Segmentation faults using classify.otu (for non sudo) + how to properly install and maintain mothur for multiple users

mothur bugs
1

Dear,

I am currently running a very out-of-the box ubuntu server (14.04.4 LTS) on a 24-core 192GB RAM machine where I have installed Mothur 1.37.0 by cloning the mothur repo into /usr/local/[some folder] and then running make. Next I made symbolic links to mothur/uchime/vsearch in /usr/local/bin.
In this way I want to enable that all users can use this mothur version and don’t have to bother installing or compiling their own. Also, the whole lab works with the same version of mothur at a given time.

However, recently, some of the users reported segmentation faults using classify.otu on larger (80 samples) MiSeq-generated datasets. The funny thing is, when I run the command as sudo, these faults are not occurring.

So I don’t really know whether this qualifies as a bug or an installation issue though I would like to upgrade to the latest release (1.37.6) and install it for all users on this machine. My current approach would be to commit local changes, pull the repo again and deal with conflicts, edit the Makefile, make clean, and then sudo make . However, will this result again in segfaults for non-sudo users? Is this the correct approach?

Kind regards,

FM

ps: should this be reported rather as a github issue or here on the forum?

2

Hmm… I am not sure why sudo would make a difference, but we did have a bug in the classify.otu command that is corrected in version 1.37.6. If the taxonomy file contained float bootstrap values the command would fail. Perhaps for some datasets you are running into this issue? You can post issues here or email them to mothur.bugs@gmail.com.

3

Hi Sarah,

Thanks for the quick reply.
The datasets are not mine, though I am trying to manage the system for many users (by lack of a dedicated sysadmin). Maybe I could update mothur to 1.37.6 and ask the users to run the code again to see if issues are resolved, I think this will be easier than getting the data from them and forwarding it to you.
My only questions is how to update mothur properly from github? Is there some kind of “flowchart”?
I am not a github/linux NOOB though not an experienced user either but I would very much like to learn.
My current idea of a flowchart is something like below, in usr/local/[programs]/mothur, which would mean I don’t need to change the symbolic links in /usr/local/bin:

git commit -a -m “commit message”

commit local changes (e.g. makefile changes to compile under unix rather than mac, removed at the 1.37 commit )
* ```text
git pull
  • fix any merge conflicts (e.g. nano Makefile and remove conflicts)

git commit -a -m “fixed merge conflicts message”

local commit after resolving merge conflicts
* ```text
make clean

(only in main directory or also in source?)

make install

* get mothuring

On the sudo issue: it appears that also the same segfaults are occurring, though they are not reported (the resulting taxonomy & summary files are both incomplete). Hence indeed it was probably occuring for all types of users.

Kind regards,

FM Kerckhof
4

If you don’t have mothur installed already, you would do something like this…

git clone git@github.com:mothur/mothur.git
cd mothur
make install

If it’s already installed you would do something like this…

cd mothur
git pull
make clean; make install

I wonder also whether you have multiple copies of mothur installed - one with bugs and one without. If you do which mothur you want to make sure that it is pointing to the correct version.

Pat

5

Thanks Pat,

That appears to work just fine.