hpages
commented
4 years ago Hi Janet,
Ouch! That's an ugly one.
Compared to Linux your Mac is such a whiner ;-)
The workhorse behind readGalignmentPairs() is the scanBam() function from the Rsamtools package. And the workhorse behind scanBam() is a complex piece of C and C++ code in Rsamtools that is built on top of the HTSlib C library. The fact that you don't get the crash when you do readGAlignments() suggests that the problem is in the C++ code that implements the pairing algo (samread_mate() and bam_fetch_mate() functions in Rsamtools/src/bam_mate_iter.cpp).
This is how readGalignmentPairs() uses scanBam() to load the paired data:
library(Rsamtools)
path <- "mapToCombinedFlyYeastHumanGenomes_ATfiltReads/just_dm6_reads/zz_testR/Nnk_chip_rep3.ATfilt.combined.dm6.chr4.bam"
flags <- scanBamFlag(isPaired=TRUE, isUnmappedQuery=FALSE, hasUnmappedMate=FALSE)
what <- c("flag", "rname", "strand", "pos", "cigar", "groupid", "mate_status")
param <- ScanBamParam(flag=flags, what=what)
res1 <- scanBam(BamFile(path), param=param) # should work
res2 <- scanBam(BamFile(path, asMates=TRUE), param=param) # should crashCan you reproduce the crash with the above code? This would confirm that the crash happens in Rsamtools/src/bam_mate_iter.cpp.
Thanks!
jayoung
lshep
hi there,
I am getting a core dump trying to use readGAlignmentPairs to read in a bam file (actually a set of bam files). I can use readGAlignments on the same bam file without any trouble.
I get a similar issue whether I'm running R on a node of our linux cluster or on my mac. On the linux cluster it seems to happen every time I try to read the file, and on the mac it's a bit more hit and miss - sometimes it works fine, but repeating the same command a few seconds later causes R to crash. Weird.
Some code is below. I think I'm using the latest release versions of everything. I'm happy to upload a bam file somewhere if that's useful.
thanks!
Janet
on linux:
and on the mac
here's the crazy long R-crash message my mac shows (it's a lot more verbose than the linux crash was....)