Hi,

I've been running my data set with current SILVA release as the reference. I've been incresing the MAPQ with --sam-qual but it seems to have no effect on filtering the matched reads. Issue is that I never get any unmatched reads which seems hard to believe with ONT data.

Also, the output in Exact_affiliations.tsv ending tmp directory file have zero as their sam FLAG. I understood that this file is taken from the sam file produced after mapping. I'm not sure if everything is working as should and have I interpreted all corretly but I would like to be able to see the sam file to understand is the issue arises.

I'm attaching here the command (nothign changes even if I set --sam-qual to be anything between 0 -30)

/projappl/project_2005629/NanoASV/workflow/nanoasv --dir /scratch/project_2007947/FYGE2045/testi4 --out /scratch/project_2007947/FYGE2045/OUT_testi6 --database /users/hmviit/projappl_project_2005629/NanoASV/resources/SINGLELINE_SILVA_138.2_SSURef_tax_silva.fasta --quality 10 --minlength 1200 --maxlength 1600 --id-vsearch 0.8 --num-process 4 --sam-qual 30

the output and error files produced from the run, and one Exact_affiliations.tsv file as an example of all being zeros.

barcode22_Exact_affiliations.tsv

errors_nanoasv_30122203.txt

output_nanoasv_30122203.txt

My current NanoASV version is 1.2.2. and I've built NanoASV with

Best,
Heidi