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Can we add a quick file size check for the config file saving instead to speed things up? That seems better than removing all consistency checks, but clearly calculating the hashes for all things is not working.
It's hard to quantify how much effect this actually has because of caches etc. On a pretty damn fast machine running many sha256s in parallel can rip through 6.6GB of .fastq.gz in 2 seconds (20 CPU-seconds) BUT only if the cache is hot already.
Like a lot of CountESS things, if it could do the hash check in the background it would be way less annoying.
Activity
nickzoic commentedon Jan 15, 2026
this continues to be a huge problem for large .fastq files.
afrubin commentedon Mar 12, 2026
Can we add a quick file size check for the config file saving instead to speed things up? That seems better than removing all consistency checks, but clearly calculating the hashes for all things is not working.
nickzoic commentedon Mar 13, 2026
It's hard to quantify how much effect this actually has because of caches etc. On a pretty damn fast machine running many sha256s in parallel can rip through 6.6GB of .fastq.gz in 2 seconds (20 CPU-seconds) BUT only if the cache is hot already.
Like a lot of CountESS things, if it could do the hash check in the background it would be way less annoying.