flowers9

heartbeat gives false negative under heavy nfs load

30

LAmerge has always generated a lot of nfs traffic, and load on our disk server. However, with the introduction of a heartbeat based on access to the same filesystem, I've...

openfold/np/protein.py:to_pdb(): chain_tag sometimes not set

3

I found what appears to be a rare case (once in millions of proteins) where the loop in to_pdb() sometimes fails to set chain_tag before closing the chain, causing an...

name of protein != entirety of header

1

Sometimes fasta files have simple header lines, but sometimes they toss in a bunch of stuff, for example: > Seita.9G099800.1.p pacid=32690791 transcript=Seita.9G099800.1 locus=Seita.9G099800 ID=Seita.9G099800.1.v2.2 annot-version=v2.2 This is not a good...

poor shutdown/restart handling with partially written files

1

There are places in get_read_hcgt_map.py (1), phasing.py (6), run_quiver.py (1), and unzip.py (1) where the code checks to see if output files from earlier parts are present before running subsequent...