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The program crashes with the error for one of the four replicates (generated pro files).

 

[ERROR] Error while creating initial fragmentation: 0 is smaller than, or equal to, the minimum (0): m
org.apache.commons.math.exception.NotStrictlyPositiveException: 0 is smaller than, or equal to, the mi
at org.apache.commons.math.random.RandomDataImpl.nextExponential(RandomDataImpl.java:484)
at barna.flux.simulator.fragmentation.Fragmenter.processInitial(Fragmenter.java:847)
at barna.flux.simulator.fragmentation.Fragmenter.writeInitialFile(Fragmenter.java:714)
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:180)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:440)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)


[ERROR] null
java.lang.NullPointerException
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:181)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:440)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)

What does it mean?

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3 Comments

  1. I also have this issue, both with 1.2.1 and the newest nightly release. This is my PAR file:

     

    ################################################File locations

    REF_FILE_NAME /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/rnaseq/ref-transcripts.gtf
    GEN_DIR /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/multi

    ###################################################Expression

    NB_MOLECULES 5000000
    TSS_MEAN 50
    POLYA_SCALE 100
    POLYA_SHAPE 1.5
    EXPRESSION_K -0.1
    EXPRESSION_X0 14500.0
    EXPRESSION_X1 9.025E9
    ###############################################Fragmentation

    FRAGMENTATION YES
    FRAG_SUBSTRATE RNA
    FRAG_METHOD UR
    FRAG_UR_ETA 800
    FRAG_UR_D0 100
    RTRANSCRIPTION YES
    RT_MOTIF default
    RT_PRIMER RH


    #########################################################PCR

    PCR_DISTRIBUTION default
    GC_MEAN NaN
    PCR_PROBABILITY 0.05
    FILTERING YES
    SIZE_DISTRIBUTION N(400,50)

    #################################################Sequencing

    READ_NUMBER 2000000
    READ_LENGTH 100
    PAIRED_END YES
    FASTA YES
    ERR_FILE 76
    UNIQUE_IDS YES

  2. I've found the reason, my gtf contains 3 nt transcript. Since my simulation is comparative I have just removed it and now the program runs normally.

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