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Metal on Biowulf & Helix

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.

The sample file can be copied:

$ cp -r /usr/local/apps/metal/examples /data/$USER/metal

Running on Helix

$ module load metal
$ cd /data/$USER/metal/examples/GlucoseExample
$ 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.

Running an interactive job on Biowulf

It may be useful for debugging purposes to run jobs interactively. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

biowulf$ sinteractive 
salloc.exe: Granted job allocation 16535

cn999$ module load metal
cn999$ cd /data/$USER/metal/examples/GlucoseExample
cn999$ 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...] cn999$ exit exit biowulf$

Make sure to exit the job once finished.

If more memory is needed, use --mem. For example

biowulf$ sinteractive --mem=8g

Documentation

http://www.sph.umich.edu/csg/abecasis/Metal/download/metal-instructions.pdf