how to run LD KNNi and save the result using command line in remote supercomputer

[czq...@hotmail.com]

Hi, 

I are trying to run LD-KNNi imputation in our remote supercomputer due to the large data, but we only found the syntax> 

./run_pipeline.pl -h mdp_genotype.hmp.txt-NumericalGenotypePlugin -endPlugin -export output -exportType ReferenceProbablity

which i think is just used to impute missing genotypes by KNNi imputation，not LD-KNNi imputation. 

Am I right? How should I change it?

here below is my syntax:

run_pipeline.pl -Xms512m -Xmx800g -vcf filename_sorted.vcf -NumericalGenotypePlugin -endPlugin -export Imputed_filename_sorted.vcf -exportType ReferenceProbablity 

Cheers

chen

[Terry Casstevens]

run_pipeline.pl -Xms512m -Xmx800g -debug -importGuess
filename_sorted.vcf -LDKNNiImputationPlugin -endPlugin -export
Imputed_filename_sorted.vcf -exportType VCF



./run_pipeline.pl -LDKNNiImputationPlugin

./lib/ahocorasick-0.2.4.jar:./lib/avro-1.8.1.jar:./lib/biojava-alignment-4.0.0.jar:./lib/biojava-core-4.0.0.jar:./lib/biojava-phylo-4.0.0.jar:./lib/colt-1.2.0.jar:./lib/commons-codec-1.10.jar:./lib/commons-math3-3.4.1.jar:./lib/ejml-0.23.jar:./lib/forester-1.038.jar:./lib/guava-22.0.jar:./lib/htsjdk-1.138.jar:./lib/itextpdf-5.1.0.jar:./lib/javax.json-1.0.4.jar:./lib/jcommon-1.0.23.jar:./lib/je-6.0.11.jar:./lib/jfreechart-1.0.19.jar:./lib/jfreesvg-3.2.jar:./lib/jfxrt.jar:./lib/jhdf5-14.12.5.jar:./lib/json-simple-1.1.1.jar:./lib/junit-4.10.jar:./lib/log4j-1.2.13.jar:./lib/mail-1.4.jar:./lib/postgresql-9.4-1201.jdbc41.jar:./lib/slf4j-api-1.7.10.jar:./lib/slf4j-simple-1.7.10.jar:./lib/snappy-java-1.1.1.6.jar:./lib/sqlite-jdbc-3.8.5-pre1.jar:./lib/trove-3.0.3.jar:./dist/sTASSEL.jar

Memory Settings: -Xms512m -Xmx1536m

Tassel Pipeline Arguments: -LDKNNiImputationPlugin

[main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version:
5.2.38 Date: July 13, 2017

[main] INFO net.maizegenetics.tassel.TasselLogging - Max Available
Memory Reported by JVM: 1365 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_121

[main] INFO net.maizegenetics.tassel.TasselLogging - OS: Mac OS X

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 8

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel
Pipeline Arguments: [-fork1, -LDKNNiImputationPlugin, -runfork1]

net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
Starting net.maizegenetics.analysis.imputation.LDKNNiImputationPlugin:
time: Jul 29, 2017 14:50:44

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -

Usage:

LDKNNiImputationPlugin <options>

-highLDSSites <High LD Sites> : Number of sites in high LD to use in
imputation [2..2000] (Default: 30)

-knnTaxa <Number of nearest neighbors> : Number of neighbors to use in
imputation [2..200] (Default: 10)

-maxLDDistance <Max distance between site to find LD> : Maximum
physical distance between sites to search for LD (-1 for no distance
cutoff - unlinked chromosomes will be tested) (Default: 10000000)


[pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin -
LDKNNiImputationPlugin: preProcessParameters: Please select one
Genotype Table.


Please follow these instructions to get more information.

https://bitbucket.org/tasseladmin/tassel-5-source/wiki/docs/ReportingTassel5Issues.pdf

Best,

Terry

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