Question: Rippseeker problem with allocate space
0
gravatar for jarod_v6@libero.it
20 months ago by
Italy
jarod_v6@libero.it40 wrote:

Dear All.

I try to make some comparison using RIPSeek I have this error on Centos 7.0

> setwd("~/Desktop/Analisi_ripseek/")
> extdata.dir <- "~/Desktop/Analisi_ripseek/mitico"
> bamFiles <- list.files(extdata.dir, "accepted_hits.bam$", recursive=TRUE, full.names=TRUE)
> ctlIgM <- combineAlignGals(grep(pattern="IgM", bamFiles, value=TRUE, invert=FALSE),reverseComplement=TRUE, genomeBuild="hg19")
Processing /home/mauro/Desktop/Analisi_ripseek/mitico/RIP1-IgM_R1/accepted_hits.bam ... Error: cannot allocate vector of size 2.3 Gb

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] RIPSeeker_1.12.0           rtracklayer_1.32.2         GenomicAlignments_1.8.4    Rsamtools_1.24.0          
 [5] Biostrings_2.40.2          XVector_0.12.1             SummarizedExperiment_1.2.3 Biobase_2.32.0            
 [9] GenomicRanges_1.24.3       GenomeInfoDb_1.8.7         IRanges_2.6.1              S4Vectors_0.10.3          
[13] BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
[1] XML_3.98-1.5       bitops_1.0-6       zlibbioc_1.18.0    BiocParallel_1.6.6 tools_3.3.2        RCurl_1.95-4.8    
>
ripseeker ripseek rip • 224 views
ADD COMMENTlink written 20 months ago by jarod_v6@libero.it40
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