Closed schorlton closed 9 months ago
Hi @schorlton, this is not expected, the report runs in a few seconds only. I managed to replicate your scenario and can confirm there's a bug in the taxonomy generation for custom databases, so I will provide a fix soon. In the current version, if you change your ganon.txt
to something like:
9606.fna 9606.fna 9606
10298.fna 10298.fna 10298
5476.fna 5476.fna 5476
it will also work fine. The bug is due to a redundancy in taxonomy, where your target name (second col.) was the same as the taxonomic identifier, creating a bad .tax
file.
Thanks for the detailed report!
Thank you! Feel free to close this when ready.
Fixed in v2.0.0 #271
Ganon looks really great (thanks for the detailed docs) so I wanted to test it out on a toy example. I have ~131k mix of paired-end and single end reads. Running 1.9.0 in micromamba.
Built a database with 3 genomes (human, 1 bacteria and 1 virus) to test it out. Specifically, here was my command:
ganon build-custom --input-target file --input-file ganon.txt -d w_size -x ncbi -t 30 --hibf
ganon.txt
looks like:Each of these is a single reference genome from NCBI except 9606 which is CHM13v2.
Then ran classify with binning:
ganon classify -t 32 -b -o test_bin_w_size -d ganon/w_size -s singles.fastq -p reads_1.fastq reads_2.fastq --verbose
It ran the classification really quickly, but then looks like it stalled on generating the report. Specifically, it's using 100% of 1 thread for >25 minutes and using >40gb RAM when I killed it. I also tried building the database with the
--skip-genome-size
.Is this expected? I was surprised that the classification was so quick but the reporting took this long given the toy example. Thanks again!!
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