Segmentation fault with condition option

[jgmayer67]

Hi,

I'm new to RVTest and genetics, so if this is something simple I apologize in advance. I am trying to run a conditional analysis with one SNP as the covariate. My command line is below, as well as the error message. This runs fine without the condition option. When I add the condition option, I get a few seconds of it running and then the following occurs:

Include sample [ 49679653 ]. ./condtest.sh: line 40: 22942 Segmentation fault (core dumped) $RVTEST --inVcf $VCFIN --pheno $PEDIN --dosage DS --covar $PEDIN --pheno-name $PHEN_NAME1 --covar-name $COV_NAME --condition $COND_RANGE --peopleIncludeFile $COMP_LIST --out $ASSCOUT1 --single $STAT_TEST

There are 12333 samples, and the log file has 24736 lines of output, so it appears to have gotten into some processing before the error. I have also experimented with widening the range on the condition, same result.

Any help you can provide would be appreciated.

Thanks,

John

$RVTEST --inVcf $VCFIN --pheno $PEDIN --dosage DS --covar $PEDIN --pheno-name $PHEN_NAME1 --covar-name $COV_NAME --condition 6:32632605-32632605 --peopleIncludeFile $COMP_LIST --out $ASSCOUT1 --single $STAT_TEST

[zhanxw]

Did this segfault happen only when "--condition" is used?

Can you paste some lines from the log file?

Thanks.

On Wed, Nov 29, 2017 at 3:59 PM, jgmayer67 [email protected] wrote:

Hi,

I'm new to RVTest and genetics, so if this is something simple I apologize in advance. I am trying to run a conditional analysis with one SNP as the covariate. My command line is below, as well as the error message. This runs fine without the condition option. When I add the condition option, I get a few seconds of it running and then the following occurs:

Include sample [ 49679653 ]. ./condtest.sh: line 40: 22942 Segmentation fault (core dumped) $RVTEST --inVcf $VCFIN --pheno $PEDIN --dosage DS --covar $PEDIN --pheno-name $PHEN_NAME1 --covar-name $COV_NAME --condition $COND_RANGE --peopleIncludeFile $COMP_LIST --out $ASSCOUT1 --single $STAT_TEST

There are 12333 samples, and the log file has 24736 lines of output, so it appears to have gotten into some processing before the error. I have also experimented with widening the range on the condition, same result.

Any help you can provide would be appreciated.

Thanks,

John

$RVTEST --inVcf $VCFIN --pheno $PEDIN --dosage DS --covar $PEDIN --pheno-name $PHEN_NAME1 --covar-name $COV_NAME --condition 6:32632605-32632605 --peopleIncludeFile $COMP_LIST --out $ASSCOUT1 --single $STAT_TEST

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[jgmayer67]

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

[limjyvictor]

Hi,

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

Thanks! Victor

[nhalliga]

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.