Is my running failed in sort step?

[czq...@hotmail.com]

Dear all,

I  am running the sorting step in Tassel. It finished in 3 minutes for 4G data, but I found there is an error in the reporting file as below. 

Memory Settings: -Xms512m -Xmx400g

Tassel Pipeline Arguments: -debug -SortGenotypeFilePlugin -inputFile GS_Fullsib_delete15badseq_indel_biallelic_GQ6_DP2_MAF0.01_Maxmiss0.9.vcf.recode.vcf -outputFile GS_Fulls

ib_delete15badseq_indel_biallelic_GQ6_DP2_MAF0.01_Maxmiss0.9_sorted_debug.vcf -fileType VCF

[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: 364089 MB

[main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_131

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

[main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 13

[main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -SortGenotypeFilePlugin, -inputFile, GS_Fullsib_delete15badseq_indel_biallelic_GQ6_DP2_MAF0.01_Maxmiss0.9.vcf.recode.vcf, -outputFile, GS_Fullsib_delete15badseq_indel_biallelic_GQ6_DP2_MAF0.01_Maxmiss0.9_sorted_debug.vcf, -fileType, VCF, -runfork1]

net.maizegenetics.analysis.data.SortGenotypeFilePlugin

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.analysis.data.SortGenotypeFilePlugin: time: Nov 5, 2017 12:41:48

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

SortGenotypeFilePlugin Parameters

inputFile: GS_Fullsib_delete15badseq_indel_biallelic_GQ6_DP2_MAF0.01_Maxmiss0.9.vcf.recode.vcf

outputFile: GS_Fullsib_delete15badseq_indel_biallelic_GQ6_DP2_MAF0.01_Maxmiss0.9_sorted_debug.vcf

fileType: VCF

[pool-1-thread-1] ERROR net.maizegenetics.dna.map.PositionListBuilder - validateOrdering: Position      Chr:MA_10       Pos:24775       Name:SMA_10_24775       Variants:G/C

    MAF:NaN Ref:G and Position      Chr:MA_5        Pos:86572       Name:SMA_5_86572        Variants:C/T    MAF:NaN Ref:C out of order.

BuilderFromVCF data timing 35.1043s 

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.analysis.data.SortGenotypeFilePlugin: time: Nov 5, 2017 12:44:35

[pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.analysis.data.SortGenotypeFilePlugin: time: Nov 5, 2017 12:44:35: progress: 100%

[pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.analysis.data.SortGenotypeFilePlugin  Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.

any suggestions?

Cheers

chen

[Terry Casstevens]

I suspect that your output file was created correctly. That error
message is showing what was out of order. Not indicating a problem.

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[czq...@hotmail.com]

Hi Terry, 

Thanks.  I would like to continue ask one more question. After this sort, I did imputation for genotype using LDKNNi imputation. But I find there still exist some missing values after imputation. 

I was wondering whether it is possible or not?

Cheers

Chen

[Terry Casstevens]

I don't know the details of that function. Maybe someone else will
reply. But I don't think it necessarily fills in every missing value.

> https://groups.google.com/d/msgid/tassel/ddf97f99-490e-47f1-8b34-a311f36026dd%40googlegroups.com.

[czq...@hotmail.com]

Hi Terry,

I saw the paper published in Nature Genetics mentioned that LD-KNNimputaion may not impute all genotypes once, at least in that paper. The LD-KNN imputation was run several times iteratively to reach user requirement.

below is the link to that paper: 

https://www.nature.com/ng/journal/v46/n7/full/ng.3007.html

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

I am not sure how it works in Tassel. Hopefully someone could answer this.

Cheer

Chen