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some error message from BFAST match

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  • xiangwulu
    replied
    found a solution for my problem.
    bfast gives error when align reads contains non a t c g n base.

    Leave a comment:


  • xiangwulu
    replied
    had similar error too, like the following:


    In function "AlignedEndRead": Fatal Error[ReadFileError]. Variable/Value: a->reads, a->qual, and a->numEntries.
    Message: Could not read from file.
    The file stream error was:: Success
    ***** Exiting due to errors *****

    Leave a comment:


  • fenciso
    replied
    ok, it works.

    Thanks

    Leave a comment:


  • nilshomer
    replied
    Originally posted by fenciso View Post
    Hi,
    II am new using bfast, I have a question: How can I define the mask values??, in index option.

    Thanks
    Welcome! In general, if you have a new question, post to a new thread. Use the "-m" option, and see the appendix in the bfast manual for the recommended settings.

    Leave a comment:


  • fenciso
    replied
    Hi,
    II am new using bfast, I have a question: How can I define the mask values??, in index option.

    Thanks

    Leave a comment:


  • nilshomer
    replied
    You need more disk space: "No space left on device".

    Leave a comment:


  • lei
    started a topic some error message from BFAST match

    some error message from BFAST match

    hi,

    I got some error message when I use BFAST for solid data mapping:

    error 1:

    In function "RGMatchPrint": Fatal Error[WriteFileError]. Message: Could not write m->readLength, m->qualLength, m->read, m->qual, m->maxReached, and m->numEntries.
    The file stream error was:: No space left on device
    ***** Exiting due to errors *****

    Does it mean I don't have enough memory or space to run it? But I run it on a cluster, it should have enough memory or space.

    error 2:

    In function "RGMatchPrint": Fatal Error[WriteFileError]. Message: Could not write masks[i].
    The file stream error was:: No space left on device
    ***** Exiting due to errors *****

    error 3:

    ************************************************************
    Searching for main indexes...
    ************************************************************

    In function "GetIndexFileNames": Fatal Error[OutOfRange]. Variable/Value: /icgc/lsdf/mb/analysis_final/reference/bfastCS/hg19.fa.cs.
    Message: Could not find any indexes with the given prefix.
    ***** Exiting due to errors *****

    For this error, I do have indexes there. Sometimes it can find them, sometimes it reports this error. So I don't understand why.
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