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?
I'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.
Thanks,
Lilly
Hello lillyhchen!
It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/69850/
This is typically not recommended as it runs the risk of annoying people in both communities.
OK, there seems to be something weird here. The content by lillyhchen is 21 months old and the user has not been seen recently, The post shows an edit by moderator zx8754 with new content that does not seem pertinent to this question.
What is happening here? Paging Pierre Lindenbaum Devon Ryan Istvan Albert