SHZ66 / zinba

Automatically exported from code.google.com/p/zinba
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Segault on running zinba function #59

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago
Hi, It looks like thealignability and basealigncount work ok, but then I get a 
segfault on running zinba itself. If you might have any suggestions that would 
be really helpful

1) What operating system are you using?

Ubuntu 12.04

2) What error message was displayed?

Traceback:
 1: .C("buildWindows", as.character(seq), as.character(input), as.character(align),     as.character(twoBit), as.integer(winSize), as.integer(offset),     as.integer(cnvWinSize), as.integer(cnvOffset), a
s.character(filetype),     as.character(filelist), as.integer(extension), 
as.character(outdir),     PACKAGE = "zinba")
 2: buildwindowdata(seq = seq, align = align, input = input, twoBit = twoBit,     winSize = winSize, offset = offset, cnvWinSize = cnvWinSize,     cnvOffset = cnvOffset, filelist = filelist, filetype = f
iletype,     extension = extension, outdir = outfile_subdir)
 3: 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, me
thod = "mixture",     refinepeaks = refinepeaks, selectmodel = TRUE, selectchr 
= "chr22",     selecttype = selecttype, selectcovs = selectcovs, FDR = FDR,     
interaction = interaction, peakconfidence = 
peakconfidence)
 4: zinba(refinepeaks = 1, seq = "/lustre/---.bed",     filetype = "bed", threshold = 0.05, align = "/lustre/---/zinba_align_results",     , numProc = 1, twoBit = "/lustre/---/zinba_files/hg19.2bit",     outfile = "/lustre/---/atac",     extension = 250, basecountfile = "/lustre/---/basealignoutput.out")
 5: eval(expr, envir, enclos)
 6: eval(ei, envir)
 7: withVisible(eval(ei, envir))
 8: source("run_zinba.r")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 

3) What was the exact command you used that resulted in the error?

library(zinba)

generateAlignability(
    mapdir="/---/zinba_files", #mappability directory from unpacked mappability files
    outdir="/---/zinba_align_results", #directory for processed files, used later in analysis
    athresh=30, #number of hits per read allowed during mapping process
    extension=250, #average fragment library length
    twoBitFile="/---/zinba_files/hg19.2bit" #path to downloaded genome build file in .2bit format
)

basealigncount(
    inputfile="/---/12596_1#6.bed", #mapped sample reads
    outputfile="/---/basealignoutput.out", # output path
    extension=250, #average fragment library length
    filetype="bed", #either "bed", "bowtie", or "tagAlign"
    twoBitFile="/---/zinba_files/hg19.2bit" #path to downloaded genome build file in .2bit format
)

zinba(
    refinepeaks=1, #refine peaks? 1 for yes, 0 for no
    seq="/---/12596_1#6.bed", #path to mapped experimental reads
    #input="", #path to mapped input reads if available (default is "none")
    filetype="bed", #either 'bed', 'bowtie', or 'tagAlign'
    threshold=0.05, #FDR threshold, default is 0.05
    align="/---/zinba_align_results",, #path to alignability directory
    numProc=1, #number of CPUs to use, must be less than max available   (default 1)
    twoBit="/---/zinba_files/hg19.2bit", #path to genome build in .2bit format
    outfile="/---/zinba_results/atac", #prefix for outputted files
    extension=250, #average fragment library length (size selected)

    ###################
    #OPTIONAL PARAMETERS
    ###################

    basecountfile="/---/basealignoutput.out" #path to basecount file if refinepeaks is 1
    #broad=, #broad setting, TRUE or FALSE (default)
    #printFullOut=, #print original data with enrichment estimates, 1 for yes (more space required), 0 for no (default)
    #interaction=, #whether or not to considering interaction during model selection, TRUE (default) or FALSE
    #mode=, #either "peaks" for peak calling (default) or "CNV" for calling likely amplified CNV regions for reads in "seq" (input reads are best)
    #FDR= #either TRUE (default) or FALSE. If false, then uses posterior probability to threshold peaks using 1-threshold
)

4) Please copy and paste any additional screen output that resulted from
running the command

