mothur

MacOS vs. Ubuntu issue

I recently was running through the MiSeq SOP on a Mac (version 10.14.6) and Ubuntu. I download the same test data from mothur.org, and the latest mothur release for either MacOS (Mothur.OSX-10.14.zip) or Ubuntu. (Mothur.Ubuntu_20.zip) from github. All went completely moothly when running the code in Ubuntu but have run into an error when working oni the Mac. Specifically, when I run this line:
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)

The error that I receive is shown below. I am not sure what the issue is and would appreciate any advice you can give me on how to fix this.

PS I used this Mac during the workshop in December 2020, but it was a different mothur release (version 1.44.3). I didn’t encounter any issues then with the MiSeq SOP and example data on either a Mac or Ubuntu.

Thanks!

sh: /Users --uchim /Users: No such file or directory
Error in reading your fastafile, at position -1. Blank name.
It took 0 secs to check 0 sequences.

Removing group: F3D0 because all sequences have been removed.

Removing group: F3D1 because all sequences have been removed.

Removing group: F3D141 because all sequences have been removed.

Removing group: F3D142 because all sequences have been removed.

Removing group: F3D143 because all sequences have been removed.

Removing group: F3D144 because all sequences have been removed.

Removing group: F3D145 because all sequences have been removed.

Removing group: F3D146 because all sequences have been removed.

Removing group: F3D147 because all sequences have been removed.

Removing group: F3D148 because all sequences have been removed.

Removing group: F3D149 because all sequences have been removed.

Removing group: F3D150 because all sequences have been removed.

Removing group: F3D2 because all sequences have been removed.

Removing group: F3D3 because all sequences have been removed.

Removing group: F3D5 because all sequences have been removed.

Removing group: F3D6 because all sequences have been removed.

Removing group: F3D7 because all sequences have been removed.

Removing group: F3D8 because all sequences have been removed.

Removing group: F3D9 because all sequences have been removed.

Removing group: Mock because all sequences have been removed.

We found an error with the assembly of the parameters sent to the vsearch program. Could you try this version, Release Version 1.45.1 · mothur/mothur · GitHub?

I ran through the program with the test data, and all looks great (on the Mac). Thanks so much for your help!

I recently upgraded mothur and i also get a similar error running precluster (with ubuntu).

Linux version
Using Boost,HDF5,GSL
mothur v.1.45.3

after running precluster it says:

/usr/local/bin//vsearch: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.21’ not found (required by /usr/local/bin//vsearch)

Error in reading your fastafile, at position -1. Blank name.

It took 0 secs to check 0 sequences.

Removing group: sample1 because all sequences have been removed.

Removing group: sample2 because all sequences have been removed.

etc for all the samples.

i still have samples with sequences should i continue? or downgrade to a different version?

/usr/local/bin//vsearch: /usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.21’ not found (required by /usr/local/bin//vsearch)

Thanks for bringing this issue to our attention. This is an error message from the vsearch program.The chimera.vsearch command is a wrapper for the vsearch program. In recent versions we included a newer version of vsearch. The error indicates the vsearch executable was not built for use with your OS. You can download vsearch executables and source here, Release VSEARCH 2.17.1 · torognes/vsearch · GitHub.

Building from source is straightforward:

wget https://github.com/torognes/vsearch/archive/v2.17.1.tar.gz
tar xzf v2.17.1.tar.gz
cd vsearch-2.17.1
./autogen.sh
./configure
make
make install # as root or sudo make install

If you don’t have autoconf installed you will need to run the following first:

sudo apt-get update -y
sudo apt-get install -y autoconf

I will also build out a version of vsearch for Ubuntu 20 for our next release.

great, did that and i no longer get the error.

Thanks for the help