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
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/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
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_folderand even if I go into the preprocess folder, where I see the file, I get the same error.
I created a sh job I :
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