charcoal
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confused about some text in output of stage2 `stage2/*postprocess.txt`
In text files stage2/*postprocess.txt
, there are sections that postprocess mashmap alignments, parsing them to determine percent identity for each contig against each contaminant genome.
ex:
removing 9kb with 5kb dirty, contig name NODE_1608_length_9168_cov_9.2029.
5kb aligns to GCA_900554435.1:USHC01000102.1 at 98.4%
(d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola;s__Phocaeicola sp900554435)
** disagreement at rank 'phylum'; genome p__Firmicutes_A, source p__Bacteroidota
I'm confused because stage2
isn't required for target clean
, but this file says that it removes contigs/kb as dirty based on mashmap alignment results. My understanding is that it would be more accurate to state, "identified 9kb with 5kb dirty, contig name NODE_1608_length_9168_cov_9.2029.
5kb aligns to GCA_900554435.1:USHC01000102.1 at 98.4%" OR "verified 9kb contaminant with 5kb dirty, contig name NODE_1608_length_9168_cov_9.2029.
5kb aligns to GCA_900554435.1:USHC01000102.1 at 98.4%"
Am i interpreting this file wrong?
line in code that produces this message: https://github.com/dib-lab/charcoal/blob/latest/charcoal/postprocess_alignments.py#L133