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Cromwell

Hi,

I am new to WDL / Cromwell. We have Sungrid engine in-house.

We want to develop our pipeline using Scatter-Gather WDL and run using cromwell.

  1. How to define the queue name to which jobs will submit to?

  2. Also when i try to submit a job, i am getting the following

[2016-04-18 11:28:34,294] [info] SgeBackend [0acfda24:hello]: qsub returnCode=0, job ID=15565651
[2016-04-18 11:28:34,296] [info] SgeBackend [0acfda24:hello]: 'rc' file does not exist yet
[2016-04-18 11:28:44,298] [info] SgeBackend [0acfda24:hello]: 'rc' file does not exist yet
[2016-04-18 11:28:49,299] [info] SgeBackend [0acfda24:hello]: 'rc' file does not exist yet
[2016-04-18 11:28:54,300] [info] SgeBackend [0acfda24:hello]: 'rc' file does not exist yet
[2016-04-18 11:28:59,301] [info] SgeBackend [0acfda24:hello]: 'rc' file does not exist yet
[2016-04-18 11:29:04,312] [info] SgeBackend [0acfda24:hello]: SGE job completed (returnCode=0)

Command used: java -Dbackend.backend=sge -jar cromwell-0.18.jar run hello.wdl hello.json

Please help me in this regard?

Thank you
Chandra

Answers

  • KateNKateN Cambridge, MAMember, Broadie, Moderator admin
    1. Unfortunately, the queue name is hard coded. You would need to modify the source code and compile in order to define the queue name.

    2. I had a developer take a look at your output, and I was told that the message 'rc' file does not exist yet is simply the engine looking for a file that will exist once the job has completed. It is not an error, although the message seems to be misleading. You can tell that your job completed successfully by the returnCode=0; Cromwell will return 0 if it completes successfully, or any other number if the job failed in some way.

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