Hi,
I am running a paired analysis for 2 tumor samples following the
vignette for 5.0/6.0. Here is how I run it:
gi <- getGenomeInformation(cdf)
si <- getSnpInformation(cdf)
cs <- AffymetrixCelSet$byName("ICGC,6.0,testSet", cdf=cdf)
acc <- AllelicCrosstalkCalibration(cs)
csC <- process(acc, verbose=verbose)
plm <- AvgCnPlm(csC, mergeStrands=TRUE, combineAlleles=TRUE, shift=
+300)
if (length(findUnitsTodo(plm)) > 0) {
# Fit CN probes quickly (~5-10s/array + some overhead)
units <- fitCnProbes(plm, verbose=verbose)
str(units)
# int [1:945826] 935590 935591 935592 935593 935594 935595 ...
# Fit remaining units, i.e. SNPs (~5-10min/array)
units <- fit(plm, verbose=verbose)
str(units)
}
ces <- getChipEffectSet(plm)
fln <- FragmentLengthNormalization(ces)
cesN <- process(fln, verbose=verbose)
cesC <- extract(cesN, c(1,3)) ## test arrays
cesT <- extract(cesN, c(5,4)) ## control arrays
cbs <- CbsModel(cesT, cesC)
ce <- ChromosomeExplorer(cbs)
process(ce, arrays=1, chromosomes=1, verbose=verbose)
After this point I get the following segfault:
20090827 16:03:19|Generating ChromosomeExplorer report...
20090827 16:03:19| Setting up ChromosomeExplorer report files...
20090827 16:03:19| Copying template files...
20090827 16:03:19| Source path: /soft/lib64/R/library/aroma.core/
reports/includes
20090827 16:03:19| Destination path: reports/includes
20090827 16:03:20| Copying template files...done
20090827 16:03:20| Setting up ChromosomeExplorer report files...done
20090827 16:03:20| Explorer output version: 3
20090827 16:03:20| Compiling ChromosomeExplorer.onLoad.js.rsp...
20090827 16:03:20| Source: /soft/lib64/R/library/aroma.core/reports/
templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
20090827 16:03:20| Output path: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired
20090827 16:03:20| Scanning directories for available chip types...
20090827 16:03:20| Detected chip types: GenomeWideSNP_6
20090827 16:03:20| Scanning directories for available chip
types...done
20090827 16:03:20| Scanning image files for available zooms...
20090827 16:03:20| Detected (or default) zooms: 1, 2, 4, 8, 16, 32,
64
20090827 16:03:20| Scanning image files for available zooms...done
20090827 16:03:20| Scanning directory for subdirectories...
20090827 16:03:20| Detected (or default) sets: cbs
20090827 16:03:20| Scanning directory for subdirectories...done
20090827 16:03:20| Compiling RSP...
20090827 16:03:20| Compiling RSP...done
20090827 16:03:20| Compiling ChromosomeExplorer.onLoad.js.rsp...done
Loading required package: Cairo
20090827 16:03:21| Using reference tuple:
ChipEffectSetTuple:
Name: ICGC
Tags: 6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Chip types: GenomeWideSNP_6
CnChipEffectSet:
Name: ICGC
Tags: 6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Path: plmData/ICGC,6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/
GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full,monocell
Number of arrays: 2
Names: 001ND-GenomeWideSNP6, 003ND-GenomeWideSNP6
Time period: 2009-08-17 17:52:48 -- 2009-08-17 17:52:48
Total file size: 53.90MB
RAM: 0.01MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
RAM: 0.00MB
20090827 16:03:21| Chip-effect tags:
20090827 16:03:21| Reference tags: 5eec0710efc02dd1b5050cb04ae98a78
20090827 16:03:21| Array #1 ('01TD-GenomeWideSNP6') of 1 on chromosome
1...
20090827 16:03:21| Loading results from file...
20090827 16:03:21| Pathname: cbsData/ICGC,6.0,testSet,ACC,ra,-XY,AVG,
+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/01TD-
GenomeWideSNP6,chr01,5eec0710efc02dd1b5050cb04ae98a78.xdr
20090827 16:03:22| Fit object: DNAcopy
20090827 16:03:22| Loading results from file...done
20090827 16:03:22| Calling onFit.CopyNumberSegmentationModel()
hooks...
20090827 16:03:22| Plotting 01TD-GenomeWideSNP6 for chromosome 01
[245.20MB]...
20090827 16:03:22| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0128.png
20090827 16:03:22| Dimensions: 94258x400
20090827 16:03:22| Ticks by: 0.010000
20090827 16:03:22| Plotting graph...
