Problems running strelka2
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Entering edit mode
7 months ago
arne.zibat • 0

Hi everybody,

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]

Version: 2.9.10

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!

variant calling ngs strelka • 202 views
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