Trimming 5bp in QIIME2 2024.5 Amplicon

[jen.herting]

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 (Johannah Hagen)]

Hi @jen.herting,
Welcome to the :qiime2: 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]

[jphagen (Johannah Hagen)]

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:

Handling ambiguous nucleotides in database construction

Hi @devonorourke & @Nicholas_Bokulich, I have had similar issues with I characters when using vsearch and other similar tools. Keep in mind that I stands for the chemical Inosine / deoxyInosine, which you can order as part of your oligos (e.g. from IDT). That is, it functions literally as an ambiguous N base. So, wherever you find and I replace with N. For example, take a look at the CO1 blocking primer we made in our swine diet paper. As for the U --> T bit… In the past, when I put that set o…

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