Loading required package: GLAD
[1] "Have fun with GLAD"
[1] "For smoothing it is possible to use either"
[1] "the AWS algorithm (Polzehl and Spokoiny, 2002)"
[1] "or the HaarSeg algorithm (Ben-Yaacov and Eldar, 2008)"
[1] ""
[1] "If you use the package with AWS, please cite:"
[1] "Hupe et al. (2004) and Polzehl and Spokoiny (2002)"
[1] ""
[1] "If you use the package with HaarSeg, please cite:"
[1] "Hupe et al. (2004) and (Ben-Yaacov and Eldar, 2008)"
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
*** caught segfault ***
address 0x2aaab8232000, cause 'memory not mapped'
Traceback:
1: dev.off()
2: tryCatch({ verbose && enter(verbose, "Plotting graph") opar
<- par(xaxs = "r") suppressWarnings({ newPlot(this, xlim =
xlim, ylim = ylim, flavor = "ce", unit = unit, ...)
drawXAxisRuler(xrange = c(0, nbrOfBases)/10^unit, ticksBy =
ticksBy) if (!identical(this$.plotCytoband, FALSE))
{ drawCytoband(this, chromosome = chromosome, unit =
unit) } cnLevels <- c(1/2, 1, 3/2) for (level in
cnLevels) { abline(h = log2(level), col = "blue", lty =
2) } rawCns <- extractRawCopyNumbers(fit) verbose
&& print(verbose, rawCns, level = -50) n <- nbrOfLoci(rawCns,
na.rm = TRUE) stext(text = sprintf("n=%d", n), side = 4, pos =
0, line = 0, cex = 0.8) pointsRawCNs(fit, unit =
unit, ...) cnRegions <- extractCopyNumberRegions(fit)
verbose && print(verbose, cnRegions, level = -50) drawLevels
(cnRegions, lwd = 4, col = "black", xScale = 1/10^unit)
drawExtraAnnotations(fit) onFitAddGenotypeCalls(fit, callList =
callList, arrayName = arrayName, resScale = 10^unit *
resScale, ...) }) stext(chipType, side = 4, pos = 1, line = 0,
cex = 0.8) verbose && exit(verbose)}, error = function(ex)
{ print(ex)}, finally = { par(opar) if (!imageFormat %in% c
("screen", "current")) dev.off()})
3: doTryCatch(return(expr), name, parentenv, handler)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
5: tryCatchList(expr, classes, parentenv, handlers)
6: tryCatch({ arrayFullName <- gsub("^(.*),chr[0-9][0-9].*$", "\
\1", fullname) arrayName <- gsub("^([^,]*).*$", "\\1",
arrayFullName) nbrOfBases <- genome$nbrOfBases[chromosome]
widthMb <- nbrOfBases/10^unit if (is.null(xlim)) { xlim <- c
(0, getChromosomeLength(chromosome))/10^unit } verbose && enter
(verbose, sprintf("Plotting %s for chromosome %02d [%.2fMB]",
arrayName, chromosome, widthMb)) for (zz in seq(along = zooms))
{ zoom <- zooms[zz] imgName <- sprintf("%s,chr%02d,x%04d.
%s", arrayFullName, chromosome, zoom, imageFormat)
pathname <- filePath(path, imgName) pathname <- gsub(" ", "_",
pathname) if (!imageFormat %in% c("screen", "current"))
{ if (skip && isFile(pathname))
{ next } } ticksBy <-
10^ceiling(log10(pixelsPerTick/(zoom * pixelsPerMb))) width <-
round(zoom * widthMb * pixelsPerMb + sum(xmargin)) verbose &&
printf(verbose, "Pathname: %s\n", pathname) verbose && printf
(verbose, "Dimensions: %dx%d\n", width, height)
verbose && printf(verbose, "Ticks by: %f\n", ticksBy) if (!
is.null(plotDev)) plotDev(pathname, width = width, height
= height) tryCatch({ verbose && enter(verbose,
"Plotting graph") opar <- par(xaxs = "r")
suppressWarnings({ newPlot(this, xlim = xlim, ylim =
ylim, flavor = "ce", unit =
unit, ...) drawXAxisRuler(xrange = c(0, nbrOfBases)/
10^unit, ticksBy = ticksBy) if (!
identical(this$.plotCytoband, FALSE)) { drawCytoband
(this, chromosome = chromosome, unit =
unit) } cnLevels <- c(1/2, 1,
3/2) for (level in cnLevels) { abline
(h = log2(level), col = "blue", lty =
2) } rawCns <- extractRawCopyNumbers
(fit) verbose && print(verbose, rawCns, level =
-50) n <- nbrOfLoci(rawCns, na.rm =
TRUE) stext(text = sprintf("n=%d", n), side = 4, pos =
0, line = 0, cex = 0.8) pointsRawCNs
(fit, unit = unit, ...) cnRegions <-
extractCopyNumberRegions(fit) verbose && print(verbose,
cnRegions, level = -50) drawLevels(cnRegions, lwd = 4,
col = "black", xScale = 1/10^unit)
drawExtraAnnotations(fit) onFitAddGenotypeCalls(fit,
callList = callList, arrayName = arrayName, resScale
= 10^unit *
resScale, ...) }) stext(chipType, side = 4, pos
= 1, line = 0, cex = 0.8) verbose && exit
(verbose) }, error = function(ex) { print
(ex) }, finally = { par(opar) if (!
