Closed OliverBryan closed 6 months ago
@mfl15 do you mind helping @jsrdrgz out with this? From a slack conversation it looks like it might be a bit nuanced to fix this (as the previous fix to a bug introduced a new one) and definitely points to a missing integration test somewhere.
@dkoslicki sure, no problems
Working with data from https://frl.publisso.de/data/frl:6425521/marine/short_read/marmgCAMI2_sample_0_reads.tar.gz as the sample data, both
yacht train
andyacht run
run into a similar error using the GTDB database available usingyacht download
.First I ran
yacht sketch sample --infile ./sample/anonymous_reads.fq --kmer 31 --scaled 1000 --outfile sample.sig.zip
and then I first attempted to use the pretrained gtdb database usingyacht download pretrained_ref_db --database gtdb --db_version rs214 --k 31 --ani_thresh 0.9995 --outfolder ./
. Then, after unzipping this and attempting to run yacht I got the following error:In an attempt to fix this, I tried to train the gtdb database myself using
yacht download default_ref_db --database gtdb --db_version rs214 --gtdb_type reps --k 31 --outfolder ./ref
and thenyacht train --ref_file ./ref/gtdb-rs214-reps.k31.zip --ksize 31 --num_threads 32 --ani_thresh 0.95 --prefix 'gtdb_ani_thresh_0.95' --outdir ./
and then I got the following error: