Can't run fastqc in cmd windows

Question

[anasofiamoreira94]

Hi, I installed fastqc on windows from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. i can run it from the bat file, but I can not run it from command line. I continue to have this error: "'fastqc' is not recognized as an internal or external command,operable program or batch file.". Also, I added this variable to my windows path. Thanks

[GenoMax]

By opening a terminal window (Windows key --> Command Prompt). Are you referring to not having it pop open the GUI, which it does by default?

[anasofiamoreira94]

Of course, but when I do this, I get this error: "'fastqc' is not recognized as an internal or external command, operable program or batch file." I edited the post to clarify the issue.

Answer 1

[GenoMax]

Dir_with_FastQC>java -Xmx250m -classpath .;./sam-1.103.jar;./jbzip2-0.9.jar uk.ac.babraham.FastQC.FastQCApplication ju.fq
Started analysis of ju.fq
Analysis complete for ju.fq

In this case ju.fq is the file I am analyzing.

[anasofiamoreira94]

This worked, thank you so much.

[anasofiamoreira94]

I'm sorry to bother again, but now I'm calling FASTQC in python, like this: check_output('C:\FastQC>java -Xmx250m -classpath .;.\sam-1.103.jar;.\jbzip2-0.9.jar uk.ac.babraham.FastQC.FastQCApplication' + alt.fq, shell=True). And now I continue to get this error: 'C:\FastQC' is not recognized as an internal or external command,operable program or batch file. Thanks

[GenoMax]

Someone else will need to comment on python but note that my example above showed running the program from inside FastQC directory (generated after downloading and uncompressing the program). You could add that directory to your $PATH and see if that works. Something like

set PATH=%PATH%;C:\path_to\FastQC_dir

This part C:\FastQC> is just the windows terminal prompt so can't be included in your call.

[MarkiMark]

To deal with

"java.lang.outofmemoryerror thrown from the uncaughtexceptionhandler in thread"

I had to change "-Xmx250m" --> "-Xmx6144M" (from windows10 using the CLI)