mothur

Chimera.vsearch (error: correct segmentation fault)

#1

Hi,
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,
Ajay

#2

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

#3

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,

Thanks,
Ajay

#4

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, https://github.com/mothur/mothur/releases/tag/v.1.41.1.

#5

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

Thanks,
Ajay

#6

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

#7

Could you send your input files to mothur.bugs@gmail.com?

#8

Did this problem get resolved? I’m running v1.41.1 with the MiSeq_SOP data following the tutorial commands exactly, and I get the same error using the command:

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)

Here is the start of the errors for items missing from the count table:

[ERROR]: M00967_43_000000000-A3JHG_1_1108_21757_2509 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_2107_5623_1741 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_1108_23117_1744 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_1112_23716_1885 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_1114_28335_1017 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_1101_14287_1231 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_1101_18615_1103 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_2113_15153_658 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_1112_4269_1548 is not in your count table. Please correct.
[ERROR]: M00967_43_000000000-A3JHG_1_1108_12142_2550 is not in your count table. Please correct.

#9

I just updated to v1.41.3 and I am still getting the same error.

#10

I’m getting the same problem.
I’m running mothur using the version 1.40.3. I’ll update for version 1.41.1, but as I saw that some of you got the same problem even with the update.
Does anyone has new insights bout the problem?
I appreciate any help.
Thanks,
Mariana.

#11

I need some help with this as well… I’m using version 1.41.0 and the tutorial:(https://www.mothur.org/wiki/MiSeq_SOP#Preparing_for_analysis) and downloaded the example files from the three links within it:
Example data from Schloss lab
SILVA-based bacterial reference alignment
mothur-formatted version of the RDP training set (v.9)

I’m happy to provide more details if that will help uncover what’s wrong.

#12

This could be the vsearch version. Vsearch changed their output string for the sequence names in newer versions. This was causing bugs with mothur for people who updated their version of vsearch. For version 1.42 and after mothur will be compatible with vsearch version 2.11.1, https://github.com/torognes/vsearch/releases/tag/v2.11.1. For mothur versions before 1.42, you will need vsearch version 2.3.4, https://github.com/torognes/vsearch/releases/tag/v2.3.4.

#13

I downloaded vsearch version 2.3.4. It went a little farther with that, but the chimera.vsearch is now reporting an error about a fastafile:

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 8 processors.
Checking sequences from stability.trim.contigs.good.unique.good.filter.unique.precluster.fasta …
sh: /home/XXX/modulefilesMothur/vsearch-2.3.4/vsearch: Is a directory
Error in reading your fastafile, at position -1. Blank name.

(I replaced part of the filepath with XXX.)

#14

It looks like mothur is not finding the vsearch executable program, but instead is finding a directory named vsearch from your path. Is the vsearch executable located within the vsearch directory? If so, are you able to put it into a location mothur can find it? For example, could you put it in the mothur directory? Or could you put it in /home/XXX/modulefilesMothur/vsearch-2.3.4 directory and remove the vsearch directory from /home/XXX/modulefilesMothur/vsearch-2.3.4/? In version 1.42.0 you can set a specific location for vsearch using the vsearch parameter as follows:

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, vsearch=/home/XXX/modulefilesMothur/vsearch-2.3.4/vsearch/vsearch)

If you want to try out our beta version of 1.42, you can find it here, https://github.com/mothur/mothur/releases/tag/v1.42.0_Beta_Release.