fastQC

papori · 02-02-2012, 06:43 AM

Hi,
i am trying to test my data quality by fastQC.
i have PE data.
When i execute this line:
./fastqc file.fastq

i am getting this warning:
...........
Approx 100% complete for file.fastq
Analysis complete for file.fastq
(.:922): Gtk-WARNING **: cannot open display:

and i am getting a corrupt zip file:
-rw-r--r--. 1 root root 6924 Feb 1 06:26 i-a_file.fastq.zip

Can anyone help??

B.R
pap

Bukowski · 02-02-2012, 08:18 AM

It's trying to launch the graphical interface to FastQC. Try specifying --outdir and setting an output directory, it should just write the files into there without launching the GUI.

Perhaps you are su'd into the root account? I wouldn't generally advise running any application as the root user by the way.

cahillcahill · 02-04-2012, 03:12 AM

A quality control tool for high throughput sequence data.
Language is Java

papori · 02-04-2012, 02:48 PM

i just had to upgrade my java to 1.6
Thanks!

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02-02-2012, 06:43 AM	#1
papori Senior Member Location: berd Join Date: Dec 2010 Posts: 181	fastQC Hi, i am trying to test my data quality by fastQC. i have PE data. When i execute this line: ./fastqc file.fastq i am getting this warning: ........... Approx 100% complete for file.fastq Analysis complete for file.fastq (.:922): Gtk-WARNING **: cannot open display: and i am getting a corrupt zip file: -rw-r--r--. 1 root root 6924 Feb 1 06:26 i-a_file.fastq.zip Can anyone help?? B.R pap

02-02-2012, 08:18 AM	#2
Bukowski Senior Member Location: UK Join Date: Jan 2010 Posts: 390	It's trying to launch the graphical interface to FastQC. Try specifying --outdir and setting an output directory, it should just write the files into there without launching the GUI. Perhaps you are su'd into the root account? I wouldn't generally advise running any application as the root user by the way. Last edited by Bukowski; 02-02-2012 at 08:21 AM.

02-04-2012, 03:12 AM	#3
cahillcahill Junior Member Location: UK Join Date: Feb 2012 Posts: 5	A quality control tool for high throughput sequence data. Language is Java

02-04-2012, 02:48 PM	#4
papori Senior Member Location: berd Join Date: Dec 2010 Posts: 181	i just had to upgrade my java to 1.6 Thanks!