Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
Update: July 26, 2019
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
This section of the forum is now closed; we are working on a new support model for WDL that we will share here shortly. For Cromwell-specific issues, see the Cromwell docs and post questions on Github.
call caching error with softlink output files
Redmar_van_den_Berg
Member ✭✭
When call-caching is enabled for a workflow that has soft-linked files as output for some of the tasks, cromwell will not produce any output.
task softlink {
command {
date >> outfile.txt
ln -s outfile.txt datum
}
output {
File datum = "datum"
}
}
workflow wf {
call softlink
}
As far as I can tell, it attempts to link the soft-linked output file into the root directory where cromwell is run, which fails. However, it will then still report the final outputs, even though the file is missing.
[email protected]~/devel/wdl$ cromwell run softlink.wdl [2017-01-23 07:52:51,20] [warn] Localization via hard link has failed: /home/redmar/devel/wdl/cromwell-executions/wf/dbfff823-ce16-4fa8-909f-6f8ee7c763fa/call-softlink/execution/datum -> /home/redmar/devel/wdl/outfile.txt [2017-01-23 07:52:51,21] [warn] Localization via copy has failed: /home/redmar/devel/wdl/outfile.txt [INFO] [01/23/2017 07:52:51.289] [cromwell-system-akka.dispatchers.engine-dispatcher-33] [akka://cromwell-system/user/SingleWorkflowRunnerActor/WorkflowManagerActor/WorkflowActor-dbfff823-ce16-4fa8-909f-6f8ee7c763fa/WorkflowExecutionActor-dbfff823-ce16-4fa8-909f-6f8ee7c763fa] WorkflowExecutionActor-dbfff823-ce16-4fa8-909f-6f8ee7c763fa [UUID(dbfff823)]: Workflow wf complete. Final Outputs: { "wf_softlink_datum": "file:///home/redmar/devel/wdl/cromwell-executions/wf/dbfff823-ce16-4fa8-909f-6f8ee7c763fa/call-softlink/execution/datum" }
[email protected]:~/devel/wdl$ cat /home/redmar/devel/wdl/cromwell-executions/wf/dbfff823-ce16-4fa8-909f-6f8ee7c763fa/call-softlink/execution/datum cat: /home/redmar/devel/wdl/cromwell-executions/wf/dbfff823-ce16-4fa8-909f-6f8ee7c763fa/call-softlink/execution/datum: No such file or directory
Tagged:
Answers
I will forward this to our dev team, as this sounds like a bug.
Hello,
May I ask what version of Cromwell you are using? I believe this issue has been fixed recently, and when I test using Cromwell develop, I can't reproduce this issue case anymore.
I'm using the latest version of cromwell, version 24