I am using SRA-FASTQ-to-bam-kit in on windows to allign large human WGS fastq files [100-150gb], BWA has latest version. Kit works through .bat file and it uses -t 4 option by default. My laptop has i5 7300HQ processor which has 2 cores but works as 4 core [like most of intel processors]. When i change to -t 1 it makes bamfile 2-3 times faster than with -t 4 or -t 2, and there is no difference in bam file size that it outputs, its the same with any options, it just works faster with -t 1. My question is - should i stay with 1 thread option or i can loose "quallity" of bam file using it, i want maximal quality no matter what time it will take. When i switch to 1 thread it shows that it reads 10000043 bp, with 4 - 40000043 bp, is it really affects bam file?
If this could help : BWA-MEM get different results with different threads
Hello serganover ,
how much RAM is available?
More threads need more RAM. And if you haven't enough the system has to swap and the whole process becomes slower.
fin swimmer
Hi.I have 24gb of ram. BWA always uses 5-6gb of ram no matter how many threads i set. The bat file uses this script:
bin\bwa mem -t 1 ref.fa %FILE:~0,-7%.fastq | bin\samtools.exe view -bS - > %FILE:~0,-7%.bam............i just drag and drop fastq onto bat file and it starts making bam