Dear Henrik,
Yes this seems obvious. I tried again, but the error remained. Also the TEMP
directory for writing is world rwx and has plenty of space left.
However the directory where the gzip file should be located does not exist:
'/scratch/tmp/RtmpwSx59C
I have manually generated the '/scratch/tmp/RtmpwSx59C' directory. With that
the 'process(fln, verbose=verbose)' runs now. So it seems that the
generation/selection of the TMP directory for writing/reading is causing the
error.
Here is the output from traceback()
> traceback()
19: gzfile(file, mode)
18: saveRDS(list(base = base, value = ret0), dest)
17: installed.packages()
16: findBasePkgs()
15: match(x, table, nomatch = 0L)
14: pkgs %in% findBasePkgs()
13: isBasePkgs(environmentName(where[[name]]))
12: cleanup.Globals(globals)
11: cleanup(globals)
10: getGlobalsAndPackages(expr, envir = envir, tweak = tweak, resolve = resolve,
persistent = persistent)
9: exportGlobals(expr, envir = envir, target = NULL, tweak = tweakExpression,
resolve = TRUE)
8: evaluator(expr, envir = envir, substitute = FALSE, ...)
7: (function (expr, envir = parent.frame(), substitute = TRUE, evaluator =
plan(),
...)
{
if (substitute)
expr <- substitute(expr)
if (!is.function(evaluator)) {
stop("Argument 'evaluator' must be a function: ", typeof(evaluator))
}
future <- evaluator(expr, envir = envir, substitute = FALSE,
...)
if (!inherits(future, "Future")) {
stop("Argument 'evaluator' specifies a function that does not return
a Future object: ",
paste(sQuote(class(future)), collapse = ", "))
}
future
})({
verbose && enter(verbose, "Getting theta estimates")
theta <- extractTheta(ce, units = cellMatrixMap, drop = FALSE,
verbose = less(verbose, 5))
verbose && str(verbose, theta)
verbose && summary(verbose, theta)
verbose && exit(verbose)
verbose && enter(verbose, "Calculating total signals")
if (ncol(theta) > 1) {
y <- theta
y[is.na(y)] <- 0
for (cc in 2:ncol(y)) {
y[, 1] <- y[, 1] + y[, cc]
}
y <- y[, 1, drop = TRUE]
}
else {
y <- theta[, 1, drop = TRUE]
}
verbose && cat(verbose, "Total thetas:")
verbose && str(verbose, y)
verbose && exit(verbose)
verbose && enter(verbose, "Normalizing log2 signals")
if (shift != 0)
y <- y + shift
y <- log2(y)
verbose && cat(verbose, "Log2 signals:")
verbose && str(verbose, y)
yN <- .normalizeFragmentLength(y, fragmentLengths = fl, targetFcns =
targetFcns,
subsetToFit = subset, onMissing = onMissing, ...)
