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snakemake-workflows / dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
MIT License
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fail in render_scenario rule #122

Open moeinzadeh opened 2 years ago

moeinzadeh commented 2 years ago

Dear everyone, I have problem running the snakemake. The stdout/stderr looks like this:

Error in rule render_scenario:
    jobid: 39
    output: results/scenarios/A.yaml
    log: logs/render-scenario/A.log (check log file(s) for error message)

RuleException:
CalledProcessError in line 20 of path_to1/dna-seq-varlociraptor/workflow/rules/calling.smk:
Command 'set -euo pipefail; path_to2/bin/python3.10 path_to1/dna-seq-varlociraptor/.snakemake/scripts/tmpe3uwiuwx.render-scenario.py' returned non-zero exit status 1.
  File "path_to1/dna-seq-varlociraptor/workflow/rules/calling.smk", line 20, in __rule_render_scenario
  File "path_to3/miniconda3/envs/snakemake/lib/python3.10/concurrent/futures/thread.py", line 58, in run

the content of logs/render-scenario/A.log is:

path_to1/dna-seq-varlociraptor$ cat logs/render-scenario/A.log
Traceback (most recent call last):
  File "path_to1/dna-seq-varlociraptor/.snakemake/scripts/tmpe3uwiuwx.render-scenario.py", line 15, in <module>
    Template(template.read()).render(
  File "path_to2/miniconda3/envs/snakemake/lib/python3.10/site-packages/jinja2/environment.py", line 1291, in render
    self.environment.handle_exception()
  File "path_to2/miniconda3/envs/snakemake/lib/python3.10/site-packages/jinja2/environment.py", line 925, in handle_exception
    raise rewrite_traceback_stack(source=source)
  File "<template>", line 14, in top-level template code
jinja2.exceptions.UndefinedError: pandas.core.series.Series object has no element 0

The content of sample.tsv and the units.tsv are:

sample.tsv

path_to1/practic_available_sms/dna-seq-varlociraptor$ cat config/samples.tsv 
sample_name alias   group   platform    purity  panel
A   A   A   ILLUMINA    NA  NA

units.tsv


(base)path_to1/dna-seq-varlociraptor$ cat config/units.tsv 
sample_name unit_name   fq1 fq2 sra adapters    umis
A   UNAME   path_to_fastq/illumina/fastq/sample_R1.fastq.gz path_to_fastq/illumina/fastq/sample_R2.fastq.gz NA  "-a ACGCGATCG -A GCTAGCGTACT"   NA

Could you please help me solve this issue? All the best, Hossein

dlaehnemann commented 2 years ago

What's the entry in config["calling"]["scenario"] (which is usually read in from config/config.yaml) and what does the file specified by this entry contain?

From what I can see from the traceback, the script workflow/scripts/render_scenario.py fails here: https://github.com/snakemake-workflows/dna-seq-varlociraptor/blob/0c09ed63fa6e4808df01bac2837ce08006104531/workflow/scripts/render-scenario.py#L11

And it sounds like this is due to something in line 14 of the scenario.yaml template you are using.

maryamghr commented 2 years ago

Dear David, Following this issue, does this tool applicable in germline SV detection for non-cancer samples? if yes, what is the config setting? Thank you in advance, Maryam