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  1. UGENE
  2. UGENE-3889

Problems during exporting large number of repeats

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Cannot Reproduce
    • Affects Version/s: 1.15
    • Fix Version/s: None
    • Component/s: Basic-Nucl
    • Sprint:
      DEV-12/02/2015, DEV-05/03/2015
    • Affect Type:
      Userdefined

      Description

      This is a user request. The procedure was:

      My file is the reference genome of Plasmodium falciparum (PlasmoDB-10.0_Pfalciparum3D7_Genome.fasta )from the website plasmoDB (http://plasmodb.org/common/downloads/release-10.0/Pfalciparum3D7/fasta/data/ )
      
      I made a fusion of all chromosomes and organelle (mitochondrion and Apicoplast). Then I run the repeat research.
      
      Finds repeats settings were
      Windows size = 50pb
      Minimum Identity per window = 100%
      
      No minimum distance between repeats
      No maximum distance between repeats
      
      Region to process whole sequence
      
      Save Annotations to new table
      
      group name = auto
      Annotation name = repeat_unit 
      
      And no items have been selected in the "advanced" tab.
      Unfortunately, I didn’t get the crash report so I didn’t send you this log file. I will try to find it. 
      

      The result was:

      But I was not able to export the result.  
      I get a file ( 188 mb). It was hard to save it. It takes a long time but I managed it.
      But when I try to export the annotation with all my repeat (742832 repeat) It doesn’t work and the software crashed… When I check the memory of my computer only 4.95 Go was used (I have more than 30 Go) and under 5% of my UC are used
      

      The memory issues must be solved and the export of annotations must work properly.

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              Assignee:
              Unassigned
              Reporter:
              oigl Olga Golosova
              Watchers:
              1 Start watching this issue

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                Updated:
                Resolved:

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