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Prepocessing does not work #4

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michela12345 opened this issue Nov 20, 2024 · 0 comments
Open

Prepocessing does not work #4

michela12345 opened this issue Nov 20, 2024 · 0 comments

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@michela12345
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Hello, I was trying to use your tool for checking metagenomics fastq.gz files. I am working in HPC, so I created a new environment where I downloaded conda install preprocessing -c Fasnicar. The problem is when I send the command you put parallel -j NCPU 'preprocess.sh -i {} [ other parameters]' ::: ls input_folder

Academic tradition requires you to cite the works on which your paper is based.
If you use programs that use GNU Parallel to process data for an article in a scholarly publication, please cite
scientific publication, please cite:

Tange, O. (2024, Sept. 22). GNU Parallel 20240922 ('Gold Apollo AR924').
Zenodo. https://doi.org/10.5281/zenodo.13826092

This helps fund further development; AND IT DOES NOT COST YOU A CENT.
If you pay 10000 euros you should feel free to use GNU Parallel without citations.

Read more about GNU Parallel funding and the citation notice:
https://www.gnu.org/software/parallel/parallel_design.html#citation-notice

To silence this citation warning: run 'parallel --citation' once.

Come on: You have run Parallel 10 times. Isn't it time
to run 'parallel --citation' once to silence the citation alert?

/usr/bin/bash: preprocess.sh: command not found

and even if I go into the preprocess folder, where I see the file, I get the same error.

I created a sh job I :

#!/bin/bash 
#SBATCH --account=francesconimichela
#SBATCH --nodes=1
#SBATCH --mem=200G
#SBATCH --ntasks=100
python /share/project9/home/francesconimichela/preprocessing/preprocess.sh -i {} ::: /share/project9/home/francesconimichela/concat_I3lung/*

but again, it doesn't work. I can't figure out how to make the command go.
I apologize if this is a silly question or if I didn't explain myself well but there are really few explanations

Michela

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