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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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DAG printing breaks for ChIP-seq with --cutntag --useSpikeInForNorm #890

Closed katsikora closed 1 year ago

katsikora commented 1 year ago

Building DAG of jobs... Error: : syntax error in line 2 near 'Spikein' Traceback (most recent call last): File "/package/mamba/envs/snakePipes-2.7.2/bin/ChIP-seq", line 193, in main() File "/package/mamba/envs/snakePipes-2.7.2/bin/ChIP-seq", line 189, in main cf.print_DAG(args,snakemake_cmd, file,defaults) File "/package/mamba/envs/snakePipes-2.7.2/lib/python3.11/site-packages/snakePipes/common_functions.py", line 664, in print_DAG subprocess.check_call("dot -Tpdf -o{}/{}_pipeline.pdf".format(args.outdir, workflowName), stdin=DAGproc.stdout, shell=True) File "/package/mamba/envs/snakePipes-2.7.2/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'dot -Tpdf -o/data/manke/processing/sikora/snakepipes_cutntag/analysis/ChIP-seq_pipeline.pdf' returned non-zero exit status 1.

katsikora commented 1 year ago

importing logging to solve this doubles the main log output