Fastqc error message

Question

[mariemh23]

Hello,

I work on Mac OS Sierra. I have downloaded Fastqc tool. It works correctly when I use it interactively but when I try to use it with command line, it shows me this error message : impossible de trouver ou charger la classe principale uk.ac.babraham.FastQC.FastQCApplication .

Any ideas. Thank you

[PoGibas]

Post command that you tried.

[mariemh23]

Hi,

I just typed on my terminal fastqc

[Pierre Lindenbaum]

I just typed on my terminal fastqc

show us exactly what you typed, including the linux prompt and the error message. And switch your message s to english

export LANG=en_US.UTF-8

[mariemh23]

sh-3.2# fastqc
Error: Could not find or load main class uk.ac.babraham.FastQC.FastQCApplication

[GenoMax]

You did not move any of the contents of fastqc folder after you downloaded and uncompressed the file?

[mariemh23]

No, i just download the source code and i unzipped it into my download directory.

I have just realized that when I type fastqc -h it shows me this Sh-3.2 # fastqc -h

             FastQC - A high throughput sequence QC analysis tool

SYNOPSIS

Fastqc seqfile1 seqfile2 .. seqfileN

     Fastqc [-o output dir] [- (no) extract] [-f fastq | bam | sam]             [-c contaminant file] seqfile1 .. seqfileN etc

However, when I type a command line like this

Sh-3.2 # fastqc - / Users / mariemh / Desktop / accriditation \ h3A / data / Dog10_R1.fastq.txt -o / Users / mariemh / Desktop / Error: Could not find or load main class uk.ac.babraham.FastQC.FastQCApplication

Answer 1

[eug]

Do you use bioconda's fastqc? It'll help to remove additional channels (not default and bioconda) and reinstall fastqc:

conda config --get channels
conda config --remove channels 'conda-forge'
conda install -n env_name -c bioconda fastqc==0.11.5