imageFormat %in% c("screen", "current")) dev.off
() }) }}, error = function(ex) { cat("ERROR caught in ",
hookName, "():\n", sep = "") print(ex)}, finally = { gc <- gc
() verbose && print(verbose, gc) verbose && exit(verbose)})
7: fcn(...)
8: doTryCatch(return(expr), name, parentenv, handler)
9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
10: tryCatchList(expr, classes, parentenv, handlers)
11: tryCatch({ result <- fcn(...) tmp[["result"]] <- result
failedHooks[kk] <- FALSE}, error = function(ex) { tmp
[["exception"]] <<- ex})
12: callHooks.list(hooks, ...)
13: callHooks(hooks, ...)
14: callHooks.default(hookName, fit = fit, chromosome = chr, fullname
= fullname)
15: callHooks(hookName, fit = fit, chromosome = chr, fullname =
fullname)
16: fit.CopyNumberSegmentationModel(this, ..., .retResults =
FALSE, verbose = verbose)
17: fit(this, ..., .retResults = FALSE, verbose = verbose)
18: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
"png", plotband = plotband, arrays = arrays, ...)
19: plot(model, path = path, imageFormat = "png", plotband =
plotband, arrays = arrays, ...)
20: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes
= chromosomes, zooms = zooms, ..., verbose = less(verbose))
21: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
zooms = zooms, ..., verbose = less(verbose))
22: process.ChromosomeExplorer(ce, arrays = 1, chromosomes = 1,
verbose = verbose)
23: process(ce, arrays = 1, chromosomes = 1, verbose = verbose)
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: 2
Save workspace image? [y/n/c]: c
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 379904 20.3 667722 35.7 626840 33.5
Vcells 2264224 17.3 5329055 40.7 7803825 59.6
20090827 16:03:33| Plotting graph...done
20090827 16:03:33| Plotting 01TD-GenomeWideSNP6 for chromosome 01
[245.20MB]...done
20090827 16:03:33| Calling onFit.CopyNumberSegmentationModel()
hooks...done
20090827 16:03:33| Array #1 ('01TD-GenomeWideSNP6') of 1 on chromosome
1...done
20090827 16:03:33|Generating ChromosomeExplorer report...done
Here is my session info:
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
base
other attached packages:
[1] GLAD_2.0.0 Cairo_1.4-5
DNAcopy_1.18.0
[4] aroma.affymetrix_1.1.0 aroma.apd_0.1.6
R.huge_0.1.8
[7] affxparser_1.16.0 aroma.core_1.1.2
aroma.light_1.12.2
[10] matrixStats_0.1.6 R.rsp_0.3.4
R.filesets_0.5.2
[13] digest_0.3.1 R.cache_0.1.7
R.utils_1.1.7
[16] R.oo_1.4.8 R.methodsS3_1.0.3
loaded via a namespace (and not attached):
[1] RColorBrewer_1.0-2 tools_2.9.0
I checked the folder "reports/ICGC/6.0,testSet,ACC,ra,-XY,AVG,+300,A
+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/". 8 png files are generated for
chr1, all of which except the one fore 128X are OK. The last one is
corrupt.Following a suggestion given before, I deleted the folder
"reports/ICGC/6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY,paired" and
re-run the same script.This time R quited by itself. What could be the
problem?
Here is the second error by the way:
20090827 16:22:42|Generating ChromosomeExplorer report...
20090827 16:22:42| Setting up ChromosomeExplorer report files...
20090827 16:22:42| Copying template files...
20090827 16:22:42| Source path: /soft/lib64/R/library/aroma.core/
reports/includes
20090827 16:22:42| Destination path: reports/includes
20090827 16:22:42| Copying template files...done
20090827 16:22:42| Setting up ChromosomeExplorer report files...done
20090827 16:22:42| Copying ChromosomeExplorer.html...
20090827 16:22:42| Source pathname: /soft/lib64/R/library/aroma.core/
reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html
20090827 16:22:42| Destination pathname: reports/ICGC/
6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY,paired/
ChromosomeExplorer.html
20090827 16:22:43| Copying ChromosomeExplorer.html...done
20090827 16:22:43| Explorer output version: 3
20090827 16:22:43| Compiling ChromosomeExplorer.onLoad.js.rsp...
