Ward D

This didn't occur anymore with chunksize increases (release 3.5.2). I'll close this for now, but feel free to re-open if it pops back up.

This is not an issue with your tmp directory ? 512MB is an oddly specific size, otherwise, would you mind sharing (somehow) the bam file that causes this behavior ?

Thanks for the additional info, it'd be great if you could share the problematic and a working bam file somehow. Do you have a way of making these available ?

Just per update, I've received the files, this is now work in progress.

It seems the chance for a truncated bam in 3.5.5 is decreased, but not completely removed. I'm aiming to have a true fix for this in the upcoming weeks.

Can you share the content of `/scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/profiles/snakepipes_genericprofile/config.yaml` More specifically, all the lines above 'set-resources' Aside from this, note that 3.0.0 will fail due to the fq problem (cfr. #1075), probably...

Hi Hanrong, --local could be replicated by specifying 'shared/profiles/local' as snakemakeProfile under your defaults.yaml file (snakePipes info to retrieve this one). -j within the local configuration can be replicated by...

This is fixed in the develop branch, but not released yet. As a workaround you can pip install from develop. Do note you probably need to cap pulp as well...

Hi Katarzyna, Can you add a reproducible example ? I can then have a look.

Yea, I got rid of it when simplifying runAndCleanup. I figured real time stdout/stderr in console is enough information, and we don't need to flush the buffer on every line....