verbose && cat(verbose, "Normalized log2 signals:")
verbose && summary(verbose, yN)
rho <- y - yN
y <- yN <- NULL
rho <- 2^rho
verbose && cat(verbose, "Normalization scale factors:")
verbose && summary(verbose, rho)
stopifnot(length(rho) == nrow(theta))
ok <- which(is.finite(rho))
verbose && str(verbose, ok)
theta[ok, ] <- theta[ok, ]/rho[ok]
ok <- rho <- NULL
verbose && cat(verbose, "Normalized thetas:")
verbose && str(verbose, theta)
verbose && summary(verbose, theta)
verbose && exit(verbose)
verbose && enter(verbose, "Creating CEL file for results, if missing")
isFile <- isFile(pathname)
pathnameT <- pushTemporaryFile(pathname, isFile = isFile,
verbose = verbose)
ceN <- createFrom(ce, filename = pathnameT, path = NULL,
verbose = less(verbose))
verbose && exit(verbose)
if (inherits(ce, "SnpChipEffectFile")) {
ceN$mergeStrands <- ce$mergeStrands
if (inherits(ce, "CnChipEffectFile")) {
ceN$combineAlleles <- ce$combineAlleles
}
}
setCdf(ceN, cdf)
verbose && enter(verbose, "Storing normalized signals")
ok <- which(is.finite(cellMatrixMap))
cells <- cellMatrixMap[ok]
data <- theta[ok]
ok <- theta <- NULL
verbose2 <- -as.integer(verbose) - 5
pathnameN <- getPathname(ceN)
.updateCel(pathnameN, indices = cells, intensities = data,
verbose = verbose2)
cells <- data <- ceN <- NULL
verbose && exit(verbose)
popTemporaryFile(pathnameT, verbose = verbose)
dfZ <- getChecksumFile(pathname)
gc <- gc()
verbose && print(verbose, gc)
pathname
}, envir = <environment>)
6: do.call(future::future, args = future.args, envir = assign.env)
5: futureAssign(name, expr, envir = envir, assign.env = assign.env,
substitute = FALSE)
4: futureAssignInternal(target, expr, envir = envir, substitute = FALSE)
3: res[[kk]] %<=% {
verbose && enter(verbose, "Getting theta estimates")
theta <- extractTheta(ce, units = cellMatrixMap, drop = FALSE,
verbose = less(verbose, 5))
verbose && str(verbose, theta)
verbose && summary(verbose, theta)
verbose && exit(verbose)
verbose && enter(verbose, "Calculating total signals")
if (ncol(theta) > 1) {
y <- theta
y[is.na(y)] <- 0
for (cc in 2:ncol(y)) {
y[, 1] <- y[, 1] + y[, cc]
}
y <- y[, 1, drop = TRUE]
}
else {
y <- theta[, 1, drop = TRUE]
}
verbose && cat(verbose, "Total thetas:")
verbose && str(verbose, y)
verbose && exit(verbose)
verbose && enter(verbose, "Normalizing log2 signals")
if (shift != 0)
y <- y + shift
y <- log2(y)
verbose && cat(verbose, "Log2 signals:")
verbose && str(verbose, y)
yN <- .normalizeFragmentLength(y, fragmentLengths = fl, targetFcns =
targetFcns,
subsetToFit = subset, onMissing = onMissing, ...)
verbose && cat(verbose, "Normalized log2 signals:")
verbose && summary(verbose, yN)
rho <- y - yN
y <- yN <- NULL
rho <- 2^rho
verbose && cat(verbose, "Normalization scale factors:")
verbose && summary(verbose, rho)
stopifnot(length(rho) == nrow(theta))
ok <- which(is.finite(rho))
verbose && str(verbose, ok)
theta[ok, ] <- theta[ok, ]/rho[ok]
ok <- rho <- NULL
verbose && cat(verbose, "Normalized thetas:")
verbose && str(verbose, theta)
verbose && summary(verbose, theta)
verbose && exit(verbose)
verbose && enter(verbose, "Creating CEL file for results, if missing")
isFile <- isFile(pathname)
pathnameT <- pushTemporaryFile(pathname, isFile = isFile,
verbose = verbose)
ceN <- createFrom(ce, filename = pathnameT, path = NULL,
verbose = less(verbose))
verbose && exit(verbose)
if (inherits(ce, "SnpChipEffectFile")) {
ceN$mergeStrands <- ce$mergeStrands
if (inherits(ce, "CnChipEffectFile")) {
ceN$combineAlleles <- ce$combineAlleles
}
}
setCdf(ceN, cdf)
verbose && enter(verbose, "Storing normalized signals")
ok <- which(is.finite(cellMatrixMap))
cells <- cellMatrixMap[ok]
data <- theta[ok]
ok <- theta <- NULL
verbose2 <- -as.integer(verbose) - 5
pathnameN <- getPathname(ceN)
.updateCel(pathnameN, indices = cells, intensities = data,
verbose = verbose2)
cells <- data <- ceN <- NULL
verbose && exit(verbose)
popTemporaryFile(pathnameT, verbose = verbose)
dfZ <- getChecksumFile(pathname)
gc <- gc()
verbose && print(verbose, gc)
pathname
}
2: process.FragmentLengthNormalization(fln, verbose = verbose)
1: process(fln, verbose = verbose)
-----Ursprüngliche Nachricht-----
Von: aroma-affymetrix@googlegroups.com
[mailto:aroma-affymetrix@googlegroups.com] Im Auftrag von Henrik Bengtsson
Gesendet: Mittwoch, 13. Juli 2016 17:45
An: aroma-affymetrix <aroma-affymetrix@googlegroups.com>
Betreff: Re: [aroma.affymetrix] troubles in doing PCR fragment length
normalization AROMA3.0
That looks like a hiccup in the file system or something. Did you try again?
