Question: Cannot run stringtie
0
gravatar for mark.pekarsky
9 months ago by
mark.pekarsky20 wrote:

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 • 342 views
ADD COMMENTlink modified 8 months ago • written 9 months ago by mark.pekarsky20

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

ADD REPLYlink written 9 months ago by Asaf8.3k
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

ADD REPLYlink modified 9 months ago • written 9 months ago by mark.pekarsky20

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.

ADD REPLYlink written 9 months ago by WouterDeCoster44k

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

ADD REPLYlink modified 9 months ago • written 9 months ago by Kevin Blighe63k
1
gravatar for mark.pekarsky
8 months ago by
mark.pekarsky20 wrote:

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.

ADD COMMENTlink written 8 months ago by mark.pekarsky20
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