Hi,
I encountered this error message while testing step 2 on my own data:
Error in mainMarkerInCPP(genoType, traitType, genoIndex_prev, genoIndex, :
Mat::elem(): index out of bounds
Calls: SPAGMMATtest -> SAIGE.Marker -> mainMarkerInCPP
Execution halted
This is the log:
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS
Matrix products: default
BLAS/LAPACK: /scratch/midway3/zepengmu/miniconda3/envs/RSAIGE/lib/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.14.2 optparse_1.7.1 RhpcBLASctl_0.21-247.1
[4] SAIGEQTL_0.1.0
loaded via a namespace (and not attached):
[1] compiler_4.1.3 Matrix_1.4-1 Rcpp_1.0.7
[4] getopt_1.20.3 RcppNumerical_0.6-0 grid_4.1.3
[7] RcppParallel_5.1.5 lattice_0.20-45
$vcfFile
[1] "merged_chr1-22.merged.phased.vcf.gz"
$vcfFileIndex
[1] ""
$vcfField
[1] "DS"
$savFile
[1] ""
$savFileIndex
[1] ""
$bgenFile
[1] ""
$bgenFileIndex
[1] ""
$sampleFile
[1] "harmonised_smp_3study.txt"
$bedFile
[1] ""
$bimFile
[1] ""
$famFile
[1] ""
$AlleleOrder
[1] "alt-first"
$idstoIncludeFile
[1] ""
$rangestoIncludeFile
[1] "chr21_15922410-15922910.region.txt"
$chrom
[1] "21"
$is_imputed_data
[1] FALSE
$minMAF
[1] 0
$minMAC
[1] 4
$minGroupMAC_in_BurdenTest
[1] 5
$minInfo
[1] 0
$maxMissing
[1] 0.15
$impute_method
[1] "best_guess"
$LOCO
[1] FALSE
$GMMATmodelFile
[1] "chr21_15922410-15922910.rda"
$varianceRatioFile
[1] "chr21_15922410-15922910.varianceRatio.txt"
$GMMATmodel_varianceRatio_multiTraits_File
[1] ""
$SAIGEOutputFile
[1] "chr21_15922410-15922910"
$markers_per_chunk
[1] 3000
$groups_per_chunk
[1] 100
$is_output_moreDetails
[1] FALSE
$is_overwrite_output
[1] TRUE
$maxMAF_in_groupTest
[1] "0.0001,0.001,0.01"
$maxMAC_in_groupTest
[1] "0"
$annotation_in_groupTest
[1] "lof,missense;lof,missense;lof;synonymous"
$groupFile
[1] ""
$sparseGRMFile
[1] ""
$sparseGRMSampleIDFile
[1] ""
$relatednessCutoff
[1] 0
$MACCutoff_to_CollapseUltraRare
[1] 10
$cateVarRatioMinMACVecExclude
[1] "10,20.5"
$cateVarRatioMaxMACVecInclude
[1] "20.5"
$weights.beta
[1] "1;25"
$r.corr
[1] 0
$markers_per_chunk_in_groupTest
[1] 100
$condition
[1] ""
$SPAcutoff
[1] 2
$dosage_zerod_cutoff
[1] 0.2
$dosage_zerod_MAC_cutoff
[1] 10
$is_single_in_groupTest
[1] FALSE
$is_SKATO
[1] FALSE
$is_equal_weight_in_groupTest
[1] FALSE
$is_output_markerList_in_groupTest
[1] FALSE
$is_Firth_beta
[1] FALSE
$pCutoffforFirth
[1] 0.01
$is_fastTest
[1] FALSE
$is_noadjCov
[1] TRUE
$is_sparseGRM
[1] FALSE
$pval_cutoff_for_fastTest
[1] 0.05
$max_MAC_for_ER
[1] 4
$is_EmpSPA
[1] FALSE
$help
[1] FALSE
[1] "opt$r.corr"
[1] 0
dosage_zerod_cutoff 0.2
Any dosages <= 0.2 for genetic variants with MAC <= 10 are set to be 0 in group tests
single-variant association test will be performed
[1] "Leave-one-chromosome-out is not applied"
[1] "LOCO = FASLE and leave-one-chromosome-out is not applied"
isSparseGRM FALSE
variance Ratio null is 0.08065672
variance Ratio null_noXadj is 0.06248972
variance Ratio ratioVec_null_sample is 0.07773422
$ratioVec_sparse
[1] 0.8355189
$ratioVec_null
[1] 0.08065672
$ratioVec_null_sample
[1] 0.07773422
$ratioVec_null_noXadj
[1] 0.06248972
$ratioVec_null_eg
[1] -1
$ratioVec_sparse_eg
[1] -1
vcfFileIndex is not specified. merged_chr1-22.merged.phased.vcf.gz.csi will be used
dosageFile type is vcf
1 ranges are in rangestoIncludeFile
Open VCF done
To read the field DS
Number of meta lines in the vcf file (lines starting with ##): 40
Number of samples in the vcf file: 59
Setting position of samples in VCF files....
m_N 59
Tests will be performed for chromosome: 21 , start: 15672660 end: 16172659
pval_cutoff_for_gxe 0.001
traitType count
(2023-12-20 10:48:57) ---- Analyzing Chunk 1 : chrom InitialChunk ----
I have tried using VCF or Plink file and got the same error.
Thanks so much in advance!!
After some digging around, I realized I used --minMAF=0 --minMAC=4 which potentially conflicts with --max_MAC_for_ER (default is 4). When I used --max_MAC_for_ER=0, I do not get the error above.
Hi, I encountered this error message while testing step 2 on my own data:
This is the log:
I have tried using VCF or Plink file and got the same error. Thanks so much in advance!!