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.
[warn] Localization via hard link has failed Invalid cross-device link
Ηello, I'm trying to run GATK best practices and I've run in to a wall when the
SamToFastqAndBwaMem is executed.
First things first: in the
.inputs.json I specified my
absolute path and I get this warning:
[warn] Localization via hard link has failed:
More specifically the
SamToFastqAndBwaMem task, always exits with 1, meaning that I get this
WorkflowManagerActor Workflow 8992b121-6c74-4ab8-aba3-07ecd748ef04 failed (during ExecutingWorkflowState): Job PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem:0:1 exited with return code 1 which has not been declared as a valid return code. I suspect this
error comes from the
# else ref_alt is empty or could not be found else exit 1;
Is this true? Has anyone else encountered this error?
My version of
cromwel is 0.25