from rvtests.

Yes, if I remove the condition argument the program runs fine. Here are some of the beginning output lines:

Effective Options
--inVcf chr6.dose.emerge_ids.consented.merged.HC.vcf.gz
--out chr6.CondAnalysisTestCondion
--covar HC_RVTEST_V3_FOR_CA.ped
--covar-name erh,site,PC1,PC2,PC3
--pheno COV_PHEN_DAT_EM_GWAS_HC_RVTEST_V3_FOR_CA.ped
--pheno-name SCORE
--dosage DS
--peopleIncludeFile GOOD_BATCH.list
--single wald
--condition 6:32632605-32632605

[INFO] Program version: 20170418
[INFO] Analysis started at: Thu Nov 30 07:50:18 2017
Include sample [ 63002450 ].
Include sample [ 63008167 ].
Include sample [ 63010203 ].

about halfway through the log file, after all the include samples I get:

[INFO] Loaded [ 12333 ] samples from VCF files
[INFO] Loaded [ 13783 ] sample pheontypes
[INFO] Discard [ 1450 ] samples as they do not have genotypes
[INFO] Begin to read covariate file
[WARN] Total [ 1450 ] samples are skipped from covariate file due to missing phenotype
[WARN] Skip sample [ 16218931 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16219298 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16219621 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16219983 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16221028 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16221790 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16221903 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16222144 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16223659 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16224888 ] from covariate file due to missing phenotype
[WARN] Skip sample [ 16225310 ] from covariate file due to missing phenotype
[WARN] Skip outputting additional [ 1440 ] samples from covariate file with missing phenotypes
[INFO] Loaded 5797 male, 6535 female and 1 sex-unknonw samples from

Hope that helps.

Thanks,

John

from rvtests.

Hi,

I wonder if there is any update on this issue?
I encounter the same problem when trying to do conditional analysis.

Thanks!
Victor

from rvtests.

I am having the same problem. I'm using rvtests on a server and requesting 64GB of memory. I want to condition on a single variant, so it's not clear how big a region to give --condition. The output/error file results follows (edited for brevity and to remove identifiers):

The following parameters are available. Ones with "[]" are in effect:

Available Options
Basic Input/Output:
--inVcf [/MY_DATA]
--inBgen [], --inBgenSample [], --inKgg []
--out [MY_results_conditioned_on_1SNP]
--outputRaw
Specify Covariate: --covar [covar.txt], --covar-name [c1,c2,c3,c4,c5,c6,c7,c8,c9,c10], --sex
Specify Phenotype: --pheno [Pheno.txt], --inverseNormal
--useResidualAsPhenotype, --mpheno [], --pheno-name []
--qtl, --multiplePheno []
Specify Genotype: --dosage [DS], --multipleAllele
Chromosome X Options: --xLabel [], --xParRegion []
People Filter: --peopleIncludeID [], --peopleIncludeFile []
--peopleExcludeID [], --peopleExcludeFile []
Site Filter: --rangeList [], --rangeFile [], --siteFile []
--siteDepthMin [], --siteDepthMax [], --siteMACMin []
--annoType []
Genotype Filter: --indvDepthMin [], --indvDepthMax [], --indvQualMin []
Association Model: --single [wald,score], --burden [], --vt []
--kernel [], --meta []
Family-based Models: --kinship [], --xHemiKinship [], --kinshipEigen []
--xHemiKinshipEigen [], --boltPlink []
--boltPlinkNoCheck
Grouping Unit : --geneFile [], --gene [], --setList [], --setFile []
--set []
Frequency Cutoff: --freqUpper [], --freqLower []
Missing Data: --impute [], --imputePheno, --imputeCov
Conditional Analysis: --condition [11:5303063-5303064]
Auxiliary Functions: --noweb, --hide-covar, --numThread [], --outputID
--help

Effective Options
--inVcf /MY_DATA
--out MY_results_conditioned_on_1SNP
--covar covar.txt
--covar-name c1,c2,c3,c4,c5,c6,c7,c8,c9,c10
--pheno Pheno.txt
--dosage DS
--single wald,score
--condition 11:5303063-5303064

[INFO] Program version: 20171009
[INFO] Analysis started at: Mon Dec 17 10:57:43 2018
[INFO] Loaded [ 1076 ] samples from genotype files
[INFO] Loaded [ 1044 ] sample phenotypes

[INFO] Loaded 538 male, 506 female and 0 sex-unknown samples from rvvPheno.txt
Include sample [ A BUNCH OF SAMPLES ].

/var/spool/torque/mom_priv/jobs/32387356.nyx.arc-ts.umich.edu.SC: line 19: 18495 Segmentation fault (core dumped) rvtest --inVcf /MY_DATA --pheno Pheno.txt --covar covar.txt --covar-name c1,c2,c3,c4,c5,c6,c7,c8,c9,c10 --dosage DS --condition 11:5303063-5303064 --out MY_results_conditioned_on_1SNP --single wald,score

Note that there is a segmentation fault. The command to analyze the data worked without --condtion. This also failed with --condition 11:5303063-5303063 and --condition 11:5303063. I really only want to condition on a single SNP in an imputed dataset.

This is the log file from rvtests:
[INFO] Program version: 20171009
[INFO] Git Version: 5a2e770cdc1cc583febd2a5555b65624e595e7bf
[INFO] Parameters BEGIN

ParameterList created by nhalliga on nyx6152.arc-ts.umich.edu at Mon Dec 17 10:57:43 2018

--inVcf "/MY_DATA" --out "MY_results_conditioned_on_1SNP" --covar "covar.txt" --covar-name "c1,c2,c3,c4,c5,c6,c7,c8,c9,c10" --pheno "Pheno.txt" --dosage "DS" --single "wald,score" --condition "11:5303063-5303064"
[INFO] Parameters END

Thanks.

from rvtests.