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Old 05-20-2012, 10:14 PM   #1
KYR
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Location: Toronto

Join Date: May 2012
Posts: 18
Default 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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