I am trying to set up strelka2 (version 2.9.10) for comparison reasons. I followed instructions for installation and configuration - all works. Running the configureStrelkaSomaticWorkflow.py sets up the appropriate script and dirs without any problem. When running the command indicated by the configure command, there is always only the --help output shown with stdout. Seems that the run command is missing something. Reading the docs does not give any hint. Did anybody experienced the same issue?
python /home/TEST/STRELKA2/test_sample/strelkaSomaticWorkflow/runWorkflow.py -m local -j 1
As described, the only output I get is:
Usage: runWorkflow.py [options]
Options: --version show program's version number and exit -h, --help show this help message and exit -m MODE, --mode=MODE select run mode (local|sge) -q QUEUE, --queue=QUEUE specify scheduler queue name -j JOBS, --jobs=JOBS number of jobs, must be an integer or 'unlimited' (default: Estimate total cores on this node for local mode, 128 for sge mode) -g MEMGB, --memGb=MEMGB gigabytes of memory available to run workflow -- only meaningful in local mode, must be an integer (default: Estimate the total memory for this node for local mode, 'unlimited' for sge mode) -d, --dryRun dryRun workflow code without actually running command- tasks --quiet Don't write any log output to stderr (but still write to workspace/pyflow.data/logs/pyflow_log.txt)
development debug options: --rescore Reset task list to re-run hypothesis generation and scoring without resetting graph generation.
extended portability options (should not be needed by most users): --maxTaskRuntime=hh:mm:ss Specify scheduler max runtime per task, argument is provided to the 'h_rt' resource limit if using SGE (no default)
Note this script can be re-run to continue the workflow run in case of interruption. Also note that dryRun option has limited utility when task definition depends on upstream task results -- in this case the dry run will not cover the full 'live' run task set.
Error logs were empty, because analysis hasn't been started anyway.
Any help will be welcomed!