Finished aggregate feature table.
Generating iComut table.
                    Name Rows Columns
1         clinical.comut  108       5
2          cluster.comut  108       2
3       genematrix.comut  108      11
4    fold.mRNA.SMG.comut    0       0
5         arm.copy.comut  108      96
6       focal.copy.comut  108      49
7  fold.mRNA.focal.comut    0       0
8          mutation.rate  108       2
9         cnv.copy.comut    0       0
10   fold.mRNA.cnv.comut    0       0
11     mutsigcateg.comut  108       5
Generating report.
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.346d790b/out.5
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.346d790b/err.5
  adding: CPTAC3-LUAD-TP.samplefeatures.txt (deflated 73%)
  adding: pval.occ.all.SCNA.fisher.txt (deflated 72%)
  adding: pval.occ.focal.SCNA.fisher.txt (deflated 82%)
  adding: pval.exc.all.SCNA.fisher.txt (deflated 75%)
  adding: CPTAC3-LUAD-TP.fisher.arm.copy.correlation.png (deflated 23%)
  adding: CPTAC3-LUAD-TP.transposed.samplefeatures.txt (deflated 78%)
  adding: CPTAC3-LUAD-TP.fisher.all.correlation.png (deflated 41%)
  adding: pval.occ.mutation.fisher.txt (deflated 68%)
  adding: nozzle.RData (stored 0%)
  adding: CPTAC3-LUAD-TP.coMut_table.txt (deflated 85%)
  adding: pval.exc.mutation.fisher.txt (deflated 69%)
  adding: pval.exc.arm.SCNA.fisher.txt (deflated 76%)
  adding: pval.exc.focal.SCNA.fisher.txt (deflated 83%)
  adding: CPTAC3-LUAD-TP.fisher.mutation.correlation.png (deflated 18%)
  adding: CPTAC3-LUAD-TP.fisher.focal.copy.correlation.png (deflated 16%)
  adding: pval.occ.arm.SCNA.fisher.txt (deflated 75%)
  adding: nozzle.html (deflated 70%)
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.346d790b/out.5
	zip warning: ignoring FIFO (Named Pipe) - use -FI to read: tmp.346d790b/err.5
  adding: CPTAC3-LUAD-TP.samplefeatures.txt (deflated 73%)
  adding: pval.occ.all.SCNA.fisher.txt (deflated 72%)
  adding: pval.occ.focal.SCNA.fisher.txt (deflated 82%)
  adding: pval.exc.all.SCNA.fisher.txt (deflated 75%)
  adding: CPTAC3-LUAD-TP.fisher.arm.copy.correlation.png (deflated 23%)
  adding: tmp.346d790b/ (stored 0%)
  adding: stderr (stored 0%)
  adding: nozzle_report.zip (stored 0%)
  adding: CPTAC3-LUAD-TP.transposed.samplefeatures.txt (deflated 78%)
  adding: CPTAC3-LUAD-TP.fisher.all.correlation.png (deflated 41%)
  adding: pval.occ.mutation.fisher.txt (deflated 68%)
  adding: nozzle.RData (stored 0%)
  adding: CPTAC3-LUAD-TP.coMut_table.txt (deflated 85%)
  adding: pval.exc.mutation.fisher.txt (deflated 69%)
  adding: pval.exc.arm.SCNA.fisher.txt (deflated 76%)
  adding: pval.exc.focal.SCNA.fisher.txt (deflated 83%)
  adding: script (deflated 69%)
  adding: CPTAC3-LUAD-TP.fisher.mutation.correlation.png (deflated 18%)
  adding: CPTAC3-LUAD-TP.fisher.focal.copy.correlation.png (deflated 16%)
  adding: stdout