Hi,
I have the following problem running rGADEM on my fasta file.
Any advice would be greatly appreciated
I tried this code on Bio-Linux and Mac OS X Elcapitan.
These sessioninfo() follows the command lines.
Best regards,
K.Mano
>library(rGADEM)
>library(BSgenome.Hsapiens.UCSC.hg19)
> T_ac.seqs <- readDNAStringSet("chippeakanno/T_ac.fa", "fasta")
> T_ac.motif <- GADEM(T_ac.seqs, verbose = 1, genome = Hsapiens)
*** Start C Programm ***
*** caught segfault ***
address 0x1509e6eb4, cause 'memory not mapped'
Traceback:
1: .Call("GADEM_Analysis", sequenceFasta, Lengthfasta, accession, as.logical(verbose), numWordGroup, numTop3mer, numTop4mer, numTop5mer, numGeneration, populationSize, pValue, eValue, extTrim, minSpaceWidth, maxSpaceWidth, useChIPscore, numEM, fEM, widthWt, fullScan, slideWinPWM, stopCriterion, numBackgSets, weightType, bFileName, Spwm, minSites, maskR, nmotifs)
2: GADEM(T_ac.seqs, verbose = 1, genome = Hsapiens)
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:
-----------
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=ja_JP.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=ja_JP.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=ja_JP.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 rGADEM_2.16.0
[3] seqLogo_1.34.0 BSgenome_1.36.3
[5] rtracklayer_1.28.10 GenomicRanges_1.20.8
[7] GenomeInfoDb_1.4.3 Biostrings_2.36.4
[9] XVector_0.8.0 IRanges_2.2.9
[11] S4Vectors_0.6.6 BiocGenerics_0.14.0
loaded via a namespace (and not attached):
[1] XML_3.98-1.2 Rsamtools_1.20.5 bitops_1.0-6
[4] GenomicAlignments_1.4.2 futile.options_1.0.0 zlibbioc_1.14.0
[7] futile.logger_1.4.3 lambda.r_1.1.9 BiocParallel_1.2.22
[10] tools_3.2.0 RCurl_1.95-4.6
----------------
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] ja_JP.UTF-8/ja_JP.UTF-8/ja_JP.UTF-8/C/ja_JP.UTF-8/ja_JP.UTF-8
attached base packages:
[1] grid stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 rGADEM_2.24.0 seqLogo_1.42.0 BSgenome_1.44.1
[5] rtracklayer_1.36.4 GenomicRanges_1.28.4 GenomeInfoDb_1.12.2 Biostrings_2.44.2
[9] XVector_0.16.0 IRanges_2.10.2 S4Vectors_0.14.3 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] zlibbioc_1.22.0 GenomicAlignments_1.12.2 BiocParallel_1.10.1 lattice_0.20-35 tools_3.4.1
[6] SummarizedExperiment_1.6.3 Biobase_2.36.2 matrixStats_0.52.2 Matrix_1.2-11 GenomeInfoDbData_0.99.0
[11] bitops_1.0-6 RCurl_1.95-4.8 DelayedArray_0.2.7 compiler_3.4.1 Rsamtools_1.28.0
[16] XML_3.98-1.9
