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  • I followed the paramater file and useage ,the error that java nullpointerexception occurred.
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I followed the example simulation 5.2 directional RNA-seq Protocol paramater file and usage ,the error that java nullpointerexception occurred.the java version is 1.8.2,and the environment variable is correct.

the command line code is  flux-simulator -t simulator -p hg19_stranded.par

error :

Processing Fragments ********** OK (00:00:45)
51435495 mol: in 4999450, new 46436045, out 51435495
avg Len 316.02563, maxLen 1036
preparing transcript sequences *java.lang.NullPointerException
at barna.model.Graph.getRAF(
at barna.model.Graph.readSequence(
at barna.model.Graph.readSequence(
at barna.model.Graph.readSequence(
at barna.model.Transcript.getSplicedSequence(
at barna.flux.simulator.fragmentation.Fragmenter.getMapTxSeq(
at barna.flux.simulator.fragmentation.Fragmenter.process(
at barna.commons.launcher.Flux.main(

I want to know why happened this?




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  1. Try this:

    On 3rd line (GEN_DIR) of par file, the directory genomes/hg19 on your machine must contain chromosome fasta files named as the first column of the GTF file hg19_RefSeq_fromUCSC100615_sorted_nuc.gtf (chr1.fa, chr2.fa, chr3.fa, etc).