Biowulf High Performance Computing at the NIH
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:

Documentation
Important Notes

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