Fork of pfam_scan that uses hpc_hmmsearch instead of hmmscan to greatly reduce the execution time when using multiple cores.
To use hpc_pfam_search you need to have hpc_hmmsearch in your PATH and then add the Pfam modules included in this repository to your PERL5LIB:
git clone https://github.com/apcamargo/hpc_pfam_search.git
export PERL5LIB=hpc_pfam_search:$PERL5LIB
chmod +x hpc_pfam_search/hpc_pfam_search.pl
./hpc_pfam_search/hpc_pfam_search.pl -h
hpc_pfam_search also depends on Moose and BioPerl. You can install these packages in Ubuntu/Debian using the following command:
sudo apt install libmoose-perl bioperl
Benchmark comparing hpc_pfam_search to regular pfam_scan and pfam_search. The commands were executed using an input with 1,000 sequences and 32 cpu cores. Execution times were measured with hyperfine.
pfam_scan.pl
Time (mean ± σ): 345.319 s ± 1.564 s [User: 397.618 s, System: 232.994 s]
Range (min … max): 343.892 s … 347.999 s 5 runs
pfam_search.pl
Time (mean ± σ): 129.560 s ± 3.295 s [User: 168.469 s, System: 254.537 s]
Range (min … max): 126.042 s … 134.696 s 5 runs
hpc_pfam_search.pl
Time (mean ± σ): 12.331 s ± 0.054 s [User: 141.741 s, System: 1.694 s]
Range (min … max): 12.254 s … 12.402 s 5 runs