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  1. Barna Package
  2. BARNA-194

Reading gene sequences close to the chromosome border

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    Description

      [LIBRARY] Configuration
      Mode: RH
      PWM: No
      RT MIN: 200
      RT MAX: 5500

      Processing Fragments ********** OK (00:03:57)
      34569813 mol: in 34569746, new 67, out 34565024
      avg Len 214.94418, maxLen 744
      start amplification
      [INFO] Loading default PCR distribution
      preparing transcript sequences ******* ERROR
      [ERROR] Error while preparing sequences: Problems reading sequence Chr3: pos -1, len 100,
      check whether chromosomal sequence exists / has the correct size
      java.lang.RuntimeException: Problems reading sequence Chr3: pos -1, len 100,
      check whether chromosomal sequence exists / has the correct size
      at barna.model.Graph.readSequence(Graph.java:585)
      at barna.model.Graph.readSequence(Graph.java:473)
      at barna.model.Transcript.getSplicedSequence(Transcript.java:459)
      at barna.flux.simulator.fragmentation.Fragmenter.getMapTxSeq(Fragmenter.java:375)
      at barna.flux.simulator.fragmentation.Fragmenter.process(Fragmenter.java:539)
      at barna.flux.simulator.fragmentation.Fragmenter.call(Fragmenter.java:258)
      at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:424)
      at barna.flux.simulator.SimulationPipeline.call(SimulationPipeline.java:53)
      at barna.commons.launcher.Flux.main(Flux.java:212)
      Caused by: java.lang.NegativeArraySizeException
      at barna.model.Graph.readSequence(Graph.java:507)
      at barna.model.Graph.readSequence(Graph.java:473)
      at barna.model.Graph.readSequence(Graph.java:529)
      ... 8 more
      FAILED

      Attachments

        1. reopen.par
          0.6 kB
          Micha Sammeth

        Activity

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            micha Micha Sammeth
            micha Micha Sammeth
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            Dates

              Created:
              Updated: