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  1. IGB
  2. IGBF-3029

CLONE - Bug when browsing genome file

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      Description

      A user reported the following problem:

      After click in the browse button to open a genome file the program freezes and you have to force quit (OSX - 10.15.7)

      Reporter: Carlos Lax
      E-mail: carlos.lax@um.es

      For this task, check that it is still possible to browse and open a genome file. Also, contact the user and ask if you can get access to the genome file they were trying to open.

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            Hide
            aloraine Ann Loraine added a comment -

            Contacting the reporter to ask for access to the genome file:

            Hello Dr. Lax,

            Thank you for letting us know about the problem!

            If possible, could you let us know the file you were trying to open? If we can get a copy of it, it will help us figure out what the problem is.

            Warm regards,

            Ann Loraine

            cc: Omkar Marne

            Show
            aloraine Ann Loraine added a comment - Contacting the reporter to ask for access to the genome file: Hello Dr. Lax, Thank you for letting us know about the problem! If possible, could you let us know the file you were trying to open? If we can get a copy of it, it will help us figure out what the problem is. Warm regards, Ann Loraine cc: Omkar Marne
            Hide
            aloraine Ann Loraine added a comment - - edited

            User appears to be attempting to open a custom genome, as per the description in this help guide page:

            Also, see the attached PDF (igbman-852091-151221-1548-17.pdf) with the above page from the user's guide.

            Show
            aloraine Ann Loraine added a comment - - edited User appears to be attempting to open a custom genome, as per the description in this help guide page: https://wiki.bioviz.org/confluence/pages/viewpage.action?pageId=852091 Also, see the attached PDF (igbman-852091-151221-1548-17.pdf) with the above page from the user's guide.
            Hide
            omarne Omkar Marne added a comment - - edited

            I tried opening A_thaliana_Jun_2009.2bit both locally and using its url: http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit. The file opened without any delay.
            The sequence data was visible immediately after hitting Load sequence button.
            Please see attached screenshot.

            Dr. Ann Loraine Please specify the file name which the user is opening.

            Show
            omarne Omkar Marne added a comment - - edited I tried opening A_thaliana_Jun_2009.2bit both locally and using its url: http://igbquickload.org/quickload/A_thaliana_Jun_2009/A_thaliana_Jun_2009.2bit . The file opened without any delay. The sequence data was visible immediately after hitting Load sequence button. Please see attached screenshot. Dr. Ann Loraine Please specify the file name which the user is opening.
            Hide
            aloraine Ann Loraine added a comment -

            Thank you Omkar Marne for looking into it.
            I have emailed the user to ask for the file - see previous comment.
            Please move this back to "To-Do" while we wait.

            Show
            aloraine Ann Loraine added a comment - Thank you Omkar Marne for looking into it. I have emailed the user to ask for the file - see previous comment. Please move this back to "To-Do" while we wait.
            Hide
            aloraine Ann Loraine added a comment - - edited

            NF notes this could be a legit bug arising from changes made in the most recent release of IGB. Notes that many of these issues come from the user trying to load the wrong file format.

            Show
            aloraine Ann Loraine added a comment - - edited NF notes this could be a legit bug arising from changes made in the most recent release of IGB. Notes that many of these issues come from the user trying to load the wrong file format.
            Hide
            aloraine Ann Loraine added a comment - - edited

            Probably the user did not try to load a 2bit but was trying to load a fasta file. So we should test a fasta file.
            cc: Omkar Marne

            Show
            aloraine Ann Loraine added a comment - - edited Probably the user did not try to load a 2bit but was trying to load a fasta file. So we should test a fasta file. cc: Omkar Marne
            Hide
            nfreese Nowlan Freese added a comment -

            I tested a .fasta file created from the A_thaliana_Jun_2009.2bit file. There were no issues loading it as either the .fasta or as a .fasta.gz.

            Show
            nfreese Nowlan Freese added a comment - I tested a .fasta file created from the A_thaliana_Jun_2009.2bit file. There were no issues loading it as either the .fasta or as a .fasta.gz.
            Hide
            aloraine Ann Loraine added a comment -

            Closing for now. Will re-open if and when the user gets back to us with the requested info.

            Show
            aloraine Ann Loraine added a comment - Closing for now. Will re-open if and when the user gets back to us with the requested info.

              People

              • Assignee:
                omarne Omkar Marne
                Reporter:
                support Support
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                Dates

                • Created:
                  Updated:
                  Resolved: