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  • _y_s
    replied
    indeed the edit_dir, phd_dir are at the same level but strangely the command worked once I used another user than the root.

    PS: the root was only for the installation procedure

    Leave a comment:


  • v_kisand
    replied
    I guess you should first check - do you run consed from an edit_dir folder and that you have a phd_dir folder at the same level as edit_dir..

    and just a recommendation do not use root as default user

    -veljo

    Leave a comment:


  • _y_s
    replied
    Error

    I have another error while executing consed for the first time. Here is the command line followed by the warnings that I've got:

    root@ubuntu:/usr/local/genome/examples# consed

    no ~/consedrc file so no user resources will be used--that's ok
    no consedrc file so no project-specific resources--that's ok
    couldn't open readOrder.txt--that's ok
    not setting XKEYSYMDB. This is ok if you don't get any errors saying something about "Warning: translation table..."Warning: translation table syntax error: Unknown keysym name: osfActivate
    Warning: ... found while parsing ':<Key>osfActivate: ManagerParentActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfBeginLine
    Warning: ... found while parsing ':<Key>osfBeginLine: ManagerGadgetTraverseHome()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfActivate
    Warning: ... found while parsing ':<Key>osfActivate: ManagerParentActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfSelect
    Warning: ... found while parsing ':<Key>osfSelect: ManagerGadgetSelect()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfSelect
    Warning: ... found while parsing ':<Key>osfSelect: MenuBarGadgetSelect()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfActivate
    Warning: ... found while parsing ':<Key>osfActivate: ManagerParentActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfHelp
    Warning: ... found while parsing ':<Key>osfHelp: MenuHelp()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfActivate
    Warning: ... found while parsing ':<Key>osfActivate: PrimitiveParentActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfHelp
    Warning: ... found while parsing ':<Key>osfHelp: Help()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfActivate
    Warning: ... found while parsing ':<Key>osfActivate: PrimitiveParentActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfCancel
    Warning: ... found while parsing ':<Key>osfCancel: MenuEscape()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfSelect
    Warning: ... found while parsing ':<Key>osfSelect: KeySelect()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfSelect
    Warning: ... found while parsing ':<Key>osfSelect: KeySelect()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfCancel
    Warning: ... found while parsing '<Key>osfCancel: MenuEscape()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfSelect
    Warning: ... found while parsing ':<Key>osfSelect: ArmAndActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfActivate
    Warning: ... found while parsing ':<Key>osfActivate: PrimitiveParentActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfHelp
    Warning: ... found while parsing ':<Key>osfHelp: ManagerGadgetHelp()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfPrimaryPaste
    Warning: ... found while parsing ':m <Key>osfPrimaryPaste:cut-primary()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfBeginLine
    Warning: ... found while parsing ':s c <Key>osfBeginLine: ListBeginDataExtend()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfActivate
    Warning: ... found while parsing ':<Key>osfActivate: PrimitiveParentActivate()'
    Warning: String to TranslationTable conversion encountered errors
    Warning: translation table syntax error: Unknown keysym name: osfPrimaryPaste
    Warning: ... found while parsing ':m <Key>osfPrimaryPaste:cut-primary()'
    Warning: String to TranslationTable conversion encountered errors
    Fatal: The parent directory must contain either phdball_dir or else phd_dir, but it doesn't. A typical directory structure is a directory named after the project, with subdirectories named edit_dir (containing the ace files), solexa_dir (containing the solexa *_seq.txt and *_prb.txt files), sff_dir (containing the 454 sff files or links to them), phdball_dir (containg the phdballs), and chromat_dir (containing chromats of any gel-based reads). Obviously you don't need all of these. Consed is run from within edit_dir.
    Version 23.0 (120514)

    Leave a comment:


  • Markiyan
    replied
    Your ace file needs reprocessing. Remove quality from *'s.

    It looks like yours ace file has got quality assigned to the pads (stars), which is the violations of the consed ace standard. So the ace file needs reprocessing to remove *'s quality.
    BTW: same problem is present with the Lasergen NGEN 2 or 3.1 ace files...

    Leave a comment:


  • HereBeDragons
    replied
    I think your right, its just strange not to have heard about this problem before. I would expect exporting ace files from Geneious is something people do all the time. I am in contact with the Geneious tech support, we'll see how it goes...

    Leave a comment:


  • v_kisand
    replied
    never tried before but seems Geneious produces bad ace file. My error message is following:

    exception thrown: ace file error detected from source file parseAceFile.cpp at 1907
    Error in file NC_008260_bb.ace at line 3917080. Line:


    premature end of file while expecting BaseQuality line

    I use linux (fedora) and consed version 20.0.

    Contact Geneious developers, my experience is that they are quite collaborative.

    -veljo

    Leave a comment:


  • maubp
    replied
    It sounds like your ACE file may be broken. Have you tried looking at it in any other tools, which may not check this field? e.g. Tablet can view ACE assembly files,

    Leave a comment:


  • HereBeDragons
    started a topic Consed ERROR opening Geneious .ace file

    Consed ERROR opening Geneious .ace file

    Hello all,

    I am trying to open an .ace file exported from the Geneious software. Strangely, when I try to open it in Consed (consed_mac) in the graphical user interface it gives me the following error message:

    exception thrown: ace file error detected from source file parseAceFile.cpp at 1888
    Error in file Contig1.ace at line 4245. Line:
    93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93

    There must be exactly the same number of quality values as unpadded consensus bases for contig Contig_1

    ace file: Contig1.ace
    Version 19.0 (090206)
    ace file error detected from source file parseAceFile.cpp at 1888
    Error in file Contig1.ace at line 4245. Line:
    93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93 93

    There must be exactly the same number of quality values as unpadded consensus bases for contig Contig_1
    ace file = Contig1.ace
    Version 19.0 (090206)

    I JUST started using consed, but I have no idea why my .ace file would be problematic. Could anyone advise me in this? Have I done something wrong, or is this a common bug I can address? Thanks!

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