DEGseq error

[yueli]

Hi,

I try to use DEGseq to process my miRNA data which only have *.fasta file.

I used bowtie to alignment my 1.fa.txt and 2.fa.txt to the contigs.fa, then use convert2bed transform my *.sam files to *.bed files.

I made the refFlat file of miRNAs in planarian Schmidtea midterranea shown as refFlatmiR_smed.

Any suggestions are appreciated!

Li




> kidneyR1L1 <- system.file("extdata", "contigs_1.bed.txt", package="DEGseq")
> liverR1L2 <- system.file("extdata", "contigs_2.bed.txt", package="DEGseq")
> refFlat <- system.file("extdata", "refFlatmiR_smed", package="DEGseq")
> mapResultBatch1 <- c(kidneyR1L1)
> mapResultBatch2 <- c(liverR1L2)
> outputDir <- file.path(tempdir(), "DEGseqExample")
> DEGseq(mapResultBatch1, mapResultBatch2, fileFormat="bed", refFlat=refFlat, outputDir=outputDir, method="LRT")
Please wait...

mapResultBatch1:
/home/li/R/x86_64-pc-linux-gnu-library/2.15/DEGseq/extdata/contigs_1.bed.txt
mapResultBatch2:
/home/li/R/x86_64-pc-linux-gnu-library/2.15/DEGseq/extdata/contigs_2.bed.txt
file format: bed
refFlat: /home/li/R/x86_64-pc-linux-gnu-library/2.15/DEGseq/extdata/refFlatmiR_smed
Ignore the strand information when count the reads mapped to genes!
Count the number of reads mapped to each gene ...
This will take several minutes, please wait patiently!
Please wait...

SampleFiles:
/home/li/R/x86_64-pc-linux-gnu-library/2.15/DEGseq/extdata/contigs_1.bed.txt
Count the number of reads mapped to each gene.
This will take several minutes.
Please wait ...

*** caught segfault ***
address 0xfffffffffffffff8, cause 'memory not mapped'

Traceback:
1: .C(".getGeneExp", as.character(refFlat), as.character(mapResultBatch), as.integer(length(mapResultBatch)), as.character(output), as.character(fileFormat), as.integer(readLength), as.integer(needStrand), as.numeric(min.overlapPercent))
2: getGeneExp(mapResultBatch1, fileFormat, readLength, strandInfo, refFlat, GeneExp1)
3: DEGseq(mapResultBatch1, mapResultBatch2, fileFormat = "bed", refFlat = refFlat, outputDir = outputDir, method = "LRT")

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: