fastqc not found Nanopreprocess

Question

fastqc not found Nanopreprocess

samir-watson opened this issue 4 years ago · 9 comments

samir-watson commented 4 years ago

Hi,

I am getting the following error when I try run NanoPreprocess:
.command.sh: line 2: fastqc: command not found

I have fastqc installed in the conda environment Im working with so im not sure what could be the problem.

Thanks

Answer 1 · 2020-09-04T12:21:39.000Z

Hi, we don't recommend using master of pores without containers. You can use singularity with -with-singularity

Answer 2 · 2020-09-08T08:40:32.000Z

Hi,
I tried to run it without conda and just using singularity but I keep getting the same error. It seems there may be an issue with the singularity. I'll keep you updated if I get it to work. Do you have any suggestions on things to try to resolve this?

Answer 3 · 2020-09-08T08:49:44.000Z

This is quite strange. Can you verify if the singularity image is there and you can run it?

Answer 4 · 2020-09-08T09:08:29.000Z

Yes, I have two singularity images in the singularity directory When I run the mopprepr image and call fastqc I get the following output [cid:image001.png@01D685D0.5BD5AC30] From: Luca Cozzuto <notifications@github.com> Sent: 08 September 2020 10:50 To: biocorecrg/master_of_pores <master_of_pores@noreply.github.com> Cc: Samir Watson <samirwatson@mbg.au.dk>; Author <author@noreply.github.com> Subject: Re: [biocorecrg/master_of_pores] fastqc not found Nanopreprocess (#74) This is quite strange. Can you verify if the singularity image is there and you can run it? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#74 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APC6XXRAUPGK3IN6JK6GKZ3SEXV3PANCNFSM4QYHJ7TQ>.

Answer 5 · 2020-09-08T09:09:44.000Z

I cannot see sorry :(

Answer 6 · 2020-09-08T09:10:03.000Z

PS: which version of singularity are you using?

Answer 7 · 2020-09-08T09:35:26.000Z

Im using version 3.5.2-1.1.e17 This is the message when I run fastqc in the singularity (base) [samirwatson@fe1 singularity]$ ls biocorecrg-mopbasecall-0.1.img biocorecrg-mopprepr-0.6.img (base) [samirwatson@fe1 singularity]$ singularity run biocorecrg-mopprepr-0.6.img Singularity> fastqc Exception in thread "main" java.awt.HeadlessException: No X11 DISPLAY variable was set, but this program performed an operation which requires it. at java.desktop/java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:208) at java.desktop/java.awt.Window.<init>(Window.java:548) at java.desktop/java.awt.Frame.<init>(Frame.java:423) at java.desktop/java.awt.Frame.<init>(Frame.java:388) at java.desktop/javax.swing.JFrame.<init>(JFrame.java:180) at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63) at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:338) From: Luca Cozzuto <notifications@github.com> Sent: 08 September 2020 11:10 To: biocorecrg/master_of_pores <master_of_pores@noreply.github.com> Cc: Samir Watson <samirwatson@mbg.au.dk>; Author <author@noreply.github.com> Subject: Re: [biocorecrg/master_of_pores] fastqc not found Nanopreprocess (#74) PS: which versiom mof singularity are you using? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#74 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/APC6XXWPOT76U6HAU35HZN3SEXYHXANCNFSM4QYHJ7TQ>.

Answer 8 · 2020-09-08T09:40:13.000Z

It looks like is working (you should use fastqc -h or it will try to open a graphical pop up. We however use version 3.2.1 since the newer had some strange behavior.

Answer 9 · 2020-10-13T10:36:04.000Z

Hi, can we consider closed this issue?