Hi All,

I am trying to align one DNA whole genome sequence file using subread, the sequence reads are paired end, 150 bp reads. I used 'thread=64' and 216 core (9 nodes, 24 core each). but after two days it processed only 15% and I had to kill the job.

I am using the university quest, so basically I can get as many nodes/cores as I want. Is there any way by which I can accelerate the alignment.

>align(index="my_index",readfile1=c("141023_H0E72_113-JG4_L003_R1.fastq.gz"),readfile2=c("141023_H0E72_113-JG4_L003_R2.fastq.gz"), output_file=c("subread_jg4.sam"),nthreads=64,unique=TRUE,type=1)

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.4 (Santiago)

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_1.22.3
 

Thanks

Tarek