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  1. Jalview
  2. JAL-3941

cannot fetch sequnces from PFAM

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Duplicate
    • Affects Version/s: 2.11.1.6
    • Fix Version/s: 2.11.1.7
    • Component/s: None
    • Labels:
      None
    • Environment:
      linux , ubuntu 20.04
      jalview installed using jalview-2_11_1_4-linux_x64-java_8.sh

      Description

      When try to fetch PFAM using File/Fetch I am getting:
      Jalview Version: 2.11.1.6
      Jalview Installation: Source git-commit:a7e71732f [releases/Release_2_11_1_Branch]
      Build Date: 10:31:23 06 January 2022
      Java version: 1.8.0_242
      amd64 Linux 5.11.0-44-generic
      Install4j version: 8.0.11
      Install4j template version: 2.11.1.4_Fa87edcab_C930bcaf01
      Launcher version: 1.8.3-1.2.9_JVL
      LookAndFeel: Metal (javax.swing.plaf.metal.MetalLookAndFeel)
      Getdown appdir: /home/petr/opt/jalview
      Java home: /home/petr/opt/jalview/jre
      java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped' (sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target)
      at jalview.io.FileParse.<init>(FileParse.java:514)
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:180)
      at jalview.io.FormatAdapter.readFile(FormatAdapter.java:235)
      at jalview.ws.dbsources.Xfam.getSequenceRecords(Xfam.java:71)
      at jalview.gui.SequenceFetcher.fetchSingleAccession(SequenceFetcher.java:915)

      at jalview.gui.SequenceFetcher.run(SequenceFetcher.java:700)
      at java.lang.Thread.run(Thread.java:748)
      Failed to read alignment using the 'Stockholm' reader.
      java.io.IOException: Failed to read data from source: CANNOT ACCESS DATA AT URL 'https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped&#39; (sun.security.validator.ValidatorException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target)


      I testes regular installation using linux installer(2.11.1.6) and also conda installer ( 2.11.1.5)

      when tried to download https://pfam.xfam.org/family/PF03760/alignment/seed/gzipped, it return correct gziped file

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              Assignee:
              jprocter James Procter
              Reporter:
              kavonrtep Petr Novak
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                Created:
                Updated:
                Resolved: