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Old 02-02-2012, 06:43 AM   #1
papori
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Location: berd

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Default 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
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Old 02-02-2012, 08:18 AM   #2
Bukowski
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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.
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Old 02-04-2012, 03:12 AM   #3
cahillcahill
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A quality control tool for high throughput sequence data.
Language is Java
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Old 02-04-2012, 02:48 PM   #4
papori
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Default

i just had to upgrade my java to 1.6
Thanks!
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