Entering edit mode
4.4 years ago
mark.pekarsky
▴
20
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:
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stringtie: stringtie/2.0
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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!
What exactly is not working? btw, you should use
module load stringtie/2.0
to load itThank you. That is what's happening... stringtie is not loaded
and this is what's happening when
load spider
command is usedPlease 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.
This looks like an issue for your Systems Administrator, not us.