"Error while fragmenting : null" during PCR amplification

When using default parameters on a custom pro file, PCR amplification gives the following error:

[LIBRARY] Amplification
[LIBRARY] Configuration
Rounds: 15
Mean: 0.5
Standard Deviation: 0.1

Processing Fragments * FAILED
[ERROR] Error while fragmenting : null
java.lang.NullPointerException
at barna.flux.simulator.fragmentation.Amplification.getGCcontent(Amplification.java:238)
at barna.flux.simulator.fragmentation.Amplification.process(Amplification.java:181)
at barna.flux.simulator.fragmentation.Fragmenter.process(Fragmenter.java:596)
at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:264)
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] Fragmentation file /group/transreg/dreec/projects/isoforms/flux_bug/parameters.lib not found. Make sure fragmentation was done !
java.lang.RuntimeException: Fragmentation file /group/transreg/dreec/projects/isoforms/flux_bug/parameters.lib not found. Make sure fragmentation was done !
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:450)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:198)

When amplification is turned of ("PCR_DISTRIBUTION none" in the pro file), no error occurs.

Reporter: Dries Vaneechoutte
E-mail: dreec@psb.vib-ugent.be