Entering edit mode
8.0 years ago
Arash
▴
30
I have latest version of Fastqc and java environment. Fastqc file does not open the program and when I run it from terminal it makes only a zip file and not the html report. zip file is also always broken and "An error occurred while loading the archive".
Dear Arash, Hi
You have downloaded the FastQC version 0.11.5 and set the correct permission for it (using
chmod 755 fastqc) and then run./fastqcbut you don't had it's GUI ?What is your OS ?
Dear Farbod,
yes, i have downloaded the last version and have the following problom. My OS is ubunto/Linux
TNX
What OS are you using on your local machine? You need to have a separate X-windows program (on Windows, if that is your desktop OS) to see graphical output directly coming from the server.
By the way: You don't need a GUI to run fastqc. You can just do
fastqc your_seq.fq.gz -o .. That should run fastqc and put the result files (-ooption) in current directory. You can then download the html file to your local windows desktop and view with a regular browser.Hi, I run fastqc on ubunto according your command ,but after having the result in -o , i got "An error occurred while loading the archive" when i did click on it
Are you directly logged into the ubuntu machine (on console) or are you using a windows desktop to SSH into the server remotely?
fastqc is working and produce the out put, but when i click on the results, i got the following message
If an html file has been produced then see my answer above to view it on local Windows desktop.
the file format in in zip format
fastqc should produce two files. Something line
sample.htmlandsample.zip. One is a self contained html version that can be viewed standalone. The corresponding zip file contains the data that was used to make the html file. It is there in case you wish to plot etc using a different program.i just got sample.zip
How did you run the command?
fastqc seq.fq.gz -o
Based on my fastqc installation (FastQC v0.11.3) that command doesn't make sense. Assuming you want to run fastqc on the command line and not interactively, you should run
fastqc --helpand read how you should execute the program.If you are using
-ooption then tellfastqcthe name of the directory where you want to save the output e.g.-o /path_to/dir. If you want to use the current directory no need to use the-ooption.