Chimera.vsearch (error: correct segmentation fault)


I am working on Metagenome analysis using Mothur. I am very naive to this tool… and processing the data with example data-sets as mentioned in the tutorial
Everything was going fine as mentioned in the tutorial until I got stuck at chimera.vsearch command.

Using ReadLine,Boost,HDF5
mothur v.1.41.0
Last updated: 11/13/18

mothur > chimera.vsearch(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta, count=stability.trim.contigs.good.unique.good.filter.unique.precluster.count_table, dereplicate=t)

Using 88 processors.
Checking sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
[ERROR]: M00967_43_000000000-A3JHG_1_1114_15978_19655 is not in your count table. Please correct.
Segmentation fault (core dumped)

I am getting the above error.
I have not changed a single thing in the files… just going line by line as in tutorial,
Kindly let me know… where I went wrong!!

Thank you,


You are not probably use the last count_table file you created.


Hi Mariscuba,
Thanks for the reply,
I am going through the tutorial only, I have not changed file names or anything and using the last count_table file.
But the error still persist,



We had a small bug in the pre.cluster command when using a count file that was causing downstream commands to have a mismatch. It has been fixed and the change is part of 1.41.1 released today,


Hi westcott,
Thanks for the update, I will check and let you know if it is working fine!



Hi westcott, I have the exactly same problem with the latest version 1.41.1. Could you help me?


Could you send your input files to