[BUG]std::runtime_error when clumping

[jraikist]

Hi! Thank you for all the hard work!

I'm getting this weird error message after PRSice starts clumping:
`PRSice --a1 ALT --a2 REF --or OR --bp POS --chr "#CHROM" --snp ID --pvalue P --stat OR --binary-target T --memory 10000 --thread 3 --type bgen --pheno my_phenotype.psam --pheno-col my_phenotype -b plink2.my_phenotype.glm.logistic.hybrid --target /path/to/bgen_CHROM_#

PRSice 2.3.3 (2020-08-05)
PRSice
--a1 ALT
--a2 REF
--bar-levels 0.001,0.05,0.1,0.2,0.3,0.4,0.5,1
--binary-target T
--bp POS
--chr #CHROM
--clump-kb 250kb
--clump-p 1.000000
--clump-r2 0.100000
--interval 5e-05
--lower 5e-08
--memory 10000
--num-auto 22
--or
--out PRSice
--pheno my_phenotype.psam
--pheno-col my_phenotype
--pvalue P
--seed 1829857522
--snp ID
--stat OR
--target /path/to/bgen_CHROM_ #
--thread 3
--type bgen
--upper 0.5
Initializing Genotype file:
/path/to/bgen_CHROM_#
(bgen)
Start processing
plink2.my_phenotype.glm.logistic

Base file:
plink2.my_phenotype.glm.logistic.hybrid
Header of file is:
#CHROM POS ID REF ALT A1 FIRTH? TEST OBS_CT OR LOG(OR)_SE Z_STAT P ERRCODE
Reading 100%
21321942 variant(s) observed in base file, with:
812866 variant(s) located on haploid chromosome
1242079 NA stat/p-value observed
2729205 ambiguous variant(s) excluded
16526892 total variant(s) included from base file
Loading Genotype info from target

273681 people (0 male(s), 0 female(s)) observed
273681 founder(s) included
1617K SNPs processed in /path/to/bgen_CHROM_1.bgen
1756K SNPs processed in /path/to/bgen_CHROM_2.bgen
1465K SNPs processed in /path/to/bgen_CHROM_3.bgen
1463K SNPs processed in /path/to/bgen_CHROM_4.bgen
1326K SNPs processed in /path/to/bgen_CHROM_5.bgen
1318K SNPs processed in /path/to/bgen_CHROM_6.bgen
1197K SNPs processed in /path/to/bgen_CHROM_7.bgen
1135K SNPs processed in /path/to/bgen_CHROM_8.bgen
896K SNPs processed in /path/to/bgen_CHROM_9.bgen
1024K SNPs processed in /path/to/bgen_CHROM_10.bgen
1004K SNPs processed in /path/to/bgen_CHROM_11.bgen
976K SNPs processed in /path/to/bgen_CHROM_12.bgen
738K SNPs processed in /path/to/bgen_CHROM_13.bgen
671K SNPs processed in /path/to/bgen_CHROM_14.bgen
592K SNPs processed in/path/to/bgen_CHROM_15.bgen
661K SNPs processed in /path/to/bgen_CHROM_16.bgen
572K SNPs processed in /path/to/bgen_CHROM_17.bgen
580K SNPs processed in /path/to/bgen_CHROM_18.bgen
463K SNPs processed in /path/to/bgen_CHROM_19.bgen
466K SNPs processed in /path/to/bgen_CHROM_20.bgen
273K SNPs processed in /path/to/bgen_CHROM_21.bgen
289K SNPs processed in /path/to/bgen_CHROM_22.bgen
3926184 variant(s) not found in previous data
16512892 variant(s) included
Phenotype file: my_phenotype.psam
Column Name of Sample ID: #FID+IID
Note: If phenotype file does not contain a header, the column name will be displayed as the sample ID which is expected.
There are a total of 1 phenotype to process.
Start performing clumping
terminate called after throwing an instance of 'std::runtime_error'
what(): Error: Cannot read the bgen file!
Aborted`

The my_phenotype.psam looks like this:
#FID IID PAT MAT SEX my_phenotype
ID00001 ID00001 0 0 0 1
ID00002 ID00002 0 0 0 1
ID00003 ID00003 0 0 0 2
ID00004 FID00004 0 0 0 1

my_phenotype.psam is ordered according to bgen files' sample order.

Any ideas?

[choishingwan]

Think it was a bug with 2.3.3. Try and see if 2.3.5 solved the problem

…

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