Is there a way to set a seed for simulation? I would like to be able to reproduce simulations, but I don't see any options for specifying a seed.

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5 Comments

  1. Thasso Griebel

    Hi Andrew, 

    unfortunately this is currently not possible. I create a ticket (BARNA-306) and will try to implement it for the next release. 

    -Thasso

  2. Thasso Griebel

    Hey Andrew,

    I implemented the SEED feature. Its not released yet, but it already in a nightly-build. If you want, download the lates nightly from here:

    http://sammeth.net/artifactory/barna-nightly/barna/barna.simulator/1.2.1-20130503160104/flux-simulator-1.2.1-20130503160104.tgz

    and set the SEED parameter in your parameter file to a number > 0. 

  3. Andrew Tritt

    Hey Thasso,

    I downloaded the new build and ran some tests. I am not getting reproducible results. I think some downstream steps are not utilizing the global seed still.

    I can reproduce the .PRO files when I just run with --express, but when I run the rest of the pipeline, the .pro file gets modified.

     

    Andrew

    1. Thasso Griebel

      Hey,

      yes, thats one issue at the moment. The .pro file gets updated. But I am not sure where the problem is. I ran some tests here and I am able to create the same results. Maybe I am missing something. Can you maybe lay out how you call the Simulator and when you would expect to get the same results? For my local tests, I simply rerun the full pipeline with the same parameters and the same SEED. But you are trying to reuse some of the files ? Like the .pro ?

      -Thasso

      1. Andrew Tritt

        I expect all the output files to be same. If that's not possible, I expect the final FastQ file to be the same. 

        To test, I ran Flux-Simulator with the same .PAR, .GTF, and fasta sequences files, side-by-side on the same machine. I monitored the two runs, and checked the md5sum of the .PRO file shortly after they started, and they have the same hash. Once the flux-simulator completed, I checked the md5sum on all the output files (.PRO, .LIB .BED, and .FASTQ) and they all have different hashes. 

        I am using Flux-Simulator v1.2.1-20130503160104 (Flux Library: 1.22-20130503160104)

        Is that the same version you're testing?

        Andrew