Test-drive the GATK tools and Best Practices pipelines on Terra
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Problem running GATK workflow (locally) from your tutorial
I am familiar with GATK best practices, but only now have I started actually running your codes, alongside learning command lines in Unix/Linux. Hence, I am sorry for the lay question: how can I execute your tutorial on running GATK workflows from the git repository?
I have installed and run the docker, which seems to be working fine (by following your guides on setting it up). Now, when I try to execute it by
java -jar cromwell-33.1.jar run ./seq-format-validation/validate-bam.wdl --inputs ./seq-format-validation/validate-bam.inputs.json
I get some warning messages and one error message, as follows:
_[**warn**] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData [**warn**] Couldn't find a suitable DSN, defaulting to a Noop one. [**warn**] Local [ae4b78d6]: Key/s [memory, cpu, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions. [**error**] WorkflowManagerActor Workflow ae4b78d6-cf4c-4896-90aa-a88c1b2d2c87 failed (during ExecutingWorkflowState): cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1$$anon$1: Call input and runtime attributes evaluation failed for ValidateBAM: java.nio.file.NoSuchFileException: /Desktop/gatk_example_github/inputs/wgs_bam_NA12878_24RG_hg38_NA12878_24RG_small.hg38.bam at cromwell.engine.workflow.lifecycle.execution.job.preparation.JobPreparationActor$$anonfun$1.applyOrElse(JobPreparationActor.scala:65)_.
I tried troubleshooting it by reading some of the posts on the forum (i.e. Q1 and Q2), but I am still struggling to identify and fix the issue.
My strongest guess is that I have to set the the arguments for ValidateBamsWf.ValidateBAM.gatk_path_override and ValidateBamsWf.gatk_docker_override, but what should I add there?
Any help is greatly appreciated.
PS: (1) I have mounted the volume with the folders, sub-folders and files onto my docker broadinstitute/gatk:184.108.40.206, onto the preset folder my_data;
(2) I have tried to run the workflow from the docker as well (/gatk)