Traceback (most recent call last): change_permissions_recursive

[xmy1990]

Hi, Previously, I had success using pvactools on Ubuntu , but this time I encountered the following error:

Traceback (most recent call last): File "bin/pvacseq", line 8, in sys.exit(main()) File "lib/python3.7/site-packages/pvactools/tools/pvacseq/main.py", line 116, in main args[0].func.main(args[1]) File "lib/python3.7/site-packages/pvactools/tools/pvacseq/run.py", line 170, in main pvactools.lib.run_utils.change_permissions_recursive(base_output_dir, 0o755, 0o644) File "lib/python3.7/site-packages/pvactools/lib/run_utils.py", line 96, in change_permissions_recursive os.chmod(file, file_mode)

Thanks!

[xmy1990]

The result seems fine, but there is an above error in the process. Thanks!

[susannasiebert]

Thank you for this bug report. Can you please attach the full stack trace for this error? Unfortunately, the original stderr you posted doesn't include the actual error message.

Additionally, can you please post the pVACtools command you ran?

[xmy1990]

I just get the above errors. The other original stderr had no errors, it was all ok. The result was also seemed ok.

Thanks

[susannasiebert]

That is weird because it doesn't actually mention a specific error message, just the lines of the files it executed when it ran into the problem. What does the stdout say?

Again, can you please attach the command you tried to run? Are there specific steps that can be taken to replicate this issue consistently?

Without a specific error message or steps to reproduce this issue on my end there isn't much I can do to fix this.

[xmy1990]

pVACtools command ： pvacseq run \ $input_vcf \ $tumor_name \ $hla_type \ MHCflurry \ $tmp \ -e1 8,9,10,11 \ --normal-sample-name $normal_name \ --iedb-install-directory $iedb_dir \ --blastp-path $blastp_path \ -b $ic50 \ --percentile-threshold $rank_p \ -m median \ --normal-cov $normal_cov \ --normal-vaf $normal_vaf \ --tdna-cov $tumor_cov \ --tdna-vaf $tumor_vaf \ -t $number_threads

Thanks！

[susannasiebert]

Was this run under docker or a standalone installation?

[xmy1990]

standalone installation

[susannasiebert]

Unfortunately, I'm unable to replicate this issue on my end. If you can provide a set of steps to reliably replicate this issue, I'm happy to investigate further. Otherwise I will have to close this issue.

[susannasiebert]

Closing this issue due to inactivity.