I am very new to qiime2.
I am analysing MiSeq paired-end sequence files.
I merged paired-end seq files with [qiime vsearch join-pairs] cammand and now I have a problem with [qiime quality-filter q-score] command.
Here I’m attaching the command and error message.
(I didn’t attach debug info as I couldn’t find a log file which seems like a temporary file…)
MacBook-Pro:SM_raw Jeongsu$ qiime quality-filter q-score --i-demux demux-joined.qza --o-filtered-sequences demux-joined-filtered.qza --o-filter-stats demux-filter-stats.qza
Plugin error from quality-filter:
Argument to parameter ‘demux’ is not a subtype of SampleData[PairedEndSequencesWithQuality | SequencesWithQuality].
Debug info has been saved to /var/folders/vh/l4ckn9311hx8yrvvbfpnh6zh0000gn/T/qiime2-q2cli-err-jr39kklr.log
Good morning Jeongsu,
Here is the main error:
Argument to parameter ‘demux’ is not a subtype of
SampleData[PairedEndSequencesWithQuality | SequencesWithQuality].
It looks like the file
demux-joined.qza is not type that qiime is expecting.
Take a look at the Moving Projects Tutorial, in which they run
qiime quality-filter q-score, but only after running
qiime demux to make a .qza file in the right format.
qiime demux first, so that the output
.qza file is in the right format for
qiime quality-filter q-score.
Let me know what you find!
While @colinbrislawn’s advice is generally correct, I suspect your goal is to use
deblur in which case quality filtering is important and also means your reads must be merged.
In that case the workflow looks more like this:
qiime vsearch join-pairs (like you’ve done)
qiime quality-filter q-score-joined (this accepts
Let us know how that goes!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.