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  • KYR
    Member
    • May 2012
    • 18

    #1

    CNVnator : Error message Please Help!

    I typed the following in unix and at step 3 CALCULATING STATISTICS CNVnator output an error message.. I have no clue what does it mean..

    Here is what I typed :

    Code:
    ./cnvnator -genome mm9 -root /home/chr1-bam1.root -chrom chr1 -tree /home/chr1-bam1.bam
    ./cnvnator -genome mm9 -root /home/chr1-bam1.root -chrom chr1 -his 100 -d /01.Reference/mm9
    ./cnvnator -root /home/chr1-bam1.root -chrom chr1 -stat 100
    And Here is the output on the last step CALCULATING STATISTICS :

    Code:
    Warning in [HTML]: DISPLAY not set, setting it to 147.46.154.136:0.0
    Making statistics for chr1 ...
    Average RD per bin (1-22) is 7.69074 +- 4.41474 (before GC correction)
    Warning in [HTML]: Fit data is empty
    Warning in [HTML]: Fit data is empty
    Average RD per bin (X,Y)  is 0 +- 0 (before GC correction)
    Correcting counts by GC-content for 'chr1' ...
    Zero value of GC average.
    Bin 386844 with center 3.86844e+07 is not corrected.
    Zero value of GC average.
    Bin 633561 with center 6.3356e+07 is not corrected.
    Zero value of GC average.
    Bin 645800 with center 6.458e+07 is not corrected.
    Zero value of GC average.
    Bin 803371 with center 8.0337e+07 is not corrected.
    Zero value of GC average.
    Bin 1793725 with center 1.79372e+08 is not corrected.
    Zero value of GC average.
    Bin 1818901 with center 1.8189e+08 is not corrected.
    Making statistics for chr1 after GC correction ...
    Average RD per bin (1-22) is 7.08536 +- 3.84236 (after GC correction)
    Warning in [HTML]: Fit data is empty
    Warning in [HTML]: Fit data is empty
    Average RD per bin (X,Y)  is 0 +- 0 (after GC correction)

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