Hello,
I am new to next gen sequencing analysis. I wanted to perform chimera.vsearch command but it says invalid command
So i went and downloaded the vsearch git file to the desktop and installed it…
still mothur shows error: invalid command…
I would appreciate any help on how to overcome this problem. thank you
Thank you
Naren
vast majority of command not found errors are due to a typo. Check your spelling/caps
If it’s not a typo error, it could also be that you have an old version of mothur. chimera.vsearch is a pretty new command.
Hello dear all,
I am using the last version in Mac, and it also did not run vsearch for the chimera check.
chimera.vsearch(fasta=16S_wAMLR.trim.contigs.pcr.good.unique.good.filter.unique.precluster.fasta, count=16S_wAMLR.trim.contigs.pcr.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)
Just wanted to add information about the topic in case something might be going wrong.
Hope helps,
Carla
Is the vsearch executable in the same location as mothur or included in your PATH? Could you have an older version of mothur in your PATH? Could you post the exact error message?