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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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running on cluster Slurm #356

Closed ahmedabbas81 closed 3 years ago

ahmedabbas81 commented 4 years ago

Hello,

I am trying to run on slurm

However it produces two .sh files and ask to run them using qsub (not sbatch although I am running on slurm)

and when using sbatch HiCPro_step1_.sh , it says sbatch command not found. And also when trying qsub HiCPro_step1_.sh, it says qsub command not found.

Any suggestions

Thank you

ahmedabbas81 commented 4 years ago

It is worth noting that I am using singularity

nservant commented 4 years ago

Hi I not sure to understand why the sbatch command is not working. How do you submit jobs on your cluster ? Or how are you using singularity ?

I never really try singularity with the parallel mode ... I guess you migth need to update the .sh file to call singularity within these files ... I can try to take time to make additional tests. N