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Why BWA is working faster with 1 thread? Does default 4 thread option output better BAM file?

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?

alignment bwa bwa /
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written by serganover • serganover

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

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written by finswimmer finswimmer

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

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written by serganover • serganover

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