Fatal error: Illegal option argument when running Barque

[nanthony80]

Hi there,

I'm new to metabarcoding eDNA analysis and coding in general. I'm trying to run the Barque pipeline (https://github.com/enormandeau/barque) and it keeps failing when running the vsearch step on each sample. The version I'm using is vsearch v2.29.2_macos_x86_64.

Here's an example error message:

Running vsearch on SRR31057074_merged_tele02_nonchimeras.fasta.gz_unique.fasta.gz with database tele02_dec24.fasta.gz
Fatal error: Illegal option argument
done

My research partner can run the pipeline successfully with the latest vsearch version for linux.

If you have suggestions for how to fix this issue on a Mac (i7), I would greatly appreciate any advice.

Many thanks,
Nicole

[enormandeau]

Hi Nicole,

I never heard of such an error. Would it be possible for you to try other vsearch versions? Otherwise, I'd suggest modifying the program so that it prints the command instead of executing it and then stop it with exit to see what the command looks like.

This could potentially be due to recent changes in the Mac version of vsearch but it seems less likely.

If it is a possibility, you could send a complete copy of your barque folder (maybe with only 4-8 samples) so I could test it on my side. If you do this, please send your whole folder that produced the error AS IS minor some samples.

You can share a link to the data with me at eric [dot] normandeau [at] bio [dot] ulaval [dot] ca.

Take care