Dietmar Rieder

Hi, sorry for the late reply, can you run the following commands: ``` singularity exec -B /home/ubuntu/nextNEOpi --no-home -H /tmp -B /home/ubuntu/nextNEOpi/assets -B /tmp -B /home/ubuntu/nextNEOpi/resources -B /home/ubuntu/nextNEOpi/resources/databases/iedb:/opt/iedb -B /home/ubuntu/nextNEOpi/resources/databases/mhcflurry_data:/opt/mhcflurry_data...

Should be fixed now in v1.4.1, please reopen if not.

Should be fixed now in v1.4.1, please reopen if not.

Hi, Are you trying to create the envs manually? There is no need for it, they will be created by nextflow automatically. However, we strongly recommend to use the singularity...

Hi, I'd need to see the contents of `/home/heshen/01.project/01.neoantigen/01.project/nextneopi/test/testdata/work/49/020fb154a5b67d3d4cd282f388c509` can you make a tar.gz of it and post it?

Thanks, I'd need the input files from the work dir. Can you use the `-h` option in your tar command to dereference the symlinks and post the archive again, sorry...

Thanks, I just tried to reproduce the error with the contents of your work dir, however it did not fail and completed successfully. Can you try to do the following...

There is a `PYTHONPATH` set which should not be there: `/home/heshen/01.project/01.neoantigen/00.biosoft/hisatgenotype/hisatgenotype_modules` This could interfere with the python packages in the container. I'm not sure if it is also mounted into...

May I ask you to manually rerun the process as follows, Just to make sure it wasn't just one time error: ``` cd /home/heshen/01.project/01.neoantigen/01.project/nextneopi/test/testdata/work/49/020fb154a5b67d3d4cd282f388c509 rm -rf MHC_Class_I bash .command.run ```

We are still investigating on this, we have access to a system on which we could reproduce the issue. Meanwhile you might disable the `MHCflurry` runs by setting the `epitope_prediction_tools`...