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Solid-color space indexing for human fasta file



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  • Solid-color space indexing for human fasta file

    I am using BFAST for indexing color space data using the command:

    bfast index -f folder/human_bfast.fa -m '11111' -w 5 -A 1 -n 8

    If I try to index the fasta file with a few chromosomes, say till 17, the tool successfully creates .bif file. But if I use a bigger fasta file (ie. from chr 1 till 22) for indexing then the tool throws error:

    Currently on [contig,pos]:
    Sorting by thread...
    100.000 percent complete************************************************************
    In function "RGIndexMergeHelperFromDiskContig_8": Fatal Error[ReadFileError]. Message: Could not read in tmp lower.
    The file stream error was:: Bad file descriptor
    ***** Exiting due to errors *****
    I want to create solid color space index for human fasta for all chromosomes from 1 through 22, X,Y

    Please note that the step just prior to indexing (ie. creating reference in color space using the same fasta) was always successful. It creates .fa.cs.brg file successfully.
    Can anybody please help me with the problem ?

    Thanks in advance,

  • #2
    Try with a longer index, I think the recommended were between 12-14 long? 5 bases with no open positions does not make much sense for human. Masking strategies are described in the publications/documentations.