C. Titus Brown
C. Titus Brown
reports now include % of genome bases & hashes covered. note, right now genome size comes from mapping info. it might be nice to have a separate file so we...
We get an error like this `gzip: outputs.paper/genomes/.genomes.SRR1976948: unexpected end of file`. I spent some time tracking this down and it has something to do with the way checkpoints return...
They can be removed with: ``` find outputs -name \*.bam -size 0 -exec rm {} \; ``` What I don't understand is why they are produced in the first place...
**Please note** if this PR requires a rebuild of catlas or other big files.
**Please note** if this PR requires a rebuild of catlas or other big files. Since we need the connectivity information, and would like the abundances, this may not be possible...
ref https://github.com/sourmash-bio/sourmash/pull/1127/files#diff-47c5f70f455a0039334dd042f30fbb585c977a73ad838ee4747e5cd304ffb412 - somehow got removed. Maybe figure out why. And, in any case, add it back!
This allows Python code to emulate the behavior of `sourmash scripts manysearch` on a RocksDB without full signatures - you can now just get the overlap in hashes & the...
Running in directory `/home/ctbrown/scratch3/sourmash-midgie-raker/splits`, command: ``` sourmash scripts manysearch 's__Mesorhizobium sp000502715.sig.zip' /group/ctbrowngrp5/sra-metagenomes/20241128-k21-s1000 -k 21 -o /tmp/xxx.csv ``` Full error: ``` ksize: 21 / scaled: None / moltype: DNA / threshold:...
https://bsky.app/profile/phylogenomics.bsky.social/post/3m6b6a6xmts2y
ref https://github.com/Arcadia-Science/sourmashconsumr/issues/79