Also, if the error remains, please report what traceback() outputs (as the
first command after you get the error).
/Henrik
On Wed, Jul 13, 2016 at 4:19 AM, <thomas.grombac...@merckgroup.com> wrote:
> Hello,
>
> I have used the standard pipeline for SNP6 CEL files described in the
> CRMAv2 vignette. I did run the pipeline before several times, without any
> issue.
> Now, the fragment length normalization step failed with an error:
>
> Error in gzfile(file, mode) : cannot open the connection
>
> I am not clear where this error comes from.
> Any support or idea is welcome.
>
> Best regards,
> Thomas
>
> My sessionInfo:
>
>> sessionInfo()
>
> R version 3.2.1 (2015-06-18)
>
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
>
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
>
> [1] aroma.light_3.0.0 aroma.affymetrix_3.0.0 aroma.core_3.0.0
>
> [4] R.devices_2.14.0 R.filesets_2.10.0 R.utils_2.3.0
>
> [7] R.oo_1.20.0 affxparser_1.42.0 R.methodsS3_1.7.1
>
> loaded via a namespace (and not attached):
>
> [1] matrixStats_0.50.2 codetools_0.2-14 listenv_0.6.0 future_0.14.0
>
> [5] digest_0.6.9 R.huge_0.9.0 PSCBS_0.61.0 tools_3.2.1
>
> [9] R.cache_0.12.0 parallel_3.2.1 base64enc_0.1-3 aroma.apd_0.6.0
>
> [13] R.rsp_0.30.0 globals_0.6.1 DNAcopy_1.44.0
>
>
> The full output of the process(fln, verbose=verbose) function:
>
>> cesN <- process(fln, verbose=verbose)
>
>
> 20160713 12:50:05|Normalizing set for PCR fragment-length effects...
>
>
> 20160713 12:51:07| Identifying SNP and CN units...
>
>
> types
>
>
> 1 2 5
>
>
> 621 934968 945826
>
>
> 20160713 12:51:09| subsetToUpdate:
>
>
> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
>
>
> 20160713 12:51:09| Identifying SNP and CN units...done
>
>
> 20160713 12:51:09| Retrieving SNP information annotations...
>
>
> UflSnpInformation:
>
>
> Name: GenomeWideSNP_6
>
>
> Tags: Full,na33,hg19,dbSNP137,HB20140118
>
>
> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
>
>
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1
> 9,dbSNP137,HB20140118.ufl
>
>
> File size: 7.18 MiB (7526422 bytes)
>
>
> RAM: 0.00 MB
>
>
> Chip type: GenomeWideSNP_6,Full
>
>
> Number of enzymes: 2
>
>
> 20160713 12:51:10| Retrieving SNP information annotations...done
>
>
> 20160713 12:51:10| Identifying the subset used to fit normalization
> function(s)...
>
>
> 20160713 12:51:10| Identifying units that are SNP and CN probes...
