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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Error while running --meta cov #16

Closed drveera closed 7 years ago

drveera commented 7 years ago

I am getting this same error repeatedly for all --meta cov runs, except that line number is different for the errors. I manually checked the suggested line number in the vcf file and i see nothing abnormal in terms of formatting. Its the same for both plink generated and bcftools generated vcf files. Other analylsis like --single wald or --meta score are fine. Can u please help me here. I need to generate the covariance files to run RAREMETAL. 

Effective Options
    --inVcf sample.chr22.vcf.gz
    --out genie_rare/study1/study1_sample.chr22.vcf.gz/meta/sample.chr22.vcf.gz_cov
    --pheno sample1.fam
    --inverseNormal
    --useResidualAsPhenotype
    --meta cov
    --geneFile /faststorage/home/veera/pipelines/genie//resources/rare/refFlat_hg19.txt.gz

[INFO]  Program version: 20170228
[INFO]  Analysis started at: Sat Apr 15 14:48:38 2017
[INFO]  Loaded [ 2504 ] samples from VCF files
[INFO]  Loaded [ 1000 ] sample pheontypes
[WARN]  Total [ 1504 ] samples are dropped from VCF file due to missing phenotype.
[WARN]  Drop sample [ HG02597_HG02597 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02600_HG02600 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02601_HG02601 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02603_HG02603 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02604_HG02604 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02610_HG02610 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02611_HG02611 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02613_HG02613 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02614_HG02614 ] from VCF file due to missing phenotype
[WARN]  Drop sample [ HG02620_HG02620 ] from VCF file due to missing phenotype
[WARN]  Skip outputting additional [ 1494 ] samples due to missing phenotype.
[INFO]  Loaded 0 male, 0 female and 1000 sex-unknonw samples from sample1.fam
[INFO]  Loaded 474 cases, 526 controls, and 0 missing phenotypes
[WARN]  -- Enabling binary phenotype mode --
[WARN]  WARNING: Skip transforming binary phenotype, although you want to use residual as phenotype!
[WARN]  WARNING: Skip transforming binary phenotype, although you required inverse normalization!
[INFO]  Analysis begins with [ 1000 ] samples...
[INFO]  Meta analysis uses window size 1,000,000 to produce covariance statistics under additive model
[INFO]  Loaded [ 22480 ] genes.
[INFO]  Impute missing genotype to mean (by default)
[INFO]  Analysis started
[INFO]  Analyzed [ 57207 ] variants from [ 22480 ] genes/regions
[ti_index_core] the file out of order at line 53
zhanxw commented 7 years ago

In my observation from the log file, the line 53 of your MetaCov outputs (e.g. genie_rare/study1/study1_sample.chr22.vcf.gz/meta/sample.chr22.vcf.gz_cov.MetaScore.assoc.gz) does not have a proper order.

Can you please verify the input VCF file (sample.chr22.vcf.gz) is sorted first on chromosome and then is numerically sorted on the position column?