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  1. Barna Package
  2. BARNA-321

NullPointer when trying to set LP output

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    Description

      Command:

      flux-capacitor -i bamfile -a annotation_file -o ouptut --threads nthreads

      Output:

      [PROFILE] Scanning the input and getting the attributes.

      profiling OK (00:23:52)

      first round finished .. took 1432 sec.

      12325 single transcript loci

      377309560 mappings in file

      43276718 mappings fall in single transcript loci

      4615251872 mappings in annotation-mapped pairs

      81,121 min/max read length

      [SOLVE] Deconvolving reads of overlapping transcripts.

      decomposing [WARN] Fraction inconsistency FBtr0077393.27.homologue -2.304722170272954

      ...

      [ERROR] Failed to set lp output to:
      null
      java.lang.NullPointerException
      at java.io.FileOutputStream.<init>(FileOutputStream.java:206)
      at java.io.FileOutputStream.<init>(FileOutputStream.java:136)
      at barna.flux.capacitor.reconstruction.GraphLPsolver.run(GraphLPsolver.java:950)
      at barna.flux.capacitor.reconstruction.FluxCapacitor$LocusSolver.call(FluxCapacitor.java:1097)
      at barna.flux.capacitor.reconstruction.FluxCapacitor.explore(FluxCapacitor.java:2631)
      at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:1886)
      at barna.flux.capacitor.reconstruction.FluxCapacitor.call(FluxCapacitor.java:74)
      at barna.commons.launcher.Flux.main(Flux.java:198)

      unusual normalization factor: 0.03384014257154664
      [WARN] Unsolved system: 2L:4891851-4941363W
      [WARN] Fraction inconsistency FBtr0302984.1.homologue -2.313103458721854
      Model name: FBtr0080341.1.homologue

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            micha Micha Sammeth
            micha Micha Sammeth
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              Created:
              Updated:
              Resolved: