PREMIM and EMIM are tools for the estimation of parental and child genetic effects, based on genotype data from a variety of different child-parent configurations. PREMIM allows the extraction of child-parent genotype data from standard-format pedigree data files, while EMIM uses the extracted genotype data to perform subsequent statistical analysis.
Allocate an interactive session and run the program. Sample session:
[user@biowulf ~]$ sinteractive --gres lscratch:1 salloc.exe: Pending job allocation 52908283 salloc.exe: job 52908283 queued and waiting for resources salloc.exe: job 52908283 has been allocated resources salloc.exe: Granted job allocation 52908283 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3153 are ready for job srun: error: x11: no local DISPLAY defined, skipping [user@cn3153 ~]$ cd /lscratch/$SLURM_JOBID [user@cn3153 52908283]$ module load emim [+] Loading emim, version 3.22... [user@cn3153 52908283]$ premim $EMIM_HOME/testpedigree.ped PREMIM: Pedigree file processing program for EMIM, v3.22 -------------------------------------------------------- Copyright 2011-2016 Richard Howey, GNU General Public License, v3 Institute of Genetic Medicine, Newcastle University Log file: premim.log Input file: /usr/local/apps/emim/3.22/testpedigree.ped Child trend analysis set for parameter file (emimparams.dat). Number of subjects: 490 Males: 320 (65.3061%) Females: 170 (34.6939%) Unknown sex: 0 (0%) Affected: 92 (18.7755%) Unaffected: 398 (81.2245%) Number of SNPs: 1 Number of pedigrees: 130 Mean pedigree size: 3.76923 Standard deviation of pedigree size: 1.81098 File name: caseparenttrios Number of counted case parent trios (all SNPs): 20 Average number of counted case parent trios (per SNP): 20 Number of uncounted (Mendelian error) case parent trios: 0 File name: casemotherduos Number of counted case mother duos (all SNPs): 10 Average number of counted case mother duos (per SNP): 10 Number of uncounted (Mendelian error) case mother duos: 0 File name: casefatherduos Number of counted case father duos (all SNPs): 10 Average number of counted case father duos (per SNP): 10 Number of uncounted (Mendelian error) case father duos: 0 File name: cases Number of counted cases (all SNPs): 10 Average number of counted cases (per SNP): 10 File name: caseparents Number of counted case parents (all SNPs): 10 Average number of counted case parents (per SNP): 10 Number of uncounted (Mendelian error) case parents: 0 File name: casemothers Number of counted case mothers (all SNPs): 10 Average number of counted case mothers (per SNP): 10 File name: casefathers Number of counted case fathers (all SNPs): 10 Average number of counted case fathers (per SNP): 10 File name: conparents Number of counted control parents (all SNPs): 20 Average number of counted control parents (per SNP): 20 Number of uncounted (Mendelian error) control parents: 0 File name: conmotherduos Number of counted control mother duos (all SNPs): 10 Average number of counted control mother duos (per SNP): 10 Number of uncounted (Mendelian error) control mother duos: 0 File name: confatherduos Number of counted control father duos (all SNPs): 10 Average number of counted control father duos (per SNP): 10 Number of uncounted (Mendelian error) control father duos: 0 File name: cons Number of counted controls (all SNPs): 10 Average number of counted controls (per SNP): 10 Number of uncounted groups: 0 Run time: less than one second [user@cn3153 52908283]$ ls casefatherduos.dat casemothers.dat cases.dat conparents.dat premim.log casefathers.dat caseparents.dat confatherduos.dat cons.dat casemotherduos.dat caseparenttrios.dat conmotherduos.dat emimparams.dat [user@cn3153 52908283]$ cp $EMIM_HOME/emimmarkers.dat . [user@cn3153 52908283]$ emim ANALYSING SNP NUMBER 1 , SNPID= 1.0000000000000000 [user@cn3153 52908283]$ exit exit salloc.exe: Relinquishing job allocation 52908283 [user@biowulf ~]$
Create a batch input file (e.g. emim.sh). For example:
#!/bin/sh set -e module load emim premim $EMIM_HOME/testpedigree.ped cp $EMIM_HOME/emimmarkers.dat . emim
Submit this job using the Slurm sbatch command.
sbatch [--cpus-per-task=#] [--mem=#] emim.sh
Create a swarmfile (e.g. emim.swarm). For example:
mkdir sample1 && cd sample1 && premim ../input1.bed && emim mkdir sample2 && cd sample1 && premim ../input2.bed && emim mkdir sample3 && cd sample1 && premim ../input3.bed && emim mkdir sample4 && cd sample1 && premim ../input4.bed && emim
Submit this job using the swarm command.
swarm -f emim.swarm [-g #] [-t #] --module emimwhere
-g # | Number of Gigabytes of memory required for each process (1 line in the swarm command file) |
-t # | Number of threads/CPUs required for each process (1 line in the swarm command file). |
--module emim | Loads the emim module for each subjob in the swarm |