3b62-4685-a9f5-6f21c9c1ee5d/call-AutoCall/execution/stderr.
 [First 3000 bytes]:/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)
/usr/gitc/iaap/iaap-cli/iaap-cli: /usr/lib/libstdc++.so.6: no version information available (required by /usr/gitc/iaap/iaap-cli/iaap-cli)

[2024-07-10 12:58:08,30] [info] WorkflowManagerActor: Workflow actor for 5e861e43-3b62-4685-a9f5-6f21c9c1ee5d completed with status 'Failed'. The workflow will be removed from the workflow store.
[2024-07-10 12:58:13,66] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2024-07-10 12:58:18,14] [info] Workflow polling stopped
[2024-07-10 12:58:18,16] [info] 0 workflows released by cromid-7f01eaf
[2024-07-10 12:58:18,17] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2024-07-10 12:58:18,17] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2024-07-10 12:58:18,17] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2024-07-10 12:58:18,18] [info] Aborting all running workflows.
[2024-07-10 12:58:18,19] [info] JobExecutionTokenDispenser stopped
[2024-07-10 12:58:18,19] [info] WorkflowStoreActor stopped
[2024-07-10 12:58:18,19] [info] WorkflowLogCopyRouter stopped
[2024-07-10 12:58:18,19] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2024-07-10 12:58:18,20] [info] WorkflowManagerActor: All workflows finished
[2024-07-10 12:58:18,20] [info] WorkflowManagerActor stopped
[2024-07-10 12:58:18,33] [info] Connection pools shut down
[2024-07-10 12:58:18,33] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2024-07-10 12:58:18,33] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2024-07-10 12:58:18,33] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2024-07-10 12:58:18,33] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2024-07-10 12:58:18,33] [info] SubWorkflowStoreActor stopped
[2024-07-10 12:58:18,33] [info] JobStoreActor stopped
[2024-07-10 12:58:18,33] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2024-07-10 12:58:18,34] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2024-07-10 12:58:18,34] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2024-07-10 12:58:18,34] [info] CallCacheWriteActor stopped
[2024-07-10 12:58:18,34] [info] IoProxy stopped
[2024-07-10 12:58:18,35] [info] DockerHashActor stopped
[2024-07-10 12:58:18,36] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2024-07-10 12:58:18,36] [info] KvWriteActor Shutting down: 0 queued messages to process
[2024-07-10 12:58:18,38] [info] ServiceRegistryActor stopped
[2024-07-10 12:58:18,39] [info] Shutting down connection pool: curAllocated=2 idleQueues.size=2 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2024-07-10 12:58:18,39] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2024-07-10 12:58:18,40] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2024-07-10 12:58:18,41] [info] Shutting down connection pool: curAllocated=0 idleQueues.size=0 waitQueue.size=0 maxWaitQueueLimit=256 closed=false
[2024-07-10 12:58:18,42] [info] Database closed
[2024-07-10 12:58:18,42] [info] Stream materializer shut down
[2024-07-10 12:58:18,42] [info] WDL HTTP import resolver closed
Workflow 5e861e43-3b62-4685-a9f5-6f21c9c1ee5d transitioned to state Failed

When I ran it with the runtime attribute continueOnReturnCode=true, I wouldn't get the error but then there were also no outputs. I'm hoping someone can help me, I've tried installing ncurses with conda and that didn't work. Any advice is much appreciated. Thanks!