Dear all, I am using sequali to QC a set of ONT-generated BAM files. So far, it has always run smoothly. However, I recently came across a ~70GB BAM file, and my nextflow pipeline crashed:

Processing my_sample.bam:  96%|█████████▋| 69.1G/71.7G [10:46<00:12, 224MiB/s].command.sh: line 8:    32 Killed                  sequali -t 4 --html my_sample.html --json my_sample.json my_sample.bam

Sequali produces only a loading bar that does not inform which step it's performing. I would like to ask its developer if it's possible to produce more verbose output. However, that alone would not solve the issue. I tested the same sequali command line (which fails above) on my linux system, outside of the Nextflow pipeline, and in that case sequali completes successfully. However, I also noticed that, in this scenario, sequali first hangs for a few seconds after reaching 100% execution, then completes successfully. I wonder if this "hanging" behavior could indicate something, and I wonder if programs should comply to some rules to be executed in Nextflow. What is it that could make Nextflow kill a module's execution?

Your tool is very likely getting killed because it's trying to use your memory than the configuration provided says it will (or that is available in the machine you're running it in).

Thank you, Pontus! I'm testing with different configurations