morgan on Biowulf
MORGAN (Monte Carlo Genetic Analysis) is a collection of programs and libraries developed at the University of Washington. This software implements a number of methods for the analysis of data observed on members of a pedigree, with the main programs implementing Markov Chain Monte Carlo (MCMC) methods.
References:
- Simon C. Health Markov Chain Monte Carlo Segregation and Linkage Analysis for Oligogenic Models AJHG 2008. PubMed | PMC | Journal
Documentation
- Manual main page
- Tutorial online tutorial
Important Notes
- Module Name: morgan (see the modules page for more information)
- Example data in
$MORGAN_TEST_DATA - make links is essential for running morgan correctly
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=4g
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job
[user@cn3144 ~]$ module load morgan
[+] Loading morgan 3.4
[user@cn3144 ~]$ mkdir /data/$USER/morgan
[user@cn3144 ~]$ cd /data/$USER/morgan
[user@cn3144 morgan]$ cp -r $MORGAN_TEST_DATA/* .
[user@cn3144 morgan]$ ls -lh
drwxr-x--- 2 user user 4.0K Jul 14 10:08 Haplo
drwxr-x--- 2 user user 4.0K Jul 14 10:08 IBD
drwxr-x--- 2 user user 4.0K Jul 14 10:08 Lodscores
-rw-r----- 1 user user 7.8K Jul 14 10:08 Makefile
drwxr-x--- 2 user user 4.0K Jul 14 10:08 Map
-rw-r----- 1 user user 38 Jul 14 10:08 marker.seed
-rw-r----- 1 user user 2.6M Jul 14 10:08 morgan34_examples.tar.gz
-rw-r----- 1 user user 2.6K Jul 14 10:08 ped73.marker.missing
-rw-r----- 1 user user 3.7K Jul 14 10:08 ped73.ped
drwxr-x--- 2 user user 4.0K Jul 14 10:08 Pedcheck
drwxr-x--- 2 user user 4.0K Jul 14 10:08 PedInfo
drwxr-x--- 2 user user 4.0K Jul 14 10:08 PolyEM
-rw-r----- 1 user user 834 Jul 14 10:08 README_2019
-rw-r----- 1 user user 42 Jul 14 10:08 sampler.seed
drwxr-x--- 2 user user 4.0K Jul 14 10:08 Simulation
drwxr-x--- 3 user user 4.0K Jul 14 10:08 TraitTests
[user@cn3144 morgan]$ make links
ln -sf /usr/local/apps/morgan/3.4/Autozyg/lm_auto `pwd`/IBD/lm_auto
ln -sf /usr/local/apps/morgan/3.4/Autozyg/gl_auto `pwd`/IBD/gl_auto
ln -sf /usr/local/apps/morgan/3.4/Autozyg/lm_pval `pwd`/TraitTests/lm_pval
ln -sf /usr/local/apps/morgan/3.4/Autozyg/lm_ibdtests `pwd`/TraitTests/lm_ibdtests
ln -sf /usr/local/apps/morgan/3.4/Autozyg/lm_map `pwd`/Map/lm_map
ln -sf /usr/local/apps/morgan/3.4/Lodscore/lm_bayes `pwd`/Lodscores/lm_bayes
ln -sf /usr/local/apps/morgan/3.4/Lodscore/lm_linkage `pwd`/Lodscores/lm_linkage
ln -sf /usr/local/apps/morgan/3.4/Lodscore/gl_lods `pwd`/Lodscores/gl_lods
ln -sf /usr/local/apps/morgan/3.4/PedComp/pedcheck `pwd`/Pedcheck/pedcheck
ln -sf /usr/local/apps/morgan/3.4/Genedrop/genedrop `pwd`/Simulation/genedrop
ln -sf /usr/local/apps/morgan/3.4/Genedrop/markerdrop `pwd`/Simulation/markerdrop
ln -sf /usr/local/apps/morgan/3.4/Genedrop/ibddrop `pwd`/IBD/ibddrop
ln -sf /usr/local/apps/morgan/3.4/PedComp/kin `pwd`/IBD/kin
ln -sf /usr/local/apps/morgan/3.4/PolyEM/multivar `pwd`/PolyEM/multivar
ln -sf /usr/local/apps/morgan/3.4/IBD_Haplo/ibd_haplo `pwd`/Haplo/ibd_haplo