--------BEGIN BUILDING WINDOW DATA-------- 2014-04-30 11:48:25 

Importing reads from file /lustre/---.bed 
        Filetype is bed 
        Extension is 250 
        Getting chromosome lengths from .2bit file: /lustre/---hg19.2bit
                For chr1 length is 249250621
                For chr2 length is 243199373
                For chr3 length is 198022430
                For chr4 length is 191154276
                For chr5 length is 180915260
                For chr6 length is 171115067
                For chr7 length is 159138663
                For chrX length is 155270560
                For chr8 length is 146364022
                For chr9 length is 141213431
                For chr10 length is 135534747
                For chr11 length is 135006516
                For chr12 length is 133851895
                For chr13 length is 115169878
                For chr14 length is 107349540
                For chr15 length is 102531392
                For chr16 length is 90354753
                For chr17 length is 81195210
                For chr18 length is 78077248
                For chr20 length is 63025520
                For chrY length is 59373566
                For chr19 length is 59128983
                For chr22 length is 51304566
                For chr21 length is 48129895
                For chr6_ssto_hap7 length is 4928567
                For chr6_mcf_hap5 length is 4833398
                For chr6_cox_hap2 length is 4795371
                For chr6_mann_hap4 length is 4683263
                For chr6_apd_hap1 length is 4622290
                For chr6_qbl_hap6 length is 4611984
                For chr6_dbb_hap3 length is 4610396
                For chr17_ctg5_hap1 length is 1680828
                For chr4_ctg9_hap1 length is 590426
                For chr1_gl000192_random length is 547496
                For chrUn_gl000225 length is 211173
                For chr4_gl000194_random length is 191469
                For chr4_gl000193_random length is 189789
                For chr9_gl000200_random length is 187035
                For chrUn_gl000222 length is 186861
                For chrUn_gl000212 length is 186858
                For chr7_gl000195_random length is 182896
                For chrUn_gl000223 length is 180455
                For chrUn_gl000224 length is 179693
                For chrUn_gl000219 length is 179198
                For chr17_gl000205_random length is 174588
                For chrUn_gl000215 length is 172545
                For chrUn_gl000216 length is 172294
                For chrUn_gl000217 length is 172149
                For chr9_gl000199_random length is 169874
                For chrUn_gl000211 length is 166566
                For chrUn_gl000213 length is 164239
                For chrUn_gl000220 length is 161802
                For chrUn_gl000218 length is 161147
                For chr19_gl000209_random length is 159169
                For chrUn_gl000221 length is 155397
                For chrUn_gl000214 length is 137718
                For chrUn_gl000228 length is 129120
                For chrUn_gl000227 length is 128374
                For chr1_gl000191_random length is 106433
                For chr19_gl000208_random length is 92689
                For chr9_gl000198_random length is 90085
                For chr17_gl000204_random length is 81310
                For chrUn_gl000233 length is 45941
                For chrUn_gl000237 length is 45867
                For chrUn_gl000230 length is 43691
                For chrUn_gl000242 length is 43523
                For chrUn_gl000243 length is 43341
                For chrUn_gl000241 length is 42152
                For chrUn_gl000236 length is 41934
                For chrUn_gl000240 length is 41933
                For chr17_gl000206_random length is 41001
                For chrUn_gl000232 length is 40652
                For chrUn_gl000234 length is 40531
                For chr11_gl000202_random length is 40103
                For chrUn_gl000238 length is 39939
                For chrUn_gl000244 length is 39929
                For chrUn_gl000248 length is 39786
                For chr8_gl000196_random length is 38914
                For chrUn_gl000249 length is 38502
                For chrUn_gl000246 length is 38154
                For chr17_gl000203_random length is 37498
                For chr8_gl000197_random length is 37175
                For chrUn_gl000245 length is 36651
                For chrUn_gl000247 length is 36422
                For chr9_gl000201_random length is 36148
                For chrUn_gl000235 length is 34474
                For chrUn_gl000239 length is 33824
                For chr21_gl000210_random length is 27682
                For chrUn_gl000231 length is 27386
                For chrUn_gl000229 length is 19913
                For chrM length is 16571
                For chrUn_gl000226 length is 15008
                For chr18_gl000207_random length is 4262
                For chr18_gl000207_random length is 4262
        Importing bed formatted reads
        Skipped 0 reads
        Imported 3143646 reads
        Sorting reads ...COMPLETE

Building window data

Processing 
        Initializing to length 0
        Mapping reads to chromosome......

 *** caught segfault ***
address 0x123e0d5c, cause 'memory not mapped'

Traceback:
 1: .C("buildWindows", as.character(seq), as.character(input), as.character(align),     as.character(twoBit), as.integer(winSize), as.integer(offset),     as.integer(cnvWinSize), as.integer(cnvOffset), a
s.character(filetype),     as.character(filelist), as.integer(extension), 
as.character(outdir),     PACKAGE = "zinba")
 2: buildwindowdata(seq = seq, align = align, input = input, twoBit = twoBit,     winSize = winSize, offset = offset, cnvWinSize = cnvWinSize,     cnvOffset = cnvOffset, filelist = filelist, filetype = f
iletype,     extension = extension, outdir = outfile_subdir)
 3: 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, me
thod = "mixture",     refinepeaks = refinepeaks, selectmodel = TRUE, selectchr 
= "chr22",     selecttype = selecttype, selectcovs = selectcovs, FDR = FDR,     
interaction = interaction, peakconfidence = 
peakconfidence)
 4: zinba(refinepeaks = 1, seq = "/lustre/---.bed",     filetype = "bed", threshold = 0.05, align = "/lustre/---/zinba_align_results",     , numProc = 1, twoBit = "/lustre/---/zinba_files/hg19.2bit",     outfile = "/lustre/---/atac",     extension = 250, basecountfile = "/lustre/---/basealignoutput.out")
 5: eval(expr, envir, enclos)
 6: eval(ei, envir)
 7: withVisible(eval(ei, envir))
 8: source("run_zinba.r")

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 

Original issue reported on code.google.com by Tshah...@gmail.com on 30 Apr 2014 at 1:08