The program crashes with the error

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

Processing Fragments * FAILED
[ERROR] Error while fragmenting : fromIndex(173) > toIndex(171)
java.lang.IllegalArgumentException: fromIndex(173) > toIndex(171)
at java.util.Arrays.rangeCheck(
at java.util.Arrays.binarySearch(
at barna.flux.simulator.fragmentation.FragmentReverseTranscription.process(
at barna.flux.simulator.fragmentation.Fragmenter.process(
at barna.commons.launcher.Flux.main(

What does it stand for?

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  1. Hi Gleb, the error incurred because there was apparently a fragment with a negative length spotted. How were the input files for this simulation run created, by the flux pipeline itself or did you create your own upstream pipeline files before simulating fragmentation? Best

    1.  The .PRO  file was created  by your  expression  simulator. I  haven't modified it.

  2. Hi, I created a ticket with your observation 

    BARNA-331 - Getting issue details... STATUS  

    It would probably help us to reproduce your observations if you could make the .PAR and maybe also the .PRO file available. Please attach these files to the ticket, if possible.

    1. Of course I can, but I don't see the "attach" button on the ticket page.


      1. There are two options to attach files in the JIRA bugtracker, either via "Attach Files" in the "More Actions" or by the drag&drop area to the right of the page. To comment and/or to upload files, you have to be logged in, which you can do with our confluence account credentials.


        1. I'm logged in but there is no "Attach Files" option in the "More Actions".

          1. Right, there was a permission conflict with users created in confluence rather than jira. Now the permissions necessary for file upload are also passed to confluence users.

            1. I've uploaded the files.