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NYU-BFX / hic-bench

A set of pipelines for Hi-C and ChIP-Seq analysis.
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qsub doesn't work #2

Closed quzhouxiachuan closed 7 years ago

quzhouxiachuan commented 8 years ago

Hi

When we ran pipeline-execute command. It popped up the following error. Our cluster doesn't use OGS/ Grid Engine 2011.11 as scheduler, we use PBS to schedule jobs and msub to submit jobs. Would this be the reason? if it is, how would you recommend to deal with this situation?

Thanks! 

_ydw529@quser12 project2]$ ./code.main/pipeline-execute project yudeng2015@u.northwestern.edu
[qsub: illegal -c value]

usage: qsub [-a date_time] [-A account_string] [-b secs]
    [-c [ none | { enabled | periodic | shutdown |
    depth=<int> | dir=<path> | interval=<minutes>}... ]
    [-C directive_prefix] [-d path] [-D path]
    [-e path] [-h] [-I] [-j oe|eo|n] [-k {oe}] [-l resource_list] [-m n|{abe}]
    [-M user_list] [-N jobname] [-o path] [-p priority] [-P proxy_user [-J <jobid]]
    [-q queue] [-r y|n] [-S path] [-t number_to_submit] [-T type]  [-u user_list]
    [-w] path
      [-W additional_attributes] [-v variable_list] [-V ] [-x] [-X] [-z] [script]

[ydw529@quser12 project2]$ pwd
/home/ydw529/panos/HiC/hic-bench/project2_
tsirigos commented 8 years ago

Yes, you need to modify the pipeline to use pbs instead of qsub!