Details
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Bug
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Status: Open
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Major
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Resolution: Unresolved
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Simulator 1.2.1 (API 1.22)
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None
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None
Description
When trying to generate synthetic data (using GRCh37 and the corresponding Ensembl GTF), the Flux Simulator consistently crashes during the read generation step. The errors always look like:
[ERROR] Error while sequencing : Problems reading BED object 3 198035859 198035959 3:197960200-198043720W:ENST00000332636:2:1812:1527:1810/1 0 + . . 0
,0,0 1 100 0
java.lang.RuntimeException: Problems reading BED object 3 198035859 198035959 3:197960200-198043720W:ENST00000332636:2:1812:1527:1810/1 0 + . . 0,0,0 1
100 0
at barna.model.bed.BEDobject2.readSequence(BEDobject2.java:335)
at barna.flux.simulator.Sequencer.createQSeq(Sequencer.java:642)
at barna.flux.simulator.Sequencer$SequenceWriter.writeRead(Sequencer.java:987)
at barna.flux.simulator.Sequencer$Processor.process(Sequencer.java:820)
at barna.flux.simulator.Sequencer.sequence(Sequencer.java:280)
at barna.flux.simulator.Sequencer.call(Sequencer.java:153)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:452)
at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:54)
at barna.commons.launcher.Flux.main(Flux.java:197)
Caused by: java.lang.RuntimeException: Problems reading chromosome 3 from 198035859 to 198022528
into array of 59 from 59 to 159
at barna.model.Graph.readSequence(Graph.java:1487)
at barna.model.bed.BEDobject2.readSequence(BEDobject2.java:305)
... 8 more
Caused by: java.lang.ArrayIndexOutOfBoundsException
at barna.model.Graph.readSequence(Graph.java:1439)
... 9 more
It seems that it is, perhaps, attempting to read non-existent sequence, but I'm not sure. I've tried a number of runs and even went so far as to pad all of my chromosomes with an extra 100bp of 'N's, but I still seem to get this error.