HI there,

I am using GATK 4.5.1 and trying to run the preprocessing pipeline from the best practices. Docker is not an option for our HPC so I used singularity to download an image file and use GATK. The major changes I  made were redirecting the docker calls for gatk_path and gotc_path to a singularity exec command to use the gatk packages and a conda environment (bwa 0.7.17, picard  2.22.0, samtools 1.9) for the packages in the gotc environment. The script is called with the following command:

java -jar cromwell-49.jar run preprocessing_gatk.wdl -i preprocessing_gatk.json

I make it through the script up until the MergeBamAlignment step, where the job fails because a file cannot be found:

WorkflowManagerActor Workflow 3e51bdc3-8424-439a-91cb-240c1f458ace failed (during ExecutingWorkflowState): java.io.FileNotFound

Exception: Could not process output, file not found

I have verified that the file exists in the location the script expects it to, and used the ValidateSamFile tool to verify there are reads in there. Could there be another reason this script is failing?

I was hoping to be able to alter the other wdl scripts in a similar way (singularity and conda environments) and follow the best practices workflows on our local HPC.

Any help you can offer would be appreciated. 

Thank you, 

Shannon