Marco van Zwetselaar

Hi Tom, here are the results for the `ncbi/blast` image on my laptop - and they don't look great :-/ ``` $ time docker run --rm -e BLAST_USAGE_REPORT=false ncbi/blast blastn...

I suppose under docker the issue is worse because the containers sit on their own network, and won't see their link go down when the outside link is down (unless...

Hi Richard, thanks for your quick response. There was no output at all from the `--resume-from` command, so I can't grep for the header. FYI, here is header of the...

Hi Richard, I used samtools view broken.bam | samtools -b >fixed.bam which got rid of the `EOF` marker warning. The last few reads in the `fixed.bam` look fine. Also, no...

On a hunch, this: [2025-04-04 22:20:15.273] [error] Cmdline requires at least 4 tokens including binary name, found: looks like it may be related to the `CL:` header, which samtools will...

Yay! **I got it working** but it gets very weird. In order to capture dorado's log output (which gets instantly obliterated by the flood of dots), I redirected the process's...

Thanks Rich, I'm a bit short on time, else I'd try and track down the bug in the sources. For now you may want to add a note to the...

Confirming the fix by @vineeth-s for distro-provided samtools on Ubuntu 24.04. `proc.stdout.decode()` chokes on the tofu in the output of `samtools --version`.