If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.
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)