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Cannot run stringtie

Hi, I am new to bioinformatics so I am trying now to complete an RNAseq procedure descriped in the famoust Salzberg paper..

I am using a cluster to run all these programs so I just load modules...

I am on a stringtie step and when I am trying to run my script I have that kind of error:

-------------------------------------------------------
  stringtie: stringtie/2.0
-------------------------------------------------------
    Description:
      StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

    Properties:
      Bioinformatic libraries/apps / Logiciels de bioinformatique

    You will need to load all module(s) on any one of the lines below before the "stringtie/2.0" module is available to load.

      nixpkgs/16.09  gcc/5.4.0
      nixpkgs/16.09  gcc/7.3.0

This is my script and I don't understand why it's not running stringtie

#!/bin/bash

module load nixpkgs/16.09  gcc/5.4.0
module load nixpkgs/16.09  gcc/7.3.0

# below are modules I had to run for hisat2
module load nixpkgs/16.09  intel/2018.3

module spider stringtie/2.0

Can anyone please help to understand what is the problem?

Thank you very much!

rna-seq
• 2,704 views • link
written by mark.pekarsky • mark.pekarsky

What exactly is not working? btw, you should use module load stringtie/2.0 to load it

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written by Asaf Asaf 
Lmod is automatically replacing "intel/2016.4" with "gcc/5.4.0".


Due to MODULEPATH changes, the following have been reloaded:
  1) openmpi/2.1.1


Due to MODULEPATH changes, the following have been reloaded:
  1) openmpi/2.1.1

The following have been reloaded with a version change:
  1) gcc/5.4.0 => gcc/7.3.0     2) gcccore/.5.4.0 => gcccore/.7.3.0


Lmod is automatically replacing "gcc/7.3.0" with "intel/2018.3".


Inactive Modules:
  1) openmpi/2.1.1

The following have been reloaded with a version change:
  1) icc/.2016.4.258 => icc/.2018.3.222     2) ifort/.2016.4.258 => ifort/.2018.3.222     3) imkl/11.3.4.258 => imkl/2018.3.222

Lmod has detected the following error:  These module(s) exist but cannot be loaded as requested: "stringtie/2.0"
   Try: "module spider stringtie/2.0" to see how to load the module(s).

./stringtie_single_mitya.sh: line 19: stringtie: command not found

Thank you. That is what's happening... stringtie is not loaded

Lmod is automatically replacing "intel/2016.4" with "gcc/5.4.0".


Due to MODULEPATH changes, the following have been reloaded:
  1) openmpi/2.1.1


Due to MODULEPATH changes, the following have been reloaded:
  1) openmpi/2.1.1

The following have been reloaded with a version change:
  1) gcc/5.4.0 => gcc/7.3.0     2) gcccore/.5.4.0 => gcccore/.7.3.0


Lmod is automatically replacing "gcc/7.3.0" with "intel/2018.3".


Inactive Modules:
  1) openmpi/2.1.1

The following have been reloaded with a version change:
  1) icc/.2016.4.258 => icc/.2018.3.222     2) ifort/.2016.4.258 => ifort/.2018.3.222     3) imkl/11.3.4.258 => imkl/2018.3.222


--------------------------------------------------------------------------------------------------------------------------------------------------------------------
  stringtie: stringtie/2.0
--------------------------------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.

    Properties:
      Bioinformatic libraries/apps / Logiciels de bioinformatique

    You will need to load all module(s) on any one of the lines below before the "stringtie/2.0" module is available to load.

      nixpkgs/16.09  gcc/5.4.0
      nixpkgs/16.09  gcc/7.3.0

    Help:

      Description
      ===========
      StringTie is a fast and highly efficient assembler of RNA-Seq alignments
       into potential transcripts.


      More information
      ================
       - Homepage: http://ccb.jhu.edu/software/stringtie/





./stringtie_single_mitya.sh: line 20: stringtie: command not found

and this is what's happening when load spider command is used

• 0 views • link
written by mark.pekarsky • mark.pekarsky

Please don't post screenshot, but copy the output and errors. Images are not indexed by search engines like text is, and these are not readable on my phone.

• 0 views • link
written by WouterDeCoster WouterDeCoster

This looks like an issue for your Systems Administrator, not us.

• 0 views • link
written by Kevin Blighe Kevin Blighe

1 answer

I have the answer now - it was all due to the version, I needed to use the v1.3.4 release.

The problem is solved now.

Thanks to all contributors.

• 0 views • link
written by mark.pekarsky • mark.pekarsky

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