-p/--threads option always uses 1 more thread than is specified.

when i run bowtie2 and specify the number of threads to use(eg -p 1, -p 4), the amount of CPU usage is always 1 more core in use than is specified by the number of threads to use. for example, if i specify -p 1:

bowtie2 --no-unal -p 1 \
-x 'ref-genome-idx' \
-1 reads-R1_001.fastq.gz \
-2 reads-R2_001.fastq.gz

the cpu usage (via htop) for the process with be at ~200% indicating a usage of 2 threads, not 1:

 CPU% Command
  2.8 └─ /usr/bin/perl5.34 /opt/homebrew/bin/bowtie2 --no-unal -p 1 -x PAO1-- ...
196.0   └─ /opt/homebrew/bin/../Cellar/bowtie2/2.5.2/bin/bowtie2-align-s --w ...

likewise, for any other number of threads, it always uses n+1 CPU cores. for -p 4:

bowtie2 --no-unal -p 4 \
-x 'ref-genome-idx' \
-1 reads-R1_001.fastq.gz \
-2 reads-R2_001.fastq.gz

CPU usage (via htop):

 CPU% Command
  2.4 └─ /usr/bin/perl5.34 /opt/homebrew/bin/bowtie2 --no-unal -p 4 -x
445.4   └─ /opt/homebrew/bin/../Cellar/bowtie2/2.5.2/bin/bowtie2-align

(between 400-500% core usage because i have other jobs running, but bare system it would be ~500% indicating usage of 5 CPU cores)

this is effectively limiting cutting my sample throughput in half because when bowtie2 is in usage with 1 thread specified, every job uses 2 threads instead. is this a bug or a feature? am i missing something?

tested on:

macos sonoma 14.2.1
mac studio m2 ultra

bowtie2 version:

bowtie2 --version
/opt/homebrew/bin/../Cellar/bowtie2/2.5.2/bin/bowtie2-align-s version 2.5.2
64-bit
Built on Ventura-arm64.local
Sat Oct 14 18:03:18 UTC 2023
Compiler: InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
Options: -O3  -funroll-loops -g3 -std=c++11 -fopenmp-simd -DNO_SPINLOCK -DWITH_QUEUELOCK=1
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

BenLangmead / bowtie2

-p/--threads option always uses 1 more thread than is specified. #465