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