High-Performance Computing at the NIH
GitHub YouTube @nih_hpc RSS Feed
Metal on HPC

The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner.

 

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
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 metal
[user@cn3144 ~]$ cd /data/$USER/metal/examples/GlucoseExample
[user@cn3144 ~]$ metal << EOT 
MARKER SNP
WEIGHT N
ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE
FREQ EFFECT_ALLELE_FREQ
EFFECT BETA
STDERR SE
PVAL P_VAL

PROCESS DGI_three_regions.txt

MARKER SNP
ALLELE EFFECT_ALLELE NON_EFFECT_ALLELE
FREQ FREQ_EFFECT
WEIGHT N
EFFECT BETA
STDERR SE
PVAL PVALUE

PROCESS MAGIC_FUSION_Results.txt

MARKER SNP
DEFAULT 4108
ALLELE AL1 AL2
FREQ FREQ1
EFFECT EFFECT
STDERR SE
PVAL PVALUE

PROCESS magic_SARDINIA.tbl

ANALYZE

Press Ctrl-D to submit these commands. Two output files will be created. [...etc...] [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$