SAIGE step 2 *** caught segfault *** address 0x448, cause 'memory not mapped'

[InfoMedichem]

Hi, I ran the following command for step 2 using .bgen file for dosage on a HPC (SAIGE installed as a singularity image) and had the error below. Any suggestions?

saige step2_SPAtests.R         
--bgenFile=/scratch/filtered_array/bgen_8bit/filtered_chr22_8bits.bgen         
--bgenFileIndex=/scratch/filtered_array/filtered_chr22.bgen.bgi         
--minMAF=0.05         
--minMAC=20         
--GMMATmodelFile=/scratch/saige/gwas_tox_concat.rda         
--varianceRatioFile=/scratch/saige/gwas_tox_concat.varianceRatio.txt         
--SAIGEOutputFile=/scratch/saige/gwas_toxcov_chr22.SAIGE.bgen.txt         
--LOCO=FALSE

Loading required package: RhpcBLASctl R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.4 LTS ... ... [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. single-variant association test will be performed [1] "Leave-one-chromosome-out is not applied" P-values of genetic variants with MAC <= 4 will be calculated via effecient resampling. [1] "LOCO = FASLE and leave-one-chromosome-out is not applied" variance Ratio null is 1 dosageFile type is bgen t_SampleInBgen 8431 snpBlocks (Mbgen): 1255683 samples (Nbgen): 8431 CompressedSNPBlocks: 1 Layout: 2 Setting position of samples in Bgen files.... Number of all markers to test: 1255683 Number of markers in each chunk: 10000 Number of chunks for all markers: 126 (2023-09-28 14:27:50) ---- Analyzing Chunk 1/126: chrom InitialChunk ----

caught segfault address 0x448, cause 'memory not mapped'

Traceback: 1: mainMarkerInCPP(genoType, traitType, genoIndex_prev, genoIndex, isMoreOutput, isImputation, isFirth) 2: SAIGE.Marker(traitType, genoType, objGeno$markerInfo$genoIndex_prev, objGeno$markerInfo$genoIndex, objGeno$markerInfo$CHROM, OutputFile, OutputFileIndex, markers_per_chunk, is_output_moreDetails, is_imputed_data, is_Firth_beta, LOCO, chrom, isCondition, is_overwrite_output, objGeno$anyInclude) 3: SPAGMMATtest(vcfFile = opt$vcfFile, vcfFileIndex = opt$vcfFileIndex, vcfField = opt$vcfField, savFile = opt$savFile, savFileIndex = opt$savFileIndex, bgenFile = opt$bgenFile, bgenFileIndex = opt$bgenFileIndex, sampleFile = opt$sampleFile, bedFile = opt$bedFile, bimFile = opt$bimFile, famFile = opt$famFile, AlleleOrder = opt$AlleleOrder, idstoIncludeFile = opt$idstoIncludeFile, rangestoIncludeFile = opt$rangestoIncludeFile, chrom = opt$chrom, is_imputed_data = opt$is_imputed_data, min_MAF = opt$minMAF, min_MAC = opt$minMAC, min_Info = opt$minInfo, max_missing = opt$maxMissing, impute_method = opt$impute_method, LOCO = opt$LOCO, GMMATmodelFile = opt$GMMATmodelFile, varianceRatioFile = opt$varianceRatioFile, SAIGEOutputFile = opt$SAIGEOutputFile, markers_per_chunk = opt$markers_per_chunk, groups_per_chunk = opt$groups_per_chunk, markers_per_chunk_in_groupTest = opt$markers_per_chunk_in_groupTest, is_output_moreDetails = opt$is_output_moreDetails, is_overwrite_output = opt$is_overwrite_output, maxMAF_in_groupTest = maxMAF_in_groupTest, maxMAC_in_groupTest = maxMAC_in_groupTest, minGroupMAC_in_BurdenTest = opt$minGroupMAC_in_BurdenTest, annotation_in_groupTest = annotation_in_groupTest, groupFile = opt$groupFile, sparseGRMFile = opt$sparseGRMFile, sparseGRMSampleIDFile = opt$sparseGRMSampleIDFile, relatednessCutoff = opt$relatednessCutoff, MACCutoