Alternative to LSF

Hello,

I'm trying to compute me own mask and I faced problem that I need to use command ~bsub that is belongs to LSF platform. We don't have LSF problem, and out genomes are very short. Is there any possibility to avoid LSF?

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Yes, you can run on a local machine. Do you need help with the command to run?
  • AleksandraKhovinaAleksandraKhovina StanfordMember

    @Geraldine_VdAuwera said:
    Yes, you can run on a local machine. Do you need help with the command to run?

    Thank you for your answer! Yes, may you please explain me a bit more how to run it on local machine?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    Ok, can you tell us what you are trying to run then?
  • AleksandraKhovinaAleksandraKhovina StanfordMember

    @Geraldine_VdAuwera said:
    Ok, can you tell us what you are trying to run then?

    Okay, I'm trying to compute genome mask file that was provided on your website. When I'm trying to run the last loop, i bump into bsub command. This bsub is my problem.

    Here is the loop:

    for chr in ${chroms};
    do
    bsub -o ${outdir}/work/svmask_${chr}.log \
    -R "rusage[mem=5000]" \
    java -cp ${classpath} -Xmx4g \
    org.broadinstitute.sv.apps.ComputeGenomeMask \
    -R ${localReference} \
    -O ${outdir}/work/svmask_${chr}.fasta \
    -readLength ${readLength} \
    -sequence ${chr} \
    || exit 1
    done

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie
    edited June 2016

    Oh I see, you're trying to use GenomeSTRiP. I believe you should be able to simply remove these two lines for local execution:

    bsub -o ${outdir}/work/svmask_${chr}.log \ 
    -R "rusage[mem=5000]" \ 
    

    FYI those tools belong to another team; I'll move your question to that part of the forum so if you have any follow-up questions they will see and answer it.

  • AleksandraKhovinaAleksandraKhovina StanfordMember

    @Geraldine_VdAuwera said:
    Oh I see, you're trying to use GenomeSTRiP. I believe you should be able to simply remove these two lines for local execution:

    bsub -o ${outdir}/work/svmask_${chr}.log \ 
    -R "rusage[mem=5000]" \ 
    

    FYI those tools belong to another team; I'll move your question to that part of the forum so if you have any follow-up questions they will see and answer it.

    Thank you for moving my question
    It didn't work. After I remove these lines, I got:

    Exception in thread "main" org.broadinstitute.gatk.utils.commandline.InvalidArgumentValueException:
    Argument '--sequence' requires a value but none was provided
    at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:334)
    at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:279)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:224)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
    at org.broadinstitute.sv.commandline.CommandLineProgram.runAndReturnResult(CommandLineProgram.java:29)
    at org.broadinstitute.sv.commandline.CommandLineProgram.run(CommandLineProgram.java:25)
    at org.broadinstitute.sv.apps.ComputeGenomeMask.main(ComputeGenomeMask.java:74)

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Technically it worked in the sense that the program did run locally. But it crashed because it ran into an error:

    Argument '--sequence' requires a value but none was provided
    

    That means the ${chr} variable isn't getting assigned a value. Check that your script is getting the variables it needs.

  • AleksandraKhovinaAleksandraKhovina StanfordMember

    @Geraldine_VdAuwera said:
    Technically it worked in the sense that the program did run locally. But it crashed because it ran into an error:

    Argument '--sequence' requires a value but none was provided
    

    That means the ${chr} variable isn't getting assigned a value. Check that your script is getting the variables it needs.

    Thank you! I will explore it more!

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