Open nhoffman opened 8 years ago
Agreed and I am assuming you are referring to the --details-summary
single largest cluster qseqid.
For some history, we output up to two qseqids per --details-summary
. The latest issue the --details-summary output is from 2014-11-26: https://bitbucket.org/uwlabmed/markergene_pipeline/issues/19/starred-genus-name-without-apparent-100
Summary:
Because --max-group-size
combines species level hits with genus level hits, --details-summary
will output the largest assignment cluster or the two largest assignment clusters of the combined rank assignments. For example:
1) hits: qseqid 1 - assignment: species 1/2*/3/4 qseqid 2 - assignment: genus 1
2) --min-group-size 3
bumps qseqid 1 - assignment: genus 1
qseqid 1 - genus 1
qseqid 2 - genus 1
3) assignment becomes genus 1*
4) --details-summary outputs qseqids 1 + 2
The reason being sometimes the largest cluster is qseqid 2 so the details simply has one genus level assignment_tax_name. This is confusing because the assignment is starred and should contain at least one 100% hit to species 2.
Yes, we should simplify or redesign the --details-summary
criteria.
We need to have consistent criteria for including a single qseqid for each assignment_id in the output.