Hi Wei,

Thanks for your reply.

I am processing whole genome sequencing data, following to alignment, I want to call SNPs within different samples (100 samples). SNP data will be used to perform a downstream GWAS.

DO you think I can use exactSNP() to call SNPs or shall I stick to GATK.

Thanks

Tarek

Hi Wei,

I tried this with the unzipped file and it returns

 *** caught segfault ***
address 0x7fff9a688000, cause 'memory not mapped'

Thanks

Tarek

Hi Wei,

I have already specified isBAM =FALSE. I have added here the sessionInfo() 

>exactSNP(SNPAnnotationFile="All_20151104.vcf",readFile="CH1_0uM_subjunc.sam",isBAM=FALSE,refGenomeFile="BSgenome.Hsapiens.NCBI.GRCh38.fasta",outputFile="subread_jg4.sam.vcf",nthreads=40)

> sessionInfo()

R version 3.2.2 (2015-08-14)
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 

Hi wie,

One more questions.

I tried subread to align whole genome sequence from one sample (paired end, 150 bp reads) and 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)

Thanks

Tarek