Fastsimcoal - bwHPC Wiki Fastsimcoal - bwHPC Wiki

Fastsimcoal

From bwHPC Wiki
Jump to: navigation, search
Description Content
module load bio/fastsimcoal
License Freely available
Citing

fastsimcoal2 and fsc22:
Excoffier, L., Dupanloup, I., Huerta-Sánchez, E., Sousa, V.C.,
and M. Foll (2013) Robust demographic inference from genomic
and SNP data. PLOS Genetics, 9(10):e1003905.
fatsimcoal:
Excoffier, L. and Foll, M (2011) fastsimcoal: a continuous-time
coalescent simulator of genomic diversity under arbitrarily complex
evolutionary scenarios Bioinformatics 27: 1332-1334.

Links Fastsimcoal2 Homepage | Documentation | Softpedia
Graphical Interface No

1 Description

fastsimcoal is a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios.
While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure.
fastsimcoal can handle very complex evolutionary scenarios including an arbitrary migration matrix between samples, historical events allowing for population resize, population fusion and fission, admixture events, changes in migration matrix, or changes in population growth rates. The time of sampling can be specified independently for each sample, allowing for serial sampling in the same or in different populations.

For more informations visit the fastsimcoal2 Homepage.

2 Versions and Availability

A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the

Cluster Information System CIS
Show a list of available versions using 'module avail bio/fastsimcoal on any HPC-C5 cluster.

: EXAMPLE
$ module avail bio/fastsimcoal
------------------------ /opt/bwhpc/common/modulefiles -------------------------
bio/fastsimcoal/2.5.2


3 License

Free Software / GPL

4 Usage

4.1 Loading the module

You can load the default version of fastsimcoal with the command 'module load bio/fastsimcoal'. Example:

$ module load bio/fastsimcoal

The module will try to load modules it needs to function. If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for software name. If you wish to load a specific (older) version, you can do so using e.g.: '$ module load bio/fastsimocal/2.5.2' to load the version you desires.

: EXAMPLE!
$ module avail bio/fastsimcoal
------------------------ /opt/bwhpc/common/modulefiles --------------------------
bio/fastsimcoal/2.5.2
$ module load bio/fastsimcoal/2.5.2

4.2 Program Binaries

Show the location and contents of the installed binaries in the main folder of the software and show some informations, too. e.g.: After loading the fastsimcoal module ('module load bio/fastsimcoal') this path is also set to the local $PATH- and $FASTSIMCOAL_BIN_DIR environments.

$ ls -F $FASTSIMCOAL_BIN_DIR
example files/  fastsimcoal25.pdf*  fsc252*
  • example_files is directory
  • fastsimcoal25.pdf is the documentation
  • fsc252 is the main binary program

4.3 Disk Usage / Workspaces

Scratch files are written to the current directory by default.
Change to a local directory or to 'your local workspace' (preferred) before starting your calculations.
'fsc_repo' is an example name of a repository you created by using the command 'ws_allocate'.

$ cd $(ws_find fsc_repo)
['your-id'-fsc_repo-0]$ pwd
/work/workspace/scratch/'your-id'-fsc_repo-0
['your-id'-fsc_repo-0]$ 

In case of multi-node parallel jobs, you might need to create the directory on all nodes used.

5 Moab Submit Examples

You can copy a simple interactive example to your workspace and run it, using 'msub'
Strictly use the $FASTSIMCOAL_EXA_DIR environment-variable!

$ cd $(ws_find fsc_repo)
$ cp $FASTSIMCOAL_EXA_DIR/bwhpc-fastsimcoal-example.moab .
$ cp bwhpc-fastsimcoal-example.moab myfscjob.moab 
§ vi myfscjob.moab         # do your own modifications
$ msub myfscjob.moab       # start job submission

5.1 Excerpt from bwhpc-fastsimcoal-example.moab file

[...]
echo " "
echo "### Copying input test files for job (if required):"
echo " "
cp ${FASTSIMCOAL_EXA_DIR}/1PopBot20* .

echo " "
echo "### Calling fastsimcoal command ..."
echo " "
mpirun -v -np ${SLURM_JOB_NUM_NODES} fsc252 -d -t 1PopBot20Mb.tpl \
 -n 1000 -N 1000 -M 0.01 -l 5 -L 5 -e 1PopBot20Mb.est -q
[...]


6 Fastsimcoal-Specific Environments

To see a list of all fastsimcoal environments set by the 'module load'-command use 'env | grep FASTSIMCOAL'
or the command 'module display bio/fastsimcoal/2.5.2 (you don't need to load the module before!).

: EXAMPLE ONLY
$ module list
Currently Loaded Modulefiles:
  1) compiler/intel/14.0(default)          3) bio/fastsimcoal/2.5.2
  2) mpi/openmpi/1.8-intel-14.0(default)
$ env | grep FASTSIMCOAL
FASTSIMCOAL_EXA_DIR=/opt/bwhpc/common/bio/fastsimcoal/2.5.2/bwhpc-examples
FASTSIMCOAL_HOME=/opt/bwhpc/common/bio/fastsimcoal/2.5.2
FASTSIMCOAL_BIN_DIR=/opt/bwhpc/common/bio/fastsimcoal/2.5.2/bin
FASTSIMCOAL_VERSION=2.5.2


7 Version-Specific Information

For a more detailed information specific to a specific fastsimcoal version, see the information available via the module system with the command 'module help bio/fastsimcoal'.

$ module help bio/fastsimcoal


For a small abstract what SOFTWARENAME is about use the command

$ module whatis bio/fastsimcoal


: EXAMPLE ONLY !!!
$ module avail bio/fastsimcoal
---------------------- /opt/bwhpc/common/modulefiles ----------------------
bio/fastsimcoal/2.5.2
:
$ module whatis bio/fastsimcoal
bio/fastsimcoal      : Sequential Markov coalescent simulation of genomic data 
  under complex evolutionary models (command 'fsc252')
:
UC:[kn_pop235844@uc1n997 modulefiles]$ module help bio/fastsimcoal

----------- Module Specific Help for 'bio/fastsimcoal/2.5.2' ----------------


fastSimcoal2 (ver 2.5.2 - March, 2015)

command-line usage: fsc252 -h  -- help : prints help

This software is available in MULTITHREADING mode 
OPENMP is included, too.

Documentation:

* Get started:
   http://cmpg.unibe.ch/software/fastsimcoal2/quickstart.html
* Full manual:
   http://cmpg.unibe.ch/software/fastsimcoal2/man/fastsimcoal25.pdf
   and in the /opt/bwhpc/common/bio/fastsimcoal/2.5.2/bin - folder.
* Fastsimcoal example-data can be found here:
   /opt/bwhpc/common/bio/fastsimcoal/2.5.2/fastsimcoal-examples
* bwHPC examples and a moab example script can be found here:
   /opt/bwhpc/common/bio/fastsimcoal/2.5.2/bwhpc-examples
[...]