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 :
And Here is the output on the last step CALCULATING STATISTICS :
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
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)