Closed taylorreiter closed 2 years ago
rule make_contigs_search_taxonomy_wc:
doesn't have a command line scaled parameter, but is fed by outputs from rule prefetch_all_matches_wc:
which does have gather_scaled = config['gather_scaled'],
as a param
.
Trying to figure out what could be causing the mismatch, I searched for 1000
in the repo to see if that scaled value is lingering anywhere.
Not really relevant, but this line of code might need to be changed to *scaled
instead of *1000
The scaled value seems to be inherited in all of the correct places, so I checked the sourmash docs, and the rs207 dbs are scaled 1000 🙄
The line of code that is causing this problem is here:
https://github.com/dib-lab/charcoal/blob/latest/charcoal/contigs_search_taxonomy.py#L59-#L66
I'll update the default scaleds back to 1000.
closed with #218
215 changed the scaled value in charcoal/conf/system.conf.
@ccbaumler is using charcoal trying to run the workflow in this repo: https://github.com/taylorreiter/2022-dominating-set-differential-abundance-example, and charcoal produces the following error:
So this caused a problem for
contigs_search_taxonomy.py
run in rulemake_contigs_search_taxonomy_wc
. Woops. Hunting it down now.