missing python dependency in rule plot_stats

[pmginacio]

I got the following error running this workflow,

[Thu Oct 21 10:30:39 2021]
rule plot_stats:
    input: results/tables/calls.tsv.gz
    output: results/plots/depths.svg, results/plots/allele-freqs.svg
    log: logs/plot-stats.log
    jobid: 24
    resources: tmpdir=/tmp

Activating conda environment: /home/pedro/projects/sandbox/snake-gatk/.snakemake/conda/c8bc479b3ecf77c3e954eb4b0008039b
Activating conda environment: /home/pedro/projects/sandbox/snake-gatk/.snakemake/conda/c8bc479b3ecf77c3e954eb4b0008039b
[Thu Oct 21 10:30:40 2021]
Error in rule plot_stats:
    jobid: 24
    output: results/plots/depths.svg, results/plots/allele-freqs.svg
    log: logs/plot-stats.log (check log file(s) for error message)
    conda-env: /home/pedro/projects/sandbox/snake-gatk/.snakemake/conda/c8bc479b3ecf77c3e954eb4b0008039b

The log shows the following message,

Traceback (most recent call last):
  File "/home/pedro/projects/sandbox/snake-gatk/.snakemake/scripts/tmpjsez2vr4.plot-depths.py", line 8, in <module>
    import common
ModuleNotFoundError: No module named 'common'

[tuliocampos]

I had the same issue. Seems like the pipeline does not download the file common.py it's supposed to use. I have tried to download (from github) and run the scripts manually, using the calls.tsv.gz (or calls.tsv) file as input. It generates very large svg files that fail to be converted to png when I tried to generate the reports using "snakemake --report report.zip".

[matthewthefool]

I really struggle with this problem rn, have you solved it yet?