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griffithlab / pVACtools

http://www.pvactools.org
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pvacseq example code from "Getting Started" page #1008

Closed nitishnih closed 1 year ago

nitishnih commented 1 year ago

Hi,

I was running the example code for pvacseq shown here: https://pvactools.readthedocs.io/en/latest/pvacseq/getting_started.html#getting-started

I ran:

pvacseq download_example_data .
pvacseq run \
 pvacseq_example_data/input.vcf \
 HCC1395_TUMOR_DNA \
 HLA-A*29:02,HLA-B*45:01,DRB1*04:05 \
 all \
 pvacseq_example_output \
 -e1 8,9,10 \
 -e2 15 \
 --normal-sample-name HCC1395_NORMAL_DNA

The first command finished successfully. The second gave the following error:

Executing MHC Class I predictions
Converting .vcf to TSV
/usr/local/lib/python3.7/site-packages/vcfpy/header.py:288: DuplicateHeaderLineWarning: Seen FILTER header more than once: PASS, using firstoccurence
  DuplicateHeaderLineWarning,
normal_sample_name HCC1395_NORMAL_DNA provided but the input file is a single-sample (tumor only) VCF

If I deleted the pvacseq_example_output directory and restarted pvacseq without the --normal-sample-name option, then it worked. Am I doing something wrong or does the documentation need to be updated?

susannasiebert commented 1 year ago

This totally is a mistake on our part. The VCF should be pvacseq_example_data/annotated.expression.vcf.gz. However, I'm confused that your example worked with the VCF input.vcf because that file is no longer part of the newest example data in version 4.0. You should've received an error that a file with such name was not found. Are you using an older version of pVACtools?

nitishnih commented 1 year ago

Thanks for the response and pointing out the problem. I pulled the docker container griffithlab/pvactools:latest-slim using singularity. This was done on July 21st but I didn't know that was actually pvactools version 3.1.3. I mistakenly assumed it was the newer 4.0.1 version. I'll correct this and pull 4.0.1 explicitly. Thanks again!

susannasiebert commented 1 year ago

Thank you for pointing that out. 4.0 no longer has xs and slim versions so the latest-xs and latest-slim are outdated. I will remove them.

susannasiebert commented 1 year ago

The documentation has been updated and the latest-xs and latest-slim images have been removed. Closing this issue.