Issues running multiQC.

[pjaborges]

Hi,

I have been trying to run multiQC from the 4SeqGUI and also from the terminal but i am getting the following (see image) report.

I can see the command -> multiQC(group = group, data.folder = data.folder)
This is strange because I have specify the folder where the data is...

I am totally lost... maybe someone here can give me a hint.
A worth note is that I am relatively new on Linux and maybe I did something wrong while installing/config docker since I am a newbie on these matters.

Thanks in advance!
Paulo

[kendomaniac]

Hi Paulo,
you need to indicate in multiQC the top folder above the folders where single experiments are present.
Practically you need to have for each experiment a folder in which there are the fastq for the experiment, e.g. exp1, exp2, exp3.
These folder are placed in folder "my_experiment". multiQC function requires as input the full path to "my_experiment"

e.g. library(docker4seq)
multiQC(group="docker", data.folder="/home/user/userX/somewhereincomputer/my_experiment")
I hope it helps
Cheers
raf

[pjaborges]

Hi!

Thank you for your prompt response.

I think what I am experience is a bit more complex than that.

Somehow, seems like the command line is not passed correctly to the R console.

However, in the execution log seems to add the arguments correctly...

I also try to run directly from the console and the error is persistent.

Here is the directory structure where i have my fastq files.

Any idea what is happening? Already watch all the tutorials available ....
Help will be very much appreciated. :)

Cheers,
Paulo