>
>
> UflSnpInformation:
>
>
> Name: GenomeWideSNP_6
>
>
> Tags: Full,na33,hg19,dbSNP137,HB20140118
>
>
> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
>
>
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1
> 9,dbSNP137,HB20140118.ufl
>
>
> File size: 7.18 MiB (7526422 bytes)
>
>
> RAM: 0.00 MB
>
>
> Chip type: GenomeWideSNP_6,Full
>
>
> Number of enzymes: 2
>
>
> 20160713 12:51:10| Identifying SNPs and CN probes...
>
>
> types
>
>
> 1 2 5
>
>
> 621 934968 945826
>
>
> 20160713 12:51:11| units:
>
>
> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
>
>
> 20160713 12:51:11| Identifying SNPs and CN probes...done
>
>
> 20160713 12:51:11| Identify subset of units from genome information...
>
>
> 20160713 12:51:11| subsetToFit: -XY
>
>
> UgpGenomeInformation:
>
>
> Name: GenomeWideSNP_6
>
>
> Tags: Full,na33,hg19,dbSNP137,HB20140118
>
>
> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
>
>
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1
> 9,dbSNP137,HB20140118.ugp
>
>
> File size: 8.97 MiB (9407882 bytes)
>
>
> RAM: 0.00 MB
>
>
> Chip type: GenomeWideSNP_6,Full
>
>
> 20160713 12:51:18| Units to exclude:
>
>
> int [1:96544] 61101 61102 61103 61104 61105 61106 61107 61108 61109
> 61110 ...
>
>
> 20160713 12:51:19| Units to include:
>
>
> int [1:1784871] 1 2 3 4 5 6 7 8 9 10 ...
>
>
> 20160713 12:51:19| Identify subset of units from genome
> information...done
>
>
> 20160713 12:51:19| Reading fragment lengths...
>
>
> 20160713 12:51:19| Reading and filtering fragment lengths...
>
>
> 20160713 12:51:19| Reading fragment lengths...
>
>
> UflSnpInformation:
>
>
> Name: GenomeWideSNP_6
>
>
> Tags: Full,na33,hg19,dbSNP137,HB20140118
>
>
> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
>
>
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1
> 9,dbSNP137,HB20140118.ufl
>
>
> File size: 7.18 MiB (7526422 bytes)
>
>
> RAM: 0.00 MB
>
>
> Chip type: GenomeWideSNP_6,Full
>
>
> Number of enzymes: 2
>
>
> 20160713 12:51:26| Summary of non-filtered fragment lengths:
>
>
> int [1:1880794, 1:2] 395 4056 633 831 970 1508 4025 4557 3779 420 ...
>
>
> V1 V2
>
>
> Min. : 7.0 Min. : 7
>
>
> 1st Qu.: 430.0 1st Qu.: 628
>
>
> Median : 676.0 Median : 1078
>
>
> Mean : 915.2 Mean : 1410
>
>
> 3rd Qu.: 970.0 3rd Qu.: 1730
>
>
> Max. :32767.0 Max. :32767
>
>
> NA's :2279 NA's :447301
>
>
> 20160713 12:51:27| Reading fragment lengths...done
>
>
> 20160713 12:51:27| Filtering fragment lengths...
>
>
> 20160713 12:51:27| Filtering fragment lengths...done
>
>
> 20160713 12:51:27| Reading and filtering fragment lengths...done
>
>
> 20160713 12:51:27| Reading fragment lengths...done
>
>
> 20160713 12:51:28| Identifying units that are SNP and CN probes...done
>
>
> int [1:1784250] 622 623 624 625 626 627 628 629 630 631 ...
>
>
> 20160713 12:51:28| Identifying the subset used to fit normalization
> function(s)...done
>
>
> 20160713 12:51:28| Shift: 0
>
>
> 20160713 12:51:28| onMissing: median
>
>
> 20160713 12:51:28| Array #1 of 1213
> ('ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002')...
