Trimming 5bp in QIIME2 2024.5 Amplicon

jen.herting · November 14, 2024, 5:30pm

Hello All,
I tried running the script below to trim the first 5bp for my sequences and got the error in the screenshot below. I checked the cutadapt version 4.9 is installed.
qiime cutadapt trim-single \
--i-demultiplexed-sequences single-end-demux.qza \
--p-front 5 \
--o-trimmed-sequences single-end-demux-trimmed.qza
Plugin error from cutadapt:

Command '['cutadapt', '--cores', '1', '--error-rate', '0.1', '--times', '1', '--overlap', '3', '--minimum-length', '1', '-q', '0,0', '--quality-base', '33', '-o', '/tmp/q2-CasavaOneEightSingleLanePerSampleDirFmt-y6rg56a3/02A_0_L001_R1_001.fastq.gz', '--front', '5', '/tmp/qiime2/ajanosik/data/53a4ff74-1ff3-4f84-9ad1-84a39fad7fda/data/02A_0_L001_R1_001.fastq.gz']' returned non-zero exit status 2.

Debug info has been saved to /tmp/qiime2-q2cli-err-jgq53us_.log

Thank you!

jphagen · November 14, 2024, 6:21pm

Hi @jen.herting,
Welcome to the forum!
Can you re run your command with the --verbose parameter and then post your command and the error message here? A screenshot is great! That will give me more information on whats causing the problem here.
--Hannah

jen.herting · November 14, 2024, 9:11pm

jphagen · November 14, 2024, 9:30pm

Okay @jen.herting,
Your issue is in the snippet above, it appears that there is the number 5 in your adaptor sequence, which is not an allowed character.
To fix this I would recommend following the guidelines in this forum post:

That should fix the issue. If you run into anything else or that doesn't work for you, we are here to help
--Hannah