Running hisat2 2.2.0 I'm seeing odd max memory (RSS) usage patterns. For one and the same command line and file, I might see 12GB, 24GB and killed due to out-of-memory on separate runs. It also appears that trimmed reads occupy more memory than untrimmed reads.
I'm using the most recent Bioconda version (hisat2-2.2.0-py27he1b5a44_1):
hisat2-align-s version 2.2.0
64-bit
Built on default-56ff2f81-e3ff-4461-b225-c02e23186a2f
Wed Mar 11 23:18:14 UTC 2020
Compiler: gcc version 7.3.0 (crosstool-NG 1.23.0.450-d54ae)
Options: -O3 -m64 -msse2 -funroll-loops -g3 -DPOPCNT_CAPABILITY -std=c++11
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
(This should be conda install -c conda-forge -c bioconda hisat2 'python<3')
Running hisat2 2.2.0 I'm seeing odd max memory (RSS) usage patterns. For one and the same command line and file, I might see 12GB, 24GB and killed due to out-of-memory on separate runs. It also appears that trimmed reads occupy more memory than untrimmed reads.
I'm using the most recent Bioconda version (hisat2-2.2.0-py27he1b5a44_1):
(This should be
conda install -c conda-forge -c bioconda hisat2 'python<3')