>
>
> 20160713 12:51:28| Reading and filtering fragment lengths...
>
>
> 20160713 12:51:28| Reading fragment lengths...
>
>
> UflSnpInformation:
>
>
> Name: GenomeWideSNP_6
>
>
> Tags: Full,na33,hg19,dbSNP137,HB20140118
>
>
> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
>
>
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1
> 9,dbSNP137,HB20140118.ufl
>
>
> File size: 7.18 MiB (7526422 bytes)
>
>
> RAM: 14.36 MB
>
>
> Chip type: GenomeWideSNP_6,Full
>
>
> Number of enzymes: 2
>
>
> 20160713 12:51:33| Summary of non-filtered fragment lengths:
>
>
> int [1:1880794, 1:2] 395 4056 633 831 970 1508 4025 4557 3779 420 ...
>
>
> V1 V2
>
>
> Min. : 7.0 Min. : 7
>
>
> 1st Qu.: 430.0 1st Qu.: 628
>
>
> Median : 676.0 Median : 1078
>
>
> Mean : 915.2 Mean : 1410
>
>
> 3rd Qu.: 970.0 3rd Qu.: 1730
>
>
> Max. :32767.0 Max. :32767
>
>
> NA's :2279 NA's :447301
>
>
> 20160713 12:51:37| Reading fragment lengths...done
>
>
> 20160713 12:51:37| Filtering fragment lengths...
>
>
> 20160713 12:51:37| Filtering fragment lengths...done
>
>
> 20160713 12:51:37| Reading and filtering fragment lengths...done
>
>
> V1 V2
>
>
> Min. : 7.0 Min. : 7
>
>
> 1st Qu.: 430.0 1st Qu.: 628
>
>
> Median : 676.0 Median : 1078
>
>
> Mean : 915.2 Mean : 1410
>
>
> 3rd Qu.: 970.0 3rd Qu.: 1730
>
>
> Max. :32767.0 Max. :32767
>
>
> NA's :2279 NA's :447301
>
>
> int [1:1784250] 1 2 3 4 5 6 7 8 9 10 ...
>
>
> UflSnpInformation:
>
>
> Name: GenomeWideSNP_6
>
>
> Tags: Full,na33,hg19,dbSNP137,HB20140118
>
>
> Full name: GenomeWideSNP_6,Full,na33,hg19,dbSNP137,HB20140118
>
>
> Pathname:
> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na33,hg1
> 9,dbSNP137,HB20140118.ufl
>
>
> File size: 7.18 MiB (7526422 bytes)
>
>
> RAM: 14.36 MB
>
>
> Chip type: GenomeWideSNP_6,Full
>
>
> Number of enzymes: 2
>
>
> 20160713 12:51:40| Setting up predefined target functions...
>
>
> 20160713 12:51:40| Target type: zero
>
>
> 20160713 12:51:40| Setting up predefined target functions...done
>
>
> 20160713 12:51:40| Getting cell matrix map...
>
>
> 'UnitGroupCellMatrixMap' int [1:1880794, 1:2] 622 624 626 628 630 632
> 634
> 636 638 640 ...
>
>
> 20160713 12:51:44| Getting cell matrix map...done
>
>
> Error in gzfile(file, mode) : cannot open the connection
>
>
> In addition: Warning message:
>
>
> In gzfile(file, mode) :
>
>
> cannot open compressed file
> '/scratch/tmp/RtmpwSx59C/libloc_178_ccc298d560fce69b.rds', probable
> reason 'No such file or directory'
>
>
> 20160713 12:51:45| Array #1 of 1213
> ('ARLES_p_NCLE_DNAAffy2_S_GenomeWideSNP_6_A01_256002')...done
>
>
> 20160713 12:51:45|Normalizing set for PCR fragment-length
> effects...done
>
>
>
>
>
> --
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of
> sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google
> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
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