Open GoogleCodeExporter opened 8 years ago
1) What operating system are you using? Linux 2) What error message was displayed? --------BEGIN BUILDING WINDOW DATA-------- 2014-01-12 20:59:46 Error in twigfiles[[i]] : subscript out of bounds 3) What was the exact command you used that resulted in the error? I was ruuning the example code for Chip-seq with a change with twoBit File (hg18 to hg19) zinba( align='align_athresh1_extension200/', numProc=4,seq='test_data/data/ctcfGM12878rep3chr22.taf', basecountfile='test_data/data/ctcfGM12878rep3chr22.basecount', filetype='tagAlign', outfile='test_data/data/ctcf', twoBit='hg19.2bit', extension=200, printFullOut=1, refinepeaks=1, broad=F, input='test_data/data/inputGM12878rep3chr22.taf') 4) Please copy and paste any additional screen output that resulted from running the command > zinba(align='align_athresh1_extension200/',numProc=4,seq='test_data/data/ctcfGM1 2878rep3chr22.taf',basecountfile='test_data/data/ctcfGM12878rep3chr22.basecount' ,filetype='tagAlign',outfile='test_data/data/ctcf',twoBit='hg19.2bit',extension= 200,printFullOut=1,refinepeaks=1,broad=F,input='test_data/data/inputGM12878rep3c hr22.taf') [1] "parameters in effect:" $filelist NULL $formula NULL $formulaE NULL $formulaZ NULL $outfile [1] "test_data/data/ctcf" $seq [1] "test_data/data/ctcfGM12878rep3chr22.taf" $align [1] "align_athresh1_extension200/" $input [1] "test_data/data/inputGM12878rep3chr22.taf" $twoBit [1] "hg19.2bit" $winSize [1] 250 $offset [1] 125 $cnvWinSize [1] 1e+05 $cnvOffset [1] 2500 $basecountfile [1] "test_data/data/ctcfGM12878rep3chr22.basecount" $threshold [1] 0.05 $peakconfidence [1] 0.95 $tol [1] 1e-05 $numProc [1] 4 $buildwin [1] 1 $winGap [1] 0 $pWinSize [1] 200 $pquant [1] 1 $refinepeaks [1] 1 $printFullOut [1] 1 $method [1] "mixture" $initmethod [1] "count" $diff [1] 0 $filetype [1] "tagAlign" $extension [1] 200 $cleanup [1] FALSE $selectmodel [1] TRUE $selectchr [1] "chr22" $selecttype [1] "complete" $selectcovs [1] "input_count" $FDR [1] TRUE Loading required package: multicore Loading required package: doMC Loading required package: foreach foreach: simple, scalable parallel programming from Revolution Analytics Use Revolution R for scalability, fault tolerance and more. http://www.revolutionanalytics.com Loading required package: iterators Loading required package: parallel Attaching package: ‘parallel’ The following objects are masked from ‘package:multicore’: mclapply, mcparallel, pvec Overwriting previously existing directory test_data/data/ctcf_files/ --------BEGIN BUILDING WINDOW DATA-------- 2014-01-12 20:59:46 Error in twigfiles[[i]] : subscript out of bounds > traceback() 3: buildwindowdata(seq = seq, align = align, input = input, twoBit = twoBit, winSize = winSize, offset = offset, cnvWinSize = cnvWinSize, cnvOffset = cnvOffset, filelist = filelist, filetype = filetype, extension = extension, outdir = outfile_subdir) 2: run.zinba(align = align, numProc = numProc, seq = seq, input = input, basecountfile = basecountfile, filetype = filetype, offset = 125, buildwin = 1, outfile = outfile, threshold = threshold, twoBit = twoBit, cnvOffset = 2500, pquant = 1, winGap = winGap, cnvWinSize = 1e+05, initmethod = "count", printFullOut = 1, winSize = 250, diff = 0, pWinSize = 200, extension = extension, method = "mixture", refinepeaks = refinepeaks, selectmodel = TRUE, selectchr = "chr22", selecttype = selecttype, selectcovs = selectcovs, FDR = FDR, interaction = interaction, peakconfidence = peakconfidence) 1: zinba(align = "align_athresh1_extension200/", numProc = 4, seq = "test_data/data/ctcfGM12878rep3chr22.taf", basecountfile = "test_data/data/ctcfGM12878rep3chr22.basecount", filetype = "tagAlign", outfile = "test_data/data/ctcf", twoBit = "hg19.2bit", extension = 200, printFullOut = 1, refinepeaks = 1, broad = F, input = "test_data/data/inputGM12878rep3chr22.taf")
Original issue reported on code.google.com by ZhCong....@gmail.com on 12 Jan 2014 at 12:48
ZhCong....@gmail.com
Original issue reported on code.google.com by
ZhCong....@gmail.comon 12 Jan 2014 at 12:48