./fastqc This is the source distribution of FastQC. You need to get the compiled version if you want to run the program

[karthickbrlab]

./fastqc
This is the source distribution of FastQC. You need to get the compiled version if you want to run the program

[s-andrews]

You need to download the appropriate binary pacakge from the downloads page at:

https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc

You can then follow the installation instructions to install the program:

https://github.com/s-andrews/FastQC/blob/master/INSTALL.md

It looks like you downloaded the java source code from either the project page or the github repository, which will give this error if you try to run the launch script from that package.