Open GoogleCodeExporter opened 8 years ago
1) What operating system are you using? CentOS release 5.5 2) What error message was displayed? *** caught segfault *** address 0x2b8615db1000, cause 'memory not mapped' Traceback: 1: .C("getSeqCountProfile", as.character(inputfile2), as.character(winlist), as.double(threshold), as.character(method), as.integer(printFullOut), as.character(outputfile), as.character(twobitfile), as.character(chromosome), as.integer(winGap), as.integer(FDR^2), as.integer(binary), PACKAGE = "zinba") 2: basecountimport(inputfile = basecountfile, winlist = winlist, threshold = threshold, method = method, printFullOut = printFullOut, outputfile = bpout, twobitfile = twoBit, winGap = winGap, FDR = FDR) 3: getrefinedpeaks(winlist = winlist, basecountfile = basecountfile, bpout = bpout, peakout = peakout, twoBit = twoBit, winSize = winSize, pWinSize = pWinSize, pquant = pquant, printFullOut = printFullOut, peakconfidence = peakconfidence, threshold = threshold, method = method, winGap = winGap, extension = extension, FDR = FDR) 4: run.zinba(buildwin = 1, refinepeaks = 1, peakconfidence = 0.95, seq = "./bowtie/GM12878_faire_rep1.new.hits", input = "none", filetype = "bowtie", twoBit = "./goldenPath/hg18/bigZips/hg18.2bit", winSize = 250, offset = 125, extension = 134, basecountfile = "data/GM12878_faire_rep1.basecount", align = "align_athresh4_extension134/", formula = exp_count ~ gcPerc + align_perc + exp_cnvwin_log, formulaE = exp_count ~ 1, formulaZ = exp_count ~ gcPerc + align_perc + exp_cnvwin_log, numProc = 4, winGap = 0, outfile = "./faire", printFullOut = 1, method = "mixture") aborting ... /opt/gridengine/default/spool/compute-23-41/job_scripts/4463872: line 1: 11695 Segmentation fault Rscript runZinba.R 3) What was the exact command you used that resulted in the error? library(zinba) basecountimport( inputfile='./data/GM12878_faire_rep1.basecount', winlist='./faire_files/faire.winlist', threshold=.01, method='mixture', printFullOut=1, twobitfile='./goldenPath/hg18/bigZips/hg18.2bit', outputfile='./temp.file' ) 4) Please copy and paste any additional screen output that resulted from running the command I'm using ZINBA version 2.02.03. It's a similar problem like jing...@gmail.com report, but I'm not expert programmer at all,I need to help. Thanks!
Original issue reported on code.google.com by scu...@gmail.com on 6 Mar 2013 at 3:32
scu...@gmail.com
Original issue reported on code.google.com by
scu...@gmail.com
on 6 Mar 2013 at 3:32