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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
The text was updated successfully, but these errors were encountered:
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:
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
Dear everyone,
I have problem running the snakemake. The stdout/stderr looks like this:
the content of
logs/render-scenario/A.log
is:The content of sample.tsv and the units.tsv are:
sample.tsv
units.tsv
Could you please help me solve this issue?
All the best,
Hossein
The text was updated successfully, but these errors were encountered: