FastQC wont run

Question

[anna]

Hi I've downloaded the most recent FASTQC windows/linux zip file, unzipped it and tried to run the program by clicking the bat file. This opens the cmd for 0,5 s and then closes it again before I even have time to see the error message. Any idea what's gone wrong? I can get the program to run by putting it on a USB stick and clicking the bat file, but this is not convenient at all. I'm running windows.

Please help?

[GenoMax]

Can you try opening a windows command line shell and then running the batch file on the command prompt to see if you are able to observe the error message (if there is one).

[Mensur Dlakic]

Most likely there is no error message - the program is simply printing out its options and closing the window before you can read anything. Like genomax suggested: open a command line prompt, go to the directory where the program (or batch script) is located, and run it by typing the command rather than double-clicking.

Answer 1

[hugo.avila]

Hi, maybe try use it through a conda environment.

1)Install miniconda (or Anaconda): https://docs.conda.io/en/latest/miniconda.html 2) Once miniconda (or Anaconda) is set and is on PATH, go into the conda shell and type: conda create -n fastqc_env -c bioconda fastqc --yes

Installing and using fastqc inside conda may seens like a additional job but once conda is installed it becames a vary useful tool to avoid issues setting up programs.