how to specify threads used with hyphy gard

[lagphase]

Hello I don't see any flag for the number of threads used in hyphy gard --help

I'm running 250 genomes and the dafault is taking forever.

[stevenweaver]

Dear @lagphase,

I'm going to assume you mean number of processors. If not, feel free to correct me. Are you using standard HyPhy or HYPHYMPI?

For the former, try

hyphy CPU=1 gard with 1 being the number of CPUs you'd like to use.

For the latter, try mpirun -np 8 HYPHYMPI.

Best, Steven

[lagphase]

Hi Steven,

Thanks. Yes I meant CPUs and I'm using the standard HyPhy.

The code seems to work slightly faster. Any estimation on how long it would take for 250 sequences with 100 CPUs?

[spond]

Dear @lagphase,

It really depends on the analysis. What are you running? HyPhy will not be able to load 100 CPUs (HYPHYMPI can for FEL, MEME, and other such analyses), unless you have a large and (more importantly) long alignment. In, fact, HyPhy will run a mini-benchmark at the beginning on time-intensive tasks to guess-timate how many CPUs is worth using.

You can add ENV="VERBOSITY_LEVEL=1; to the command line, and for most analyses you will see a line that looks like this, which will also report the effective CPU load.

Current Max: -17515.127     (0 % done) LF Evals/Sec: 1571    CPU Load: 3.604 

Best, Sergei

[lagphase]

Hi Sergei,

I'm using hyphy gard to detect recombination sequences in the alignment. Yes my alignment is long and ~100 MB. Is there a way to speed up the process?

Thanks.

[spond]

Dear @lagphase,

GARD will make better use of an MPI environment. That said, it is meant for screening "gene-sized" aligments (at most 10-20kb). While GARD will attempt to run for a 100 megabase alignment, it will be very slow. How many sequences do you have? Because GARD only considers variable sites, the effective search space could be manageable if you have a few (5-20) sequences.

Best, Sergei

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