Hi, I'm fairly new to R and bioinformatics and I'm working on a project with DESeq2 in R studio. I've been trying to run the "summarizeOverlaps" function on 12 bam files. However, I let it run over the weekend and the process still hasn't finished running. I don't think it's frozen, but i'm not sure if I should try and restart it again. Does anyone know of a faster way to work around SummarizeOverlap?
As Jim says, we need more information in order to help you. Please show the code of how you are calling summarizeOverlaps(). There are several options for managing memory when counting bam files, 'yieldSize' in BamFile, ScanBamParam for reading in subsets, etc. You may want to look at the Counting reads with summarizeOverlaps vignette, specifically section 2.
SorrI'm using RStudio 3.2.1 and I'm trying to run 12 BAM files that are each about 100,000 kb in size against a UCSC txdb GRangesList. The computer I'm using is windows8 with 16gb of RAM and a 3.4 ghz processor. When I terminate the summarizeOverlap function I get this warning message:
"Warning message: running command 'env MASTER=localhost PORT=11880 OUT=/dev/null RPROG=C:/PROGRA~1/R/R-32~1.1/bin/R R_LIBS= C:/Users/lchen/Documents/R/win-library/3.2/BiocParallel/RSOCKnode.sh' had status 127"
I'm wasn't sure what status 127 meant, but I checked the folder and found that the file was still there, so i'm not sure why I keep getting this error.