Hello,

I am running the method configuration "ebert-pipeline2" from my workspace "ebert-pipeline-test". When I begin running the pipeline on a sample, Firecloud can copy the files correctly and begin the first of five tasks, but terminates such that the only message in the stderr is "[main] unrecognized command '/tmp/ggp-464013851'", where the digits change with each run. It appears this corresponds to this line in the exec file:

!/bin/bash

tmpDir=$(mktemp -d /cromwell_root/tmp.XXXXXX)
chmod 777 $tmpDir
export _JAVA_OPTIONS=-Djava.io.tmpdir=$tmpDir
export TMPDIR=$tmpDir

where the "tmp.XXXXXX" appears to be the hash seen earlier. However, this is a set of executions that are common across Firecloud methods that work such that there must be something specifically wrong with my method configuration or FireCloud, but the error message is not informative in telling me what that issue is. Any insight into what this issue may be? Thank you.

Best,
Matt Leventhal