Need help: plugin error from ITSxpress

Library Plugin Support ITSxpress
6

Hi everyone,

I encountered an issue while working with ITSxpress 2.1.3 in QIIME 2 (2024.10). I successfully installed ITSxpress 2.1.3 after resolving version conflicts with hmmer caused by q2-fragment-insertion and sepp. I removed these plugins to allow the installation of ITSxpress 2.1.3. Additionally, since I use Apple Silicon, I configured the environment as osx-64 using:

conda config --env --set subdir osx-64

I followed the instructions from ITSxpress GitHub.

After installation, I ran the following command:

qiime itsxpress trim-pair-output-unmerged \
  --i-per-sample-sequences paired-end-demux.qza \
  --p-region ITS2 \
  --p-taxa F \
  --o-trimmed trimmed.qza \
  --p-threads 12

However, I encountered the following error:

Fatal error: Unable to open file for writing (/var/folders/fj/vnpgdy7573bg5z6c3h7wfrd00000gn/T/itsxpress_jolf67tr/seq.fq)
Traceback (most recent call last):
  File "...", line 61, in _merge_reads
    p1.check_returncode()
  ...
subprocess.CalledProcessError: Command '['vsearch', '--fastq_mergepairs', ...]' returned non-zero exit status 1.

Debugging Steps

  1. I tested the plugin with a demultiplexed paired-end artifact containing only one sample, and it worked without errors.
  2. When I used an artifact containing two samples, I encountered the same error again.

Solution

After some testing, I decided to downgrade to ITSxpress 2.1.1 without reinstalling vsearch. The same command worked successfully with two samples (--p-threads 12) and multiple samples (--p-threads 20):

qiime itsxpress trim-pair-output-unmerged \
  --i-per-sample-sequences paired-end-demux.qza \
  --p-region ITS2 \
  --p-taxa F \
  --o-trimmed trimmed.qza \
  --p-threads 20

Summary

  • ITSxpress 2.1.3 seems to have an issue when processing artifacts with multiple samples.
  • Downgrading to ITSxpress 2.1.1 resolved the issue.

While downgrading to ITSxpress 2.1.1 resolves the issue, I’d like to know if there’s a fix that allows ITSxpress 2.1.3 to be installed without needing to remove the q2-fragment-insertion and sepp plugins. Any insights or suggestions would be greatly appreciated.

Thanks!

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