dfornika
commented
1 year ago Relevant error message is:
Running command:
set -u pipefail; bcftools query -u -f '%CHROM\t%POS\t%REF\t%ALT\t%ANN\t[%AD]\n' ./4c8ae5e4-e0cf-4a93-a565-e7ae6ab808ee.delly.csq.vcf.gz
Traceback (most recent call last): File "/home/dfornika/.conda/envs/tbprofiler-nf-a3a7045274879811c28a762d2c9a6c48/bin/tb-profiler", line 616, in <module> args.func(args) File "/home/dfornika/.conda/envs/tbprofiler-nf-a3a7045274879811c28a762d2c9a6c48/bin/tb-profiler", line 210, in main_profile results = tbp.reformat(results, conf, reporting_af=args.reporting_af, mutation_metadata=args.add_mutation_metadata) File "/home/dfornika/.conda/envs/tbprofiler-nf-a3a7045274879811c28a762d2c9a6c48/lib/python3.9/site-packages/tbprofiler/reformat.py", line 269, in reformat results["variants"] = select_csq(results["variants"])
File "/home/dfornika/.conda/envs/tbprofiler-nf-a3a7045274879811c28a762d2c9a6c48/lib/python3.9/site-packages/tbprofiler/reformat.py", line 88, in select_csq
csq = select_most_relevant_csq(d["consequences"])
File "/home/dfornika/.conda/envs/tbprofiler-nf-a3a7045274879811c28a762d2c9a6c48/lib/python3.9/site-packages/tbprofiler/reformat.py", line 72, in select_most_relevant_csq
ranked_csq.append([i for i,d in enumerate(rank) if d in csq["type"]][0])
IndexError: list index out of range
Cleaning up after failed run
################################# ERROR #######################################
This run has failed. Please check all arguments and make sure all input files
exist. If no solution is found, please open up an issue at
https://github.com/jodyphelan/TBProfiler/issues/new and paste or attach the
contents of the error log (SAMPLE_ID_REDACTED.errlog)
###############################################################################It looks like the error is happening here:
...where there’s a list comprehension (statement like: [x for x in ....]), then an array access of the first element ([...][0])
[i for i,d in enumerate(rank) if d in csq["type"]][0]...which is throwing an IndexError exception because that list comprehension is evaluating to an empty list, so there is no first element.
I’m looking at the latest version of TBprofiler, and it looks like the ‘reformat’ method has been rewritten:
...to use the ‘select_csq’ method from ‘pathogen-profiler’:
...which calls this ‘select_most_relevant_csq’ method:
...which seems to have been re-written compared to the version used in the TBProfiler that’s currently used in this pipeline.
So I think it would be worth trying to update TBProfiler to see if that fixes the issue.
It is not an error of tbprofiler-nf. but some samples can cause tbprofiler to fail, for unclear reasons. Could we add ignore errors for those samples so the pipeline can run on the rest of the samples?