Cannot run FASTQC on terminal

Question

[fatin nadhirah]

1) Hi, Im using Mac OS and I'm having difficulty to run fastqc using terminal. It shows like this:

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

i've downloaded many time including the zip file. What should i do?

2) Another problem is the module command. I used "module load FastQC/0.11.2" and has error message like this: -bash: module: command not found

I really need your help. Tq

[Bastien Hervé]

Could you give us the link of your download and the command line you used please.

[fatin nadhirah]

Link: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip

Command line: mfrlab:raw.reads firdausraih$ ls
FastQC  QA  QC  Tophat  data
mfrlab:raw.reads firdausraih$ cd FastQC/
mfrlab:FastQC firdausraih$ ls
Configuration       README.txt      fastqc_icon.ico     run_fastqc.bat
Help            RELEASE_NOTES.txt   jbzip2-0.9.jar      sam-1.103.jar
INSTALL.txt     Templates       net         uk
LICENSE.txt     fastqc          org
mfrlab:FastQC firdausraih$ chmod 755 fastqc
mfrlab:FastQC firdausraih$ ./fastqc -help
This is the source distribution of FastQC.  You need to get the compiled version if you want to run the program
mfrlab:FastQC firdausraih$ ./fastqc
This is the source distribution of FastQC.  You need to get the compiled version if you want to run the program
mfrlab:FastQC firdausraih$ module load fastqc
-bash: module: command not found

[Bastien Hervé]

Did you follow these steps ? https://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt

OSX: On newer versions of OSX you need to install the Java Development Kit. The normal Java runtime environment IS NOT enough. To get this go to java.com, click "Free java download", then IGNORE the big red button, and select "See all java downloads", on the next screen select "Looking for the JDK?" from the left hand menu and select the link to "JDK downloads" in the first paragraph. You can then click the "Download" button underneath JDK in the page you are taken to. Sorry this is such a pain!

If you're on Mac OS you do not need a zip file but a DMG image

FastQC v0.11.7 (Mac DMG image)

[WouterDeCoster]

I added code markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

[lieven.sterck]

It seems like your first have to compile fastQc in your system.

Also the 'module' system will not be present if it has not been installed separately (this has nothing to do with FastQC itself though) and you don't actually need it to run FastQC

[fatin nadhirah]

How to compile? I don't really understand that part

And if i may ask, how to install 'module'?

[lieven.sterck]

Follow the instructions as indicated by Bastien Hervé , (it is not actually compiling the software but anyway).

I would personally not bother installing the whole module systems if you are running this on your own personal device. Just call FastQC directly

Answer 1

[whadgar]

Download the fastqc from https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.7.zip or from github once you download the zip file -> extract the zip (It will have the Configuration folder + fastqc : which gives compiled version error ) -> Then do sudo apt-get install fastqc -> When you type fastqc in terminal it will give JAVA FILE NOT FOUND EXCEPTION ( File not found in /etc/fastqc/Configuration ) -> Now the copy the Configuration folder from the extracted zip and paste it in the /etc/fastqc/ directory.

STEP 1 ) sudo apt-get install fastqc -> It will show the JAVA ERROR ( file not found in /etc/fastqc/Configuration ) STEP 2) Copy the files from Configuration folder from downloaded zip to /etc/fastqc