Problem when running quality-filter q-score-joined on joined reads

Hi, good day!

I was trying to do sequence quality control on the joined reads (using q2-vsearch).
The QIIME2 version I’m using is 2019.10

Below is the script i use:
qiime quality-filter q-score-joined
–i-demux demux-joined.qza
–p-min-quality 20 \
–o-filtered-sequences demux-joined-filtered2.qza
–o-filter-stats demux-joined-filter-stats2.qza

These are the errors I received:
There were some problems with the command:
(1/3) Missing option “–o-filtered-sequences”. ("–output-dir" may also be
used)
(2/3) Missing option “–o-filter-stats”. ("–output-dir" may also be used)
(3/3) Got unexpected extra argument ( )
/var/spool/slurmd/job04754/slurm_script: line 22: --o-filtered-sequences: command not found

Can anyone point me in a right direction? Thank you in advance!

Good morning @pyee0417,

Welcome to the Qiime 2 forums! :qiime2:

I think I know how to solve this problem!

I noticed your command is across multiple lines.

qiime quality-filter q-score-joined
–i-demux demux-joined.qza
–p-min-quality 20 \
–o-filtered-sequences demux-joined-filtered2.qza
–o-filter-stats demux-joined-filter-stats2.qza

In linux, each command is run on one line, unless you use the \ backslash \ character to continue the same command to the next line. This should work:

qiime quality-filter q-score-joined \
--i-demux demux-joined.qza \
--p-min-quality 20 \
--o-filtered-sequences demux-joined-filtered2.qza \
--o-filter-stats demux-joined-filter-stats2.qza

Keep in touch!
Colin

Dear Colin, thank you for the reply!
I’ve edited the script and rerun.

qiime quality-filter q-score-joined
–i-demux demux-joined.qza
–p-min-quality 20 \
–o-filtered-sequences demux-joined-filtered2.qza
–o-filter-stats demux-joined-filter-stats2.qza

However, I still received the same errors:
There were some problems with the command:
(1/3) Missing option “–o-filtered-sequences”. ("–output-dir" may also be
used)
(2/3) Missing option “–o-filter-stats”. ("–output-dir" may also be used)
(3/3) Got unexpected extra argument ( )
/var/spool/slurmd/job04769/slurm_script: line 22: --o-filtered-sequences: command not found

I really would appreciate if anyone could help me. Thank you in advance!

1 Like

Hi @pyee0417, as @colinbrislawn mentioned above, this is a formatting issue. Please attach your full script and we can help point out specifically what is wrong (it looks like when you are copying-and-pasting to the forum we are losing some of your formatting). You can also send a screenshot, although the actual script is preferable.

Your command is close, but you are missing something!

Thank you for the reply!
I had actually edited my script with / at the end of every line except last line. However, they were missing every time i posted here.

Below are my script and screenshot of script (just in case there is any problem with the file, so I attached both):
qualityfilter2.txt (598 Bytes)

Thank you in advance!

Are there any spaces after the \ slashes \?

qiime quality-filter q-score-joined \ 
         Is there a space right here ^

Did you write that script yourself, or base if off another template script? If it’s a template, maybe the author of the template could help you troubleshoot this. I’m not sure how your SLURM queue is set up.

Colin

For your kind information, I scripted it based on the “sequence quality control” part in alternative methods of read-joining in QIIME 2 tutorial.

Thank you.