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griffithlab / pVACtools

http://www.pvactools.org
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ValueError: dict contains fields not in fieldnames: 'DeepImmuno WT IC50 Score', 'DeepImmuno MT IC50 Score' #1075

Closed YingYa closed 4 months ago

YingYa commented 4 months ago

Installation Type

Docker

pVACtools Version / Docker Image

4.1.0 - running via Singularity (v3.8.1)

Python Version

No response

Operating System

CentOS7

Describe the bug

Running pVACtools using Singularity on a CentOS Linux 7 HPC at work. (Docker not permitted)

The key information from the stdout: Executing MHC Class I predictions ...... Parsing prediction file for Allele HLA-B*15:01 and Epitope Length 9 - Entries 1-104

The error information from stderr: Traceback (most recent call last): File "/usr/local/bin/pvacseq", line 8, in sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/main.py", line 123, in main args[0].func.main(args[1]) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 142, in main pipeline.execute() File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 452, in execute split_parsed_output_files = self.parse_outputs(chunks) File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 413, in parse_outputs parser.execute() File "/usr/local/lib/python3.7/site-packages/pvactools/lib/output_parser.py", line 755, in execute tsv_writer.writerow(row) File "/usr/local/lib/python3.7/csv.py", line 155, in writerow return self.writer.writerow(self._dict_to_list(rowdict)) File "/usr/local/lib/python3.7/csv.py", line 151, in _dict_to_list

How to reproduce this bug

singularity exec -e -B /path/to/indir:/indir -B `pwd` /path/to/pvactools-4.1.0.sif pvacseq run /indir/test2.vcf.gz test2 HLA-A*02:01,HLA-B*15:01,HLA-B*57:01,HLA-C*03:03,HLA-C*06:02,DPA1*01:03,DPA1*02:02,DPB1*02:01,DPB1*19:01,DQA1*01:03,DQA1*02:01,DQB1*03:03,DQB1*06:03,DRB1*07:01,DRB1*13:01 all . --iedb-install-directory /opt/iedb -t 4 --minimum-fold-change 1 --tdna-vaf 0.1 --trna-vaf 0.1 -a sample_name --normal-sample-name normal2 --tumor-purity 0.25 -p /indir/test2.phased.vep.vcf.gz

Input files

No response

Log output

Traceback (most recent call last): File "/usr/local/bin/pvacseq", line 8, in sys.exit(main()) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/main.py", line 123, in main args[0].func.main(args[1]) File "/usr/local/lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 142, in main pipeline.execute() File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 452, in execute split_parsed_output_files = self.parse_outputs(chunks) File "/usr/local/lib/python3.7/site-packages/pvactools/lib/pipeline.py", line 413, in parse_outputs parser.execute() File "/usr/local/lib/python3.7/site-packages/pvactools/lib/output_parser.py", line 755, in execute tsv_writer.writerow(row) File "/usr/local/lib/python3.7/csv.py", line 155, in writerow return self.writer.writerow(self._dict_to_list(rowdict)) File "/usr/local/lib/python3.7/csv.py", line 151, in _dict_to_list

Output files

No response

susannasiebert commented 4 months ago

@YingYa thank you for this bug report. Can you please attach the input VCF file for this run so I can try to reproduce this error on my end?

YingYa commented 4 months ago

Yes. May I have your e-mail that I could share the files by google drive?

susannasiebert commented 4 months ago

Would our Google group help email alias work? It’s help@pvactools.org

YingYa commented 4 months ago

Please find the files on: https://drive.google.com/drive/folders/18_UpQMi_1ijlkDsKNAMRaWpSxG2DNcqJ?usp=sharing

susannasiebert commented 4 months ago

Unfortunately, I'm unable to reproduce this issue on my end. Would you be able to share your output directory for this run with me if you still have it? Additionally, the full stderr/stdout log would be helpful in case there are any additional errors/warnings in there.

susannasiebert commented 4 months ago

I was actually able to reproduce this error on the data for #1074. Did you, by any chance, restart this particular run? Did you encounter the following error earlier: FileNotFoundError: [Errno 2] No such file or directory: '/data/issue_1074/MHC_Class_I/tmp/deepimmuno-cnn-result.txt'? I'm trying to figure out if this error is related to a restart after the FileNotFoundError.

YingYa commented 4 months ago

Yes, I encounter the following error in other rerun samples: _FileNotFoundError: [Errno 2] No such file or directory: '/path/to/MHC_ClassI/tmp/deepimmuno-cnn-result.txt'

susannasiebert commented 4 months ago

This issue has been fixed in version 4.1.1. You will need to start your run from scratch because the FileNotFoundError results in incomplete tmp files that will lead to the ValueError from the original bug report. Please give that version a try and feel free to reopen this issue if the error persists.