Hello!

I'm trying to run the Rsubread function align() with the parameter sortReadsByCoordinates set to TRUE in order to generate sorted BAMs with BAIs. My attempts to do so encounter a fatal error at about the point when mapping is 3% completed. Error message & sessionInfo() printout copied and pasted below.

However, when I run basically the same script in the same environment, but without setting sortReadsByCoordinates (docs say default value is FALSE), the alignment runs to 100% completion. I am running this alignment on a HPC and believe I request more than enough memory (100G).

From the alignment successfully completing when sortReadsByCoordinates is not set, the problem seems to be what sortReadsByCoordinates does. Does anyone have any pointers for how to get past this issue?

Thanks!

 *** caught segfault ***
address 0xffffffff881fd31e, cause 'memory not mapped'

Traceback:
 1: align(RNAseq..REFERENCE.BASENAME..DIR, phredOffset = 33, readfile1 = FASTQ.File.Names.DIR1..TRIM,     readfile2 = FASTQ.File.Names.DIR2..TRIM, input_format = "gzFASTQ",     output_file = BAM.File.Col.Names12, sortReadsByCoordinates = TRUE)
An irrecoverable exception occurred. R is aborting now ...
/var/spool/slurmd/job49569909/slurm_script: line 15: 27053 Segmentation fault      Rscript ./ZZ..Process.RNAseq.fastq_sorted_sessionInfo.r

sessionInfo( )
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /n/app/openblas/0.2.19/lib/libopenblas_core2p-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Rsubread_2.8.1

loaded via a namespace (and not attached):
[1] compiler_4.1.1  Matrix_1.3-4    grid_4.1.1      lattice_0.20-44