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  1. Jalview
  2. JAL-1454

Jalview crashes when selecting PCA analysis

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.8.0b1
    • Fix Version/s: 2.8.1
    • Component/s: analysis
    • Labels:
      None
    • Environment:
      Windows 7, 64 bit, Launched Jalview Desktop (.jnlp) --accessed website via Chrome browser

      Description

      I am attempting to view sequences via PCA analysis. I loaded the fasta alignment into Jalview after launching and calculated a distance tree. I then selected nodes which auto-colored groups and clicked calculate principal components analysis...the analysis ran for approx 2 min and the whole program crashed. The java console didn't stay open either, it closed and I was unable to retrieve it to see what error had happened. I adjusted memory up to 1GB in the .jnlp and tried again. During the analysis it stated I had 77% memory free, it again ran for about 1.5-2 min before crashing.

      My alignment is 282 taxa (closely related). I've attached it. I can do PCA analysis on smaller alignments but the larger alignment (282 sequences) crashes the program every time.

      I will try the 64 bit java (I am running 32 bit at the moment).

        Attachments

        1. alignment.fasta
          434 kB
          Melanie Melendrez
        2. javaws2014128270530834701.trace
          16 kB
          Melanie Melendrez
        3. javaws5708831006679299358.log
          49 kB
          Melanie Melendrez

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              Assignee:
              jprocter James Procter
              Reporter:
              mmelendrez Melanie Melendrez
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                Dates

                Created:
                Updated:
                Resolved: