python snakemake
I'm launching snakemake in Gitlab CI/CD bash as Python module, so the original command looks like
python3 -m snakemake -s baseline.rules --report report_baseline.html
Only in reports I get this error and pipeline fails.
627 Traceback (most recent call last):
628 File "/home/gitlabrun/.local/lib/python3.6/site-packages/snakemake/__init__.py", line 633, in snakemake
629 keepincomplete=keep_incomplete,
630 File "/home/gitlabrun/.local/lib/python3.6/site-packages/snakemake/workflow.py", line 680, in execute
631 auto_report(dag, report)
632 File "/home/gitlabrun/.local/lib/python3.6/site-packages/snakemake/report/__init__.py", line 663, in auto_report
633 text = f.read() + rst_links
634 File "/trinity/shared/pkg/devel/python/3.6.5/lib/python3.6/encodings/ascii.py", line 26, in decode
635 return codecs.ascii_decode(input, self.errors)[0]
636 UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 452: ordinal not in range(128)
Actually I don't get the exact reason and since my local setup is working fine I can't reproduce it locally and debug. Any suggestions how to fix it are welcome.