**0**wrote:

I am using 'derfinder' to find differentially expressed regions using RNA-seq data. The tool works until some point and gets stuck after calculating p-values. Some of the intermediate files are created but it doesn't finish the analysis. Here is the log:

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Error in tools:::httpdPort <= 0L :

comparison (4) is possible only for atomic and list types

> library(derfinder)

Find out what's changed in derfinder with

news(Version == "1.2.0", package = "derfinder")

> library(GenomicRanges)

> library(BiocParallel)

> setwd("~/Research/Ring/rnaSeq/bams/");

>

> files <- Sys.glob(file.path(".","*chr20*.bam"))

> fullCov <- fullCoverage(files=files,chrs='20')

2015-06-12 14:07:26 fullCoverage: processing chromosome 20

2015-06-12 14:07:26 loadCoverage: finding chromosome lengths

2015-06-12 14:07:26 loadCoverage: loading BAM file ./E11-1.chr20.sorted.bam

2015-06-12 14:07:31 loadCoverage: loading BAM file ./E11-2.chr20.sorted.bam

2015-06-12 14:07:33 loadCoverage: loading BAM file ./E8-1.chr20.sorted.bam

2015-06-12 14:07:36 loadCoverage: loading BAM file ./E8-2.chr20.sorted.bam

2015-06-12 14:07:39 loadCoverage: applying the cutoff to the merged data

2015-06-12 14:07:39 filterData: originally there were 63025520 rows, now there are 63025520 rows. Meaning that 0 percent was filtered.

extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens

> filteredCov <- lapply(fullCov, filterData, cutoff = 2)

2015-06-12 14:07:40 filterData: originally there were 63025520 rows, now there are 3580364 rows. Meaning that 94.32 percent was filtered.

> sampleDepths <- sampleDepth(collapseFullCoverage(fullCov), 1)

2015-06-12 14:07:40 sampleDepth: Calculating sample quantiles

2015-06-12 14:07:40 sampleDepth: Calculating sample adjustments

> pheno <- data.frame(group = c("Ring","Ring","WT","WT"))

>

> models <- makeModels(sampleDepths, testvars = pheno$group)

> originalWd <- getwd()

> setwd(file.path(originalWd, 'analysisResults'))

>

> results <- analyzeChr(chr = '20', filteredCov$chr20, models, cutoffType='manual', mc.cores=6, method = 'regular', runAnnotation = 'false', BPPARAM.custom = MulticoreParam(workers = 6),

+ groupInfo = pheno$group, writeOutput = FALSE, cutoffFstat = 5e-02, nPermute = 5, seeds = 20140923 + seq_len(5), returnOutput = TRUE)

extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens

2015-06-12 14:09:07 analyzeChr: Pre-processing the coverage data

2015-06-12 14:09:18 analyzeChr: Calculating statistics

2015-06-12 14:09:18 calculateStats: calculating the F-statistics

2015-06-12 14:09:21 analyzeChr: Calculating pvalues

2015-06-12 14:09:21 analyzeChr: Using the following manual cutoff for the F-statistics 0.05

2015-06-12 14:09:21 calculatePvalues: identifying data segments

2015-06-12 14:09:21 findRegions: segmenting F-stats information

2015-06-12 14:09:21 findRegions: identifying candidate regions

2015-06-12 14:09:21 findRegions: identifying region clusters

2015-06-12 14:09:48 calculatePvalues: calculating F-statistics for permutation 1 and seed 20140924

2015-06-12 14:09:51 findRegions: segmenting F-stats information

2015-06-12 14:09:51 findRegions: identifying candidate regions

2015-06-12 14:09:51 calculatePvalues: calculating F-statistics for permutation 2 and seed 20140925

2015-06-12 14:09:53 findRegions: segmenting F-stats information

2015-06-12 14:09:53 findRegions: identifying candidate regions

2015-06-12 14:09:54 calculatePvalues: calculating F-statistics for permutation 3 and seed 20140926

2015-06-12 14:09:56 findRegions: segmenting F-stats information

2015-06-12 14:09:56 findRegions: identifying candidate regions

2015-06-12 14:09:56 calculatePvalues: calculating F-statistics for permutation 4 and seed 20140927

2015-06-12 14:09:58 findRegions: segmenting F-stats information

2015-06-12 14:09:59 findRegions: identifying candidate regions

2015-06-12 14:09:59 calculatePvalues: calculating F-statistics for permutation 5 and seed 20140928

2015-06-12 14:10:01 findRegions: segmenting F-stats information

2015-06-12 14:10:01 findRegions: identifying candidate regions

2015-06-12 14:10:01 calculatePvalues: calculating the p-values

It just gets stuck here. Any suggestions to fix?

Hi,

Can you please provide the session information? Thanks!

Best,

Leonardo

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