Great,
Thanks dpryan. I'll cross post at bioconductor support and wait for a site maintainer to get back to me.
Cheers!
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Apparently RSamtools isn't using the garbage collector. You might post this to the bioconductor support site and see if the maintainers reply.
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Hi dpryan,
So after running the loop described, my system memory states this session is using 2.579Gb RAM.
If I run gc() a few times, the system memory usage doesn't change and I get the following output:
Code:> gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1912702 102.2 3205452 171.2 3205452 171.2 Vcells 1579324 12.1 7866470 60.1 21256102 162.2 > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1912693 102.2 3205452 171.2 3205452 171.2 Vcells 1579327 12.1 6293176 48.1 21256102 162.2 > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1912693 102.2 3205452 171.2 3205452 171.2 Vcells 1579327 12.1 5034540 38.5 21256102 162.2 > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1912693 102.2 3205452 171.2 3205452 171.2 Vcells 1579327 12.1 5034540 38.5 21256102 162.2 > gc() used (Mb) gc trigger (Mb) max used (Mb) Ncells 1912693 102.2 3205452 171.2 3205452 171.2 Vcells 1579327 12.1 5034540 38.5 21256102 162.2
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Rsamtools memory leak
Hi there,
I've just updated Rsamtools to the latest version ("1.22.0") and I've noticed a weird memory leak that is crashing my system.
I have a folder of ~150 bam files that I'm trying to process, feeding in a data.frame called filter, that splits the genome into 7744 genomic coordinates
Code:> head(filter) V1 V2 V3 V4 1 GL896898 0 30180132 GL896898:0-30180132 2 GL896898 30180133 52375790 GL896898:30180133-52375790 3 GL896899 0 24984016 GL896899:0-24984016 4 GL896899 24984017 40953715 GL896899:24984017-40953715 5 GL896905 0 18438707 GL896905:0-18438707 6 GL896905 18438708 27910907 GL896905:18438708-27910907
Code:#R implementation of top library(NCmisc) #R value of all objects library(pryr) library(Rsamtools) filter=read.table('ferret_merged_sce_events.bed') fileName='AAAGCA.merge.bam' objectRam=vector() totalRam=vector() for(seq in 1:10) { message(paste("iteration", seq)) bam.dataframe <- scanBam(fileName, param=ScanBamParam(which=GRanges(seqnames = c(as.character(filter[,1])), ranges = IRanges(c(filter[,2]), c(filter[,3]) )), mapqFilter=10, what=c("rname","pos","strand"))) #measure RAM across all R objects objectRam <- c(objectRam, mem_used()[1]/10^6) #measure RAM across system totalRam <- c(totalRam, suppressWarnings(top(CPU=F)$RAM$used*10^6)) #remove scanBam object to reset for next iteration rm(bam.dataframe) #empty garbage collection gc() } plot(objectRam, type='l', xlab='iteration', ylab='Ram usage (Mb)') plot(totalRam, type='l', xlab='iteration', ylab='Ram usage (Mb)')
Any help would be greatly appreciated.Attached Files
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