20090827 16:22:43| Source: /soft/lib64/R/library/aroma.core/reports/
templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
20090827 16:22:43| Output path: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired
20090827 16:22:43| Scanning directories for available chip types...
20090827 16:22:43| Detected chip types: GenomeWideSNP_6
20090827 16:22:43| Scanning directories for available chip
types...done
20090827 16:22:43| Scanning image files for available zooms...
20090827 16:22:43| Detected (or default) zooms: 1, 2, 4, 8, 16, 32,
64, 128
20090827 16:22:43| Scanning image files for available zooms...done
20090827 16:22:43| Scanning directory for subdirectories...
20090827 16:22:43| Detected (or default) sets: cbs
20090827 16:22:43| Scanning directory for subdirectories...done
20090827 16:22:43| Compiling RSP...
20090827 16:22:43| Compiling RSP...done
20090827 16:22:43| Compiling ChromosomeExplorer.onLoad.js.rsp...done
20090827 16:22:43| Using reference tuple:
ChipEffectSetTuple:
Name: ICGC
Tags: 6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Chip types: GenomeWideSNP_6
CnChipEffectSet:
Name: ICGC
Tags: 6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY
Path: plmData/ICGC,6.0,testSet,ACC,ra,-XY,AVG,+300,A+B,FLN,-XY/
GenomeWideSNP_6
Platform: Affymetrix
Chip type: GenomeWideSNP_6,Full,monocell
Number of arrays: 2
Names: 001ND-GenomeWideSNP6, 003ND-GenomeWideSNP6
Time period: 2009-08-17 17:52:48 -- 2009-08-17 17:52:48
Total file size: 53.90MB
RAM: 0.01MB
Parameters: (probeModel: chr "pm", mergeStrands: logi TRUE,
combineAlleles: logi TRUE)
RAM: 0.00MB
20090827 16:22:43| Chip-effect tags:
20090827 16:22:43| Reference tags: 5eec0710efc02dd1b5050cb04ae98a78
20090827 16:22:43| Array #1 ('01TD-GenomeWideSNP6') of 1 on chromosome
1...
20090827 16:22:43| Loading results from file...
20090827 16:22:43| Pathname: cbsData/ICGC,6.0,testSet,ACC,ra,-XY,AVG,
+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/01TD-
GenomeWideSNP6,chr01,5eec0710efc02dd1b5050cb04ae98a78.xdr
20090827 16:22:43| Fit object: DNAcopy
20090827 16:22:43| Loading results from file...done
20090827 16:22:43| Calling onFit.CopyNumberSegmentationModel()
hooks...
20090827 16:22:43| Plotting 01TD-GenomeWideSNP6 for chromosome 01
[245.20MB]...
20090827 16:22:43| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0001.png
20090827 16:22:43| Dimensions: 836x400
20090827 16:22:43| Ticks by: 1.000000
20090827 16:22:43| Plotting graph...
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
20090827 16:22:44| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0002.png
20090827 16:22:44| Dimensions: 1571x400
20090827 16:22:44| Ticks by: 1.000000
20090827 16:22:44| Plotting graph...
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
20090827 16:22:44| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0004.png
20090827 16:22:44| Dimensions: 3042x400
20090827 16:22:44| Ticks by: 1.000000
20090827 16:22:44| Plotting graph...
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
20090827 16:22:45| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0008.png
20090827 16:22:45| Dimensions: 5985x400
20090827 16:22:45| Ticks by: 1.000000
20090827 16:22:45| Plotting graph...
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
20090827 16:22:46| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0016.png
20090827 16:22:46| Dimensions: 11870x400
20090827 16:22:46| Ticks by: 0.100000
20090827 16:22:46| Plotting graph...
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
20090827 16:22:48| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0032.png
20090827 16:22:48| Dimensions: 23640x400
20090827 16:22:48| Ticks by: 0.100000
20090827 16:22:48| Plotting graph...
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
20090827 16:22:50| Pathname: reports/ICGC/6.0,testSet,ACC,ra,-
XY,AVG,+300,A+B,FLN,-XY,paired/GenomeWideSNP_6/cbs/01TD-
GenomeWideSNP6,chr01,x0064.png
20090827 16:22:50| Dimensions: 47179x400
20090827 16:22:50| Ticks by: 0.100000
20090827 16:22:50| Plotting graph...
<simpleError in mtext(text = text, side = side, line = line, at = at,
adj = adj, cex = cex, ..., xpd = TRUE): Metric information not
available for this device>
Segmentation fault
--~--~---------~--~----~------------~-------~--~----~
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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traceback(), and 3) to post a complete code example.
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