Chimera.vsearch /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21’ not found

mothur bugs
1

Hello,

First of all thank you for providing this great resource and for having such great forums/documentation that have helped me through previous blips that have come up while using Mothur.

The issue I’m having is very similar to that found here. However unlike the solution for that problem, when I installed different versions of Mothur ensuring that they matched my OS I still had the same errors. So to break it down:

My machine:
I’m working on Umich’s Greatlakes server. Specifically their OS currently is:
NAME=“CentOS Linux”
VERSION=“7 (Core)”
ID=“centos”
ID_LIKE=“rhel fedora”
VERSION_ID=“7”
PRETTY_NAME=“CentOS Linux 7 (Core)”
ANSI_COLOR=“0;31”
CPE_NAME=“cpe:/o:centos:centos:7”
HOME_URL="https://…
BUG_REPORT_URL="https://…

CENTOS_MANTISBT_PROJECT=“CentOS-7”
CENTOS_MANTISBT_PROJECT_VERSION=“7”
REDHAT_SUPPORT_PRODUCT=“centos”
REDHAT_SUPPORT_PRODUCT_VERSION=“7”

My version of Mothur:
Linux version

Using Boost,HDF5,GSL
mothur v.1.45.2
Last updated: 4/9/21
by
Patrick D. Schloss

Department of Microbiology & Immunology

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type ‘help()’ for information on the commands that are available

Type ‘quit()’ to exit program

NOTE: Setting random seed to 19760620.

Interactive Mode

The command I’m running:
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 I’m getting:
/mydir/mothur//vsearch: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21’ not found (required by /mydir/mothur//vsearch)
Error in reading your fastafile, at position -1. Blank name.
It took 0 secs to check 0 sequences.

Removing group: 513 because all sequences have been removed.
Removing group: 513_1 because all sequences have been removed.
Removing group: 513_2 because all sequences have been removed.
Removing group: 513_2S because all sequences have been removed.
Removing group: 513_3 because all sequences have been removed.
Removing group: 513_3S because all sequences have been removed.
Removing group: 513_4 because all sequences have been removed.
Removing group: 513_4S because all sequences have been removed.
Removing group: 514 because all sequences have been removed.
Removing group: 514_1 because all sequences have been removed.
Removing group: 514_2 because all sequences have been removed.
Removing group: 514_2S because all sequences have been removed.
Removing group: 514_3 because all sequences have been removed.
Removing group: 514_3S because all sequences have been removed.
Removing group: 514_4 because all sequences have been removed.
Removing group: 514_4S because all sequences have been removed.
Removing group: 515 because all sequences have been removed.
Removing group: 515_1 because all sequences have been removed.
Removing group: 515_2 because all sequences have been removed.
Removing group: 515_2S because all sequences have been removed.
Removing group: 515_3 because all sequences have been removed.
Removing group: 515_3S because all sequences have been removed.
Removing group: 515_4 because all sequences have been removed.
Removing group: 515_4S because all sequences have been removed.
Removing group: 516 because all sequences have been removed.
Removing group: 516_1 because all sequences have been removed.
Removing group: 517 because all sequences have been removed.
Removing group: 517_2 because all sequences have been removed.
Removing group: 517_3 because all sequences have been removed.
Removing group: 517_3S because all sequences have been removed.
Removing group: 517_4 because all sequences have been removed.
Removing group: 517_4S because all sequences have been removed.
Removing group: 517_5 because all sequences have been removed.
Removing group: 517_5S because all sequences have been removed.
Removing group: 518 because all sequences have been removed.
Removing group: 518_4 because all sequences have been removed.
Removing group: 518_4S because all sequences have been removed.
Removing group: 519 because all sequences have been removed.
Removing group: 519_1 because all sequences have been removed.
Removing group: 519_3 because all sequences have been removed.
Removing group: 519_3S because all sequences have been removed.

What I’ve tried so far:
I’ve deleted my existing mothur and reinstalled Mothur.linux_7.zip and Mothur.linux_7_noReadline.zip for version 1.45.3 without luck. I also tried the version 1.45.2 referenced in the previous forum post linked above.

Any advice would be greatly appreciated!
All the best,
Ryan

2

As the error indicated this was a problem with the C library of the HPC I was using. The great staff @ UM’s greatlakes notified me that there actually is a Mothur module on the HPC which I simply switched to. Unsurprisingly this worked perfectly and I had no further problems with Mothur’s chimera.vsearch. In case anyone else runs into simiilar compiler issues in the future I have included the response from the support staff with the intent to help trouble shoot my issue:

"Generally missing library errors are due to not having the same compiler module loaded as the program was compiled with. The default complier on Greatlakes is gcc/4.8.5, which does not have GLIBCXX_3.4.21 in it, you will want to use gcc/8.2.0 or gcc/9.2.0 when compiling (you will need. Did you compile mothur on Greatlakes, or did you just download the binary?

NOTE: There are 3 versions of mothur (1.42.1, 1.42.3, 1.43.0) already installed on Greatlakes, if one of them will work for you. (You will need to load the Bioinformatics in order to load the Bioinformatics module in order to load any of the mothur modules.)"

All the best,
Ryan

3

Hi Ryan - we’re up to version 1.45.3. I’d strongly recommend not using the older versions of mothur and using the new version instead. You might ask the greatlakes people to install that for you.

Pat

4

Will do Pat - thanks for putting out a great tool!

5

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