Qiime quality-filter q-score error

[Jeongsu_Kim (Jeongsu)]

Hello guys,

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

[colinbrislawn (Colin J Brislawn)]

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.

Try running 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!

Colin

[ebolyen (Evan Bolyen)]

Hi @Jeongsu_Kim,

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)
and then
qiime quality-filter q-score-joined (this accepts SampleData[JoinedSequencesWithQuality])

Let us know how that goes!