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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1117 ] blprotein - Jalview can't load input file
    Date:
    02/28/11 17:02
    Submitted by:
    B_Fristensky
    Assigned to:
    B_Fristensky
    Category:
    bioLegato
    Priority:
    3
    Ticket group:
    Bug
    Resolution:
    Resolved
    Summary:
    blprotein - Jalview can't load input file
    Original submission:
    Linux-intel, Feb. 22 Development version

    cd $tutorials/bioLegato/phylogeny/distance
    blprotein
    File --> Open chitIII.pro.tcoffee.gde
    Select All
    Alignment --> Jalview

    Jalview launches, but gives the message:

    Couldn't load file bioxxxxxxxxx.tmp.fsa
    Problem opening file bioxxxxxxxx.tmp.fsa: FILE CANNOT BE OPENED FOR READING
    Formats currently supported are BLC, CLUSTAL.MSF, PileUp,PIR,PFAM,STH, PDF, AND JnetFile.

    File looks like a perfectly good fasta file.
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    Fixed bldna and blprotein.

    Jalview -open requires a fully-qualified path, even if the input file is in the current working directory.
    The command is therefore

    Jalview -open $PWD/in1.fsa

    This was mentioned in the comment lines for jalview.item, but somehow, the $PWD got taken out. It has been restored.

    02/28/11 17:44 B_Fristensky
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Open 03/13/11 19:15 B_Fristensky
    close_date 12/31/69 19:00 03/13/11 19:15 B_Fristensky
    resolution_id Not Resolved 02/28/11 17:44 B_Fristensky
    status_id Pending 02/28/11 17:02 B_Fristensky
    priority 5 02/28/11 17:02 B_Fristensky
    assigned_to unset 02/28/11 17:02 B_Fristensky
    resolution_id Unset 02/28/11 17:02 B_Fristensky

     

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