Question: Cannot run FASTQC on terminal
0
gravatar for fatin nadhirah
16 months ago by
fatin nadhirah0 wrote:

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

fastqc module • 3.4k views
ADD COMMENTlink modified 3 months ago by whadgar0 • written 16 months ago by fatin nadhirah0
1

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

ADD REPLYlink written 16 months ago by Bastien Hervé4.4k
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
ADD REPLYlink modified 16 months ago by WouterDeCoster40k • written 16 months ago by fatin nadhirah0
1

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)

ADD REPLYlink modified 16 months ago • written 16 months ago by Bastien Hervé4.4k

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ADD REPLYlink written 16 months ago by WouterDeCoster40k

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

ADD REPLYlink written 16 months ago by lieven.sterck5.8k

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

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

ADD REPLYlink written 16 months ago by fatin nadhirah0
1

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

ADD REPLYlink modified 16 months ago • written 16 months ago by lieven.sterck5.8k
0
gravatar for whadgar
3 months ago by
whadgar0
whadgar0 wrote:

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

ADD COMMENTlink written 3 months ago by whadgar0
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