methods for processing fungal ITS2 data in QIIME2

Library Plugin Support
1

i really realy tired to trim my its2 data using itsx, and i got error :
Error: QIIME 2 plugin 'itsxpress' has no action 'trim-pair-output-unmerged--i-per-sample-sequences'.

2

Welcome @Pena_Piana!

Looks like you are just missing a space after "unmerged"

Good luck!

5

Hi @Pena_Piana,
Could you please report the full error message? See this line:

Or re-run with the --verbose flag.

Also, please do not post duplicate questions. You posted the same question twice, and I had to merge both into this topic. I also merged your third post into this topic, as it is a question about the same method.

Thanks!

6

thank you for your help. ...
I got this error below, what I should do to fix this error message. thank you

(qiime2-2020.6) afriana@alfriana-hp-laptop-14-cm0xxx:~/Documents/alfri$ qiime itsxpress trim-pair-output-unmerged --i-per-sample-sequences sequences.qza --p-region ITS2 --p-taxa F --o-trimmed trimmed.qza
Plugin error from itsxpress:

Command '['bbmerge.sh', 'in=/tmp/qiime2-archive-ycdugho4/273e1416-f945-4ea5-aa19-8b0fd71a3200/data/S1_0_L001_R1_001.fastq.gz', 'in2=/tmp/qiime2-archive-ycdugho4/273e1416-f945-4ea5-aa19-8b0fd71a3200/data/S1_1_L001_R2_001.fastq.gz', 'out=/tmp/itsxpress_gfolnze7/seq.fq.gz', 't=1', 'maxmismatches=40', 'maxratio=0.3']' returned non-zero exit status 1.

7

Hi @Pena_Piana,
That still does not look like the full error message, please note my requests above.

In any case, I am not the itsxpress developer and cannot help troubleshoot, just trying to help you report the full necessary info. Maybe @Adam_Rivers could give you a hand if you report the full error message

8

@Pena_Piana My guess from this info would be that you need to update BBtools in your Qiime2 environment. With your Qiime environment active, run conda install -c bioconda bbmap.
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1 Like
9

An off-topic reply has been split into a new topic: ITS2 analysis SOP with QIIME 2?

Please keep replies on-topic in the future.