Genetree on XSEDE
8.3
Estimation of mutation, migration and growth rates, and ancestral inference
Bob Griffiths
Simulating probability distributions in the coalescent. Theor. Popn. Biol., 46, 131-159, 1994. R. C. Griffiths, S. Tavaré
Phylogeny / Alignment
genetree_xsede
infile
Input sequence file
haplotype_dat
genetree_invocation
perl
"/expanse/projects/ngbt/opt/comet/genetree/gtree/genetree haplotype_dat -z"
0
genetree_invocation2
perl
"&& /expanse/projects/ngbt/opt/comet/genetree/gtree/genetree haplotype_dat.# $theta_val $run_val $seed_val -A mutation_age.# -M genetree_temp.#"
2
genetree_invocation3
perl
"; wait ; chmod 770 ./output.sh ; wait ; sleep 2 ; convert_parallel.sh output.sh"
95
genetree_invocation4
perl
"; wait ; sleep 2 ; ./output.sh"
99
genetree_scheduler
scheduler.conf
perl
$run_val < 3000
perl
"threads_per_process=1\\n" .
"mem=5G\\n" .
"node_exclusive=0\\n" .
"nodes=1\\n"
genetree_scheduler2
scheduler.conf
perl
$run_val > 2999
perl
"threads_per_process=18\\n" .
"mem=36G\\n" .
"node_exclusive=0\\n" .
"nodes=1\\n"
all_output
All output
*
runtime
1
scheduler.conf
Maximum Hours to Run (click here for help setting this correctly)
perl
"runhours=$value\\n"
0.25
Maximum Hours to Run must be less than 168
perl
$runtime > 168.0
Maximum Hours to Run must be greater than 0.1
perl
$runtime < 0.1
The job will run on 1 processor as configured. If it runs for the entire configured time, it will consume $numthreads x $runtime cpu hours
perl
$runtime ne 0
Estimate the maximum time your job will need to run. We recommend testimg initially with a < 0.5hr test run because Jobs set for 0.5 h or less dependably run immediately in the "debug" queue.
Once you are sure the configuration is correct, you then increase the time. The reason is that jobs > 0.5 h are submitted to the "normal" queue, where jobs configured for 1 or a few hours times may
run sooner than jobs configured for the full 168 hours.
theta_val
Specify a value for theta
3
run_val
Specify the number of runs
3
seed_val
Specify a seed value
3
make_batchfile
Make a batch file (-b)
4
perl
($value) ? "-b":""
multifile_sum
Multiple file summary (-l)
4
perl
($value) ? "-l":""
run_allrootedtrees
Provide a migration rate file (matrix of rates, diagonals zero) (-m)
5
infile.mig
perl
(defined $value) ? "-m infile.mig":""
allow_popsizes
Provide subpopulation relative size file (array of rates) (-p)
6
pop.dat
perl
(defined $value) ? "-p pop.dat":""
num_subpops
Number of subpopulations (default - number in tree_file) (-s)
7
perl
(defined $value) ? "-s $value":""
num_segsites
Number of segregating sites + 1 (-Z)
7
perl
(defined $value) ? "-Z $value":""
max_eventspersim
Maximum events in one simulation run (default - 500) (-x)
8
pop.dat
perl
(defined $value) ? "-x $value":""
max_typesanc
Maximum types in the ancestry of the sample (-y)
8
pop.dat
perl
(defined $value) ? "-y $value":""
output_level
Output Level (-o)
8
1
2
3
4
5
6
7
perl
(defined $value) ? "-o $value":""
surface_outfile
Surface outfile_name (g m theta likelihood sd_like) (-f)
9
surf.file
perl
(defined $value) ? "-f surf.file":""
theta_1
Theta value 1 (-g)
9
perl
(defined $value) ? "-g $theta_1 $theta_2 $surface_1 $surface_2":""
theta_2
Theta value 2
surface_1
Surface point 1
surface_2
Surface point 2
outfile_name_val
Specify the output file name
perl
"> output.sh"
10