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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).

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              Assignee:
              jprocter Jim Procter
              Reporter:
              mmelendrez Melanie Melendrez
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