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Failed to read exp files error code 0

Harry
2014-04-08
2014-04-16
  • Harry
    Harry
    2014-04-08

    I am on Mac OSX 10.6. using Staden for first time
    I have run 15 .ab1 trace files through pregap and generated .exp and .zcf files
    I try to load these into gap4 using the pregap.passed file
    All files fail to load with error code 0 which I see means:
    "The reading file was not found or is of invalid format"
    The files to read are in the same folder as the pregap.passed file
    The traces looked good on a trace viewer
    Since the files were generated with pregap I assume that they were good.

    Any suggestions where I am going wrong?

     
    • James Bonfield
      James Bonfield
      2014-04-09

      Which version of the Staden Package are you using? I just tested 2.0.0b10 under 10.8.5 and it seemed OK. I don't know how to test on older MacOS releases, although in theory it is built with 10.5 and above as the deployment target.

      Does Trev work? Can it open the .ztr files?

      James

       
  • Harry
    Harry
    2014-04-10

    Thanks
    I am using 2.0.0b10
    I got someone with Mavericks to install Staden and test it and the same problem occured.
    Trev does work and I can see the ztr traces

     
  • James Bonfield
    James Bonfield
    2014-04-11

    Sorry I didn't read the issue properly initially.

    I tried using the (ancient) tutorial data downloaded from https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz/download with Gap4. On the command line:

    $ tar xfz course-1.1.tar.gz
    $ cd course-1.1/data/shotgun_data/
    $ ~/staden-2.0.0b10-MacOSX/bin/gap4 &

    Then within Gap4

    File->New
    Assembly->Normal Shotgun Assembly
    "pregap.passed" as fofn in and anything as output.
    Hit OK and it assembles, poorly. (Marvel at the hideous nature of old data.)

    Does the above work for you? If so then it would appear to be something specific about your data, in which case posting one of the experiment files may explain the problem. I'm wondering if it's something to do with the pathnames for example. Also what is your current working directory? In theory it can cope with spaces and the like, but I'm not 100% sure! Definitely spaces aren't allowed in sequence filenames.

    If the above doesn't work then perhaps it is an incompatibility between MacOS releases, although I'm clutching at straws there and I wouldn't know how to proceed.

     
    Last edit: James Bonfield 2014-04-11
  • Harry
    Harry
    2014-04-11

    Path is: /Users/harry/Documents/ToolsAndResources/SHEEP/Hydin/sequences
    Filename is of form: 2001-105_Run_AB3130XL_2014-04-07_17-02_8050_G04.ab1
    and 81_SKIP_TW1_JULY98_Run_AB3130XL_2014-04-07_17-02_8050_A04.ztr

    I was wondering if it was a path problem. Only filenames are shown in the pregap.passed file.

    Are hyphens legal?

    Thanks for looking at this

    I think I am attaching an experiment file seeing as that is what pregap.passed is pointing at. But I cannot see an upload button so I do not know if it will get included in the post.

     
  • James Bonfield
    James Bonfield
    2014-04-14

    Ah I see the issue. It's due to the entry names being too long. Gap4 has a limit of 40 (or maybe 39, I'm not sure if it includes the nul terminating character now). Sorry it didn't explain the error more sensibly.

    I know that's a bit rubbish and gap5 doesn't have this issue, but gap5 solves a different purpose to gap4 so it's not a direct replacement still. If you rename your .ab1 files and reprocess it should work.

    This can be done on the command line with something like:

    for i in *.ab1;do mv $i `echo $i | sed 's/.*AB3130XL_//'`;done
    

    (Probably best to take a backup first)

     
    Last edit: James Bonfield 2014-04-14
  • Harry
    Harry
    2014-04-16

    Thanks James
    That fixed that problem but now Gap4 crashes when I press OK for normal shotgun assembly when using default settings.
    I am working off the Babraham tutorial and have tried using two sets of reads in two different places. One set of reads had some poor quality sequences but the other was all perfect.

    The log file was unremarkable:
    Wed 16 Apr 12:51:50 2014 [67436@harry-noyess-macbook-pro-2.local] opening rw... by harry(501)
    Wed 16 Apr 12:51:50 2014 [67436@harry-noyess-macbook-pro-2.local] ...opened
    Wed 16 Apr 12:52:53 2014 [67436@harry-noyess-macbook-pro-2.local] auto assemble
    Wed 16 Apr 12:56:43 2014 [67489@harry-noyess-macbook-pro-2.local] opening rw... by harry(501)
    Wed 16 Apr 12:56:43 2014 [67489@harry-noyess-macbook-pro-2.local] ...opened
    Wed 16 Apr 12:57:02 2014 [67489@harry-noyess-macbook-pro-2.local] auto assemble

    The system log had this report for X11 events:
    The last error report was 8 seconds before the time of the auto assemble so may or may not be relevant.

    dh198119:sequences harry$ grep X11 /private/var/log/system.log | tail
    Apr 16 12:52:43 harry-noyess-macbook-pro-2 X11.bin[64853]: kCGErrorIllegalArgument: CGSAddWindowToWindowOrderingGroup: error setting window property
    Apr 16 12:52:43 harry-noyess-macbook-pro-2 org.x.startx[64771]: Wed Apr 16 12:52:43 harry-noyess-macbook-pro-2.local X11.bin[64853] <Error>: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 6566
    Apr 16 12:52:43 harry-noyess-macbook-pro-2 org.x.startx[64771]: Wed Apr 16 12:52:43 harry-noyess-macbook-pro-2.local X11.bin[64853] <Error>: kCGErrorIllegalArgument: CGSSetWindowProperty: Invalid window 0x19a6
    Apr 16 12:52:43 harry-noyess-macbook-pro-2 org.x.startx[64771]: Wed Apr 16 12:52:43 harry-noyess-macbook-pro-2.local X11.bin[64853] <Error>: kCGErrorIllegalArgument: CGSAddWindowToWindowOrderingGroup: error setting window property
    Apr 16 12:56:54 harry-noyess-macbook-pro-2 X11.bin[64853]: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 6598
    Apr 16 12:56:54 harry-noyess-macbook-pro-2 X11.bin[64853]: kCGErrorIllegalArgument: CGSSetWindowProperty: Invalid window 0x19c6
    Apr 16 12:56:54 harry-noyess-macbook-pro-2 org.x.startx[64771]: Wed Apr 16 12:56:54 harry-noyess-macbook-pro-2.local X11.bin[64853] <Error>: kCGErrorIllegalArgument: _CGSFindSharedWindow: WID 6598
    Apr 16 12:56:54 harry-noyess-macbook-pro-2 X11.bin[64853]: kCGErrorIllegalArgument: CGSAddWindowToWindowOrderingGroup: error setting window property
    Apr 16 12:56:54 harry-noyess-macbook-pro-2 org.x.startx[64771]: Wed Apr 16 12:56:54 harry-noyess-macbook-pro-2.local X11.bin[64853] <Error>: kCGErrorIllegalArgument: CGSSetWindowProperty: Invalid window 0x19c6
    Apr 16 12:56:54 harry-noyess-macbook-pro-2 org.x.startx[64771]: Wed Apr 16 12:56:54 harry-noyess-macbook-pro-2.local X11.bin[64853] <Error>: kCGErrorIllegalArgument: CGSAddWindowToWindowOrderingGroup: error setting window property