User: mhills

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mhills10
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Canada
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Posts by mhills

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Comment: C: Rsamtools memory leak
... Thanks Aaron, I think one difference is that I'm loading in more and bigger bam files than the dataset from RNAseqData.HNRNPC.bam.chr14.  I edited the code above with a second loop, to better assess the ~150 samples I'm dealing with: for(loop in 1:20) { message('loop ', loop) for(fileName in ...
written 3.6 years ago by mhills10
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Comment: C: Rsamtools memory leak
... When I reran my validation this morning I hadn't realized it was on a computer with an older version of Rsamtools installed.  I just tried again on the computer with Rsamtools 1.22.0 and I'm still seeing the memory leak, including when I run the above loop with RNAseqData.HNRNPC.bam.chr14.  Would so ...
written 3.6 years ago by mhills10
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Comment: C: Rsamtools memory leak
... Thanks Martin! I should have mentioned I've been running this all through terminal, not Rstudio. Thanks for the additional insight with the GRanges approach. I confess I don't come from a computational background, but have used GenomicRanges a bit, so will give this a go.  Thanks again! ...
written 3.6 years ago by mhills10
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Answer: A: Rsamtools memory leak
... EDIT: I'm adding this to the main section, because it'll probably look choppy in the comments, but I changed things around as recommended by Martin Morgan, and for some reason, I'm only getting an increase in system memory if param is specified within the loop, but not if it's specified outside of ...
written 3.6 years ago by mhills10
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Comment: C: Rsamtools memory leak
... Could well be related. Have you monitored RAM? Our lab is pretty small fry, so I'm only on a computer with 16Gb RAM to do all the analysis. After getting the inital error, I monitored with a separate terminal running top -p `pgrep R | tr "\\n" "," | sed 's/,$//' command, and just watched my memory s ...
written 3.6 years ago by mhills10
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Comment: C: Rsamtools memory leak
... Hi Aaron, I'm not sure; I updated Bioconductor and Rsamtools at the same time.  I'm on Bioconductor v3.2 on R v3.2.2 using Rsamtools v1.22.0. My code was working fine on Bioconductor v3.1 with Rsamtools v1.18, but after updating it poops out after it loops through ~40 samples with a memory usage er ...
written 3.6 years ago by mhills10
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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 program. I have a folder of ~150 bam files that I'm trying to sequentially process, feeding in a data.frame called filter to scanBam(which), that splits the genome into 7 ...
iranges rsamtools granges bam scanbam written 3.6 years ago by mhills10

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