Opening mothur in slurm?

Hi, this is my first post so please tell me if I am not formatting my post correctly! I am trying to open mothur in slurm in interactive mode but it hasn’t been working. Does anyone know how to resolve this? I have looked through this form/googled/played around with various commands but nothing has worked.

This is basically what I have done:

used the shebang

[elgard@gl-login1 ~]$ #!/bin/bash

set my working directory:

[elgard@gl-login1 ~]$ cd 20230405_p005_testing_pestle_data_analysis_v1

checked to make sure mothur is in there using ls (it is, but I don’t want to put the readout). Then I try to load mothur and it does not work:

[elgard@gl-login1 20230405_p005_testing_pestle_data_analysis_v1]$ module load mothur/1.48.0
Lmod has detected the following error:  These module(s) or extension(s) exist but cannot be loaded as requested: "mothur/1.48.0"
   Try: "module spider mothur/1.48.0" to see how to load the module(s).

so then as the command prompt suggests I try that and this is all that comes out:

---------------------------------------------------------------------------------------------------------------------------------------------------------
  mothur: mothur/1.48.0
---------------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      The goal of mothur is to have a single resource to analyze molecular data that is used by microbial ecologists.


    You will need to load all module(s) on any one of the lines below before the "mothur/1.48.0" module is available to load.

      Bioinformatics

    Help:
      The goal of mothur is to have a single resource to analyze molecular
      data that is used by microbial ecologists. Many of these tools are
      available elsewhere as individual programs and as scripts, which tend
      to be slow or as web utilities, which limit your ability to analyze
      your data. mothur offers the ability to go from raw sequences to the
      generation of visualization tools to describe α and β diversity.
      Examples of each command are provided within their specific pages,
      but several users have provided several analysis examples, which use
      these commands. An exhaustive list of the commands found in mothur is
      available within the commands category index.

So it says “You will need to load all module(s) on any one of the lines below before the “mothur/1.48.0” module is available to load.” but I don’t know what that means?

Some variations I have tried:

  • tried this while I had opened up a job using salloc and got the same responses
  • tried writing mothur.exe but then it says it is “unable to find” that

Some other notes:

  • when I use the module avail command, mothur doesn’t show up at all in the list
  • My host server is sftp://greatlakes-xfer.arc-ts.umich.edu

Thank you very much!

Hi - I’d encourage you to reach out to ARC-TS. I don’t actually use their module system and instead use conda to keep track of software and versions for my projects. Also, that shebang line needs to be at the top of you bash script and not entered directly at the command prompt.

Pat

This topic was automatically closed 10 days after the last reply. New replies are no longer allowed.