Sunday, October 18, 2015

GCDH height run timings

runGcdh timings:

# 51 hours
user     system    elapsed
184872.684   1347.476 186386.675

gcdhReport timings:

system.time(gcdh_report <- getQuery(gcdhReport(gcdh_res), "select * from gcdh_report"))
   user  system elapsed
291.780  79.300 371.669
bedinfo height_filtered_iprzbZ
bed file path: height_filtered_iprzbZ.bed
bim file path: height_filtered_iprzbZ.bim
fam file path: height_filtered_iprzbZ.fam
List of shifted bed files: 
[]
......
Number of SNPs: 594937
Number of individuals: 10675
Each SNP uses 2669 bytes
All SNPs use 1587886853 bytes in total

        bed file:           height_filtered_iprzbZ.bed
        bim file:           height_filtered_iprzbZ.bim
        fam file:           height_filtered_iprzbZ.fam
        Number of SNPs:        594937
        Number of obs:         10675
        Bytes / SNP:           2669

Size of bed file agrees with bim and fam files.

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