Closed peterbjarke closed 2 years ago
Hi Peter, thanks for you using KMCP.
kmcp search
reports the proportion of matched reads.
10:01:29.112 [INFO] processed queries: 595188, speed: 2.135 million queries per minute
10:01:29.112 [INFO] 100.0000% (595188/595188) queries matched
10:01:29.112 [INFO] done searching
And kmcp search
shows the number and proportion of reads belonging to targets in the profile.
10:04:30.308 [INFO] #input matched reads: 595189, #reads belonging to references in profile: 595189, proportion: 100.000000%
Maybe kmcp search
could write the basic summary to the search result file as comment lines, then kmcp search
shall read and report them again.
Many thanks for the quick answer! Yes I can see the reporting in the stderr output.
Best regards,
Peter
Maybe kmcp search could write the basic summary to the search result file as comment lines, then kmcp search shall read and report them again.
I may not do this, cause it's difficult for kmcp profile
to read the comment lines.
I'll implement this. #33
Many thanks for this open source tool! Vey well documented
When running the profiling: For example: kmcp profile search.kmcp@gtdb.kmcp.tsv.gz --taxid-map taxid.map --taxdump taxdump/ --out-prefix search.tsv.gz.k.profile --metaphlan-report search.tsv.gz.m.profile --cami-report search.tsv.gz.c.profile --binning-result search.tsv.gz.binning.gz
It is possible to report the proportion of unmatched read similar to what kraken2 does ?
Best regards,
Peter