How the data was generated: Illumina Nextseq 2000 P1 600 cycles
Command(s) used to run ITSxpress:
qiime itsxpress trim-pair-output-unmerged
--i-per-sample-sequences {project_id}/Trimming/{project_id}_Raw_trimmed.qza
--p-region ITS1
--p-taxa F
--p-cluster-id 0.995
--p-threads {threads}
--o-trimmed {project_id}/Trimming/{project_id}_its_trimmed.qza"
My Question
What are the next troubleshooting steps you recommend?
There is a number of things that can cause that error. This old post from Chris is a good place to start:
This is also helpful, because it can help calculate the expected amplicon coverage, if you know the of expected amplicon length (distribution, because there are lots of amplicons). But check the other things first!
Let us know what you try next and if you need more help!
I’m running the latest version of ITSxpress (2.1.4) on my QIIME 2 setup. Interestingly, ITSxpress works perfectly in some projects but fails in others, even though the error message doesn’t point to anything obvious, there are no missing or empty lines, and the input files look fine.
Since the plugin behaves differently depending on the dataset, it seems the issue could be related to some specific characteristic of certain input files or perhaps a rare compatibility problem, rather than an installation or version issue. The bizarre part is that switching to a different dataset using the same workflow resolves the problem, which suggests it’s not due to my environment or plugin version.
Before we contact the ITSxpress developer, can you find an example file that makes an error like this that you can post on the forum? I trust you with the decision of what samples and data you can share.
This will help the developer reproduce this error and diagnose the cause.
Thanks for your suggestion! Unfortunately, I can't share the original FASTQ files due to confidentiality agreements concerning sample data from my projects. However, I can definitely provide the error log, as well as the exact line that triggered the error. If helpful, I can also paste about 10 lines before and after the line that triggered the error, to give context.
Please let me know if this would work or if there's any other information I can share to help diagnose the issue.
