Max Cluster RNAseq trouble

[Rebeca.Pac...@mdc-berlin.de]

Hi

 

I am trying to submit a job with the Pigx pipeline in the Max Cluster,  but It gives me an error (attached the .e file). I do “qlogin” and then submit the job with “qsub runscript.sh”.

Here I attached my error file, my script (runscript.sh), the settings and sample files.
I would appreciate any help.

 

Best regards,

Rebeca

[alex....@gmail.com]

Dear Rebecca, 

The problem might be that you are trying to run the pipeline as a job.
When you run the PiGx pipeline on the cluster by enabling 'submit-to-cluster: yes', the pipeline will submit the workflow steps as single jobs via "qsub". 

However, when you submit a job via "qsub", that job does not have access to the job scheduling engine, thus the pipeline fails with the error that the system does not support cluster submission.

The solution would be to execute your "runscript.sh" as a shell script on the interactive node (after "qlogin"), rather than submitting it as a job.

Best,

Alex

[Bora Uyar]

Hi Rebeca,

In your run script you have at line 6 starting with a dot. That command is not recognized.

Can you try to run the pipeline directly? 

pigx-rnaseq -s /fast/AG_Gotthardt/rpacheco/settings.yaml /fast/AG_Gotthardt/rpacheco/sample_sheet.csv

Can you also check if you have `qsub` in your interactive session with: which qsub 

Or you could just fix the line 6 that starts with a dot. 

Best,

Bora

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Dr. Bora Uyar
Bioinformatics Scientist
Bioinformatics and Omics Data Science
Max Delbrueck Center (MDC) for Molecular Medicine
The Berlin Institute for Medical Systems Biology (BIMSB): 
Hannoversche Str. 28, 10115 Berlin 
email: bora...@mdc-berlin.de
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[Bora Uyar]

So, you have "qsub" in the system but the command about the guix profile declaration is causing the issue. 

You should be able to run any command you want as long as you do it in the interactive mode.

After you login the cluster, you do "qrsh" and then you should be able to run the pipeline with the command I suggested. 

This is just to rule out the problem with the guix profile declaration.

Can you please just run the command I asked you and see if it works?

Also it would be great if you could reply to "all" so that other people on the pigx group can contribute to the discussion.

Maybe Ricardo could help with the guix profile declaration issue. 

Best,

Bora

 

On Mon, Feb 20, 2023 at 10:16 AM Rebeca.Pac...@mdc-berlin.de <Rebeca.Pac...@mdc-berlin.de> wrote:

Hi Bora

 

I tried removing the dot but it didn’t work. Also I checked other scripts to see how I declare my guix profile and all of them contains the dot.

 

I can not run directly the lines because some cluster policies, I just can run it in a shell script.

 

Finally, when I run which qsub I obtain:

 

Thank you very much for your help! I hope we could find a solution.

 

Best regards,

Rebeca

[Alexander Blume]

Dear Rebecca,

When inspecting the contents of my ~/.guix-profile/etc/profile it says: 

```

# Source this file to define all the relevant environment variables in Bash

# for this profile.  You may want to define the 'GUIX_PROFILE' environment

# variable to point to the "visible" name of the profile, like this:

#

#  GUIX_PROFILE=/path/to/profile ; \

#  source /path/to/profile/etc/profile

#

# When GUIX_PROFILE is undefined, the various environment variables refer

# to this specific profile generation.

```

So to be on the safe side you may want to replace your command to load your environment.

Also, I wonder if you did receive my previous answer to the pigx mailing list, thus I will just include it again:

The problem might be that you are trying to run the pipeline as a job. 
When you run the PiGx pipeline on the cluster by enabling 'submit-to-cluster: yes', the pipeline will submit the workflow steps as single jobs via "qsub". 

However, when you submit a job via "qsub", that job does not have access to the job scheduling engine, thus the pipeline fails with the error that the system does not support cluster submission.

The solution would be to execute your "runscript.sh" as a shell script on the interactive node (after "qlogin"), rather than submitting it as a job.

Best,

Alex

On 20. Feb 2023, at 10:50, Bora Uyar <borauy...@gmail.com> wrote:

So, you have "qsub" in the system but the command about the guix profile declaration is causing the issue. 

You should be able to run any command you want as long as you do it in the interactive mode.

After you login the cluster, you do "qrsh" and then you should be able to run the pipeline with the command I suggested. 

This is just to rule out the problem with the guix profile declaration.

Can you please just run the command I asked you and see if it works?

Also it would be great if you could reply to "all" so that other people on the pigx group can contribute to the discussion.

Maybe Ricardo could help with the guix profile declaration issue. 

Best,

Bora

 

On Mon, Feb 20, 2023 at 10:16 AM Rebeca.Pac...@mdc-berlin.de <Rebeca.Pac...@mdc-berlin.de> wrote:

Hi Bora

 

I tried removing the dot but it didn’t work. Also I checked other scripts to see how I declare my guix profile and all of them contains the dot.

 

I can not run directly the lines because some cluster policies, I just can run it in a shell script.

 

Finally, when I run which qsub I obtain:

<image001.png>

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