Closed peterk87 closed 5 years ago
Hi @glabbe
With the changes in this pull request I am able to get the proper QC messages using the schema you linked to in #98
For ERR163996, I now get a QC FAIL
with the message:
FAIL: Mixed subtype; the positive and negative kmers were found for the same target site 62657 for subtype "4.1.2".
Command-line:
$ hansel -s tb_speciation_scheme_v1.0.5.fasta -p ERR163996_* -O output.tsv --min-kmer-freq 8
For ERR182041, I now get a QC FAIL
with the message:
FAIL: Mixed subtype; the positive and negative kmers were found for the same target site 4260268 for subtype ""4.6.1.1"".
Command-line
$ hansel -v -s tb_speciation_scheme_v1.0.5.fasta -p ERR182041_*.fastq.gz --min-kmer-freq 8 --force
I'll continue testing the other genomes next week!
Great! Thanks a lot @peterk87