ln -sf /usr/local/apps/morgan/3.4/IBD_Haplo/ibd_create `pwd`/Haplo/ibd_create
[user@cn3144 morgan]$ cd Pedcheck
[user@cn3144 Pedcheck]$ ./pedcheck check.par
MORGAN Version 3.4 ./pedcheck Tue Jul 14 10:20:07 2020
Opened input pedigree file "check.ped"
30 individuals read
Gender assigned
Component information:
compnt size founders females males unsexed observd first
1 15 5 7 7 1 5 132
2 15 5 7 7 1 5 142
total 30 10 14 14 2 10
The input pedigree was not by component and/or in chronological order (W)
There are changes to the pedigree in assignment of gender (W)
A new pedigree file will be written (W)
Opened output pedigree file "check.oped"
Opened output individuals file "indiv_oped"
hostname: cn3159
system time: 0.000 sec
user time: 0.000 sec
elapsed time: 0 hr 0 min 0 sec
[user@cn3144 Pedcheck]$ cd ../TraitTests
[user@cn3144 TraitTests]$ ./lm_ibdtests ped73_ibdt_IBD.par
MORGAN Version 3.4 ./lm_ibdtests Tue Jul 14 10:23:16 2020
=== Parsing of parameter statements completed ===
Chromosome map
..............
Inter-locus distances in cM, using Haldane map function:
----------------------------------------------------------------
10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0 10.0
+------+------+------+------+------+------+------+------+------+
M1 M2 M3 M4 M5 M6 M7 M8 M9 M10
...
************************************
p Value for Permutation Test for IBD
************************************
pos(Haldane cM) Spairs Srobdom
locus male female p-value p-value
marker-1 0.000 0.000 0.9180 0.7780
marker-2 10.000 10.000 0.8970 0.8490
marker-3 20.000 20.000 0.8410 0.7670
marker-4 30.000 30.000 0.4210 0.5520
marker-5 40.000 40.000 0.2520 0.2540
marker-6 50.000 50.000 0.3510 0.4430
marker-7 60.000 60.000 0.4770 0.3460
marker-8 70.000 70.000 0.5580 0.6230
marker-9 80.000 80.000 0.8000 0.8060
marker-10 90.000 90.000 0.5900 0.7020
*******************************
p Value for Normal Test for IBD
*******************************
pos(Haldane cM)
locus male female Spairs p-value Srobdom p-value
marker-1 0.000 0.000 -0.9542 0.8346 -0.4085 0.6617
marker-2 10.000 10.000 -1.0095 0.8261 -0.4315 0.6652
marker-3 20.000 20.000 -1.2681 0.9030 -0.4127 0.6702
marker-4 30.000 30.000 -0.8368 0.7951 -0.3361 0.6397
marker-5 40.000 40.000 -0.0012 0.5187 -0.2196 0.5812
marker-6 50.000 50.000 -0.7263 0.7726 -0.5325 0.6862
marker-7 60.000 60.000 -0.1478 0.5587 -0.3481 0.6487
marker-8 70.000 70.000 -0.2016 0.5712 -0.2803 0.6137
marker-9 80.000 80.000 -0.5499 0.7176 -0.3898 0.6507
marker-10 90.000 90.000 -0.3814 0.6202 -0.1903 0.5697
hostname: cn3159
system time: 0.030 sec
user time: 17.780 sec
elapsed time: 0 hr 0 min 18 sec
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$exit
Batch job
Most jobs should be run as batch jobs.
Create a batch input file (e.g. morgan.sh), which uses the input file 'morgan.in'. For example:
#! /bin/bash module load morgan || exit 1 cd /data/user/morgan/TraitTests ./pedcheck check.par
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=2 morgan.sh