I use flux-simulator-1.2.2-20140614022955, since in this version you have fixed the problem with the short length transcripts (<3 nt).

Now the program crashes at library preparation step

[LIBRARY] Reverse Transcription
[LIBRARY] Configuration
Mode: RH
PWM: default
RT MIN: 500
RT MAX: 5500

Processing Fragments * FAILED
[ERROR] Error while fragmenting : null
java.lang.NullPointerException
at barna.flux.simulator.fragmentation.Fragmenter.toCDF(Fragmenter.java:788)
at barna.flux.simulator.fragmentation.FragmentReverseTranscription.process(FragmentReverseTranscription.java:226)
at barna.flux.simulator.fragmentation.Fragmenter.process(Fragmenter.java:596)
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:222)
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:197)

Could you please help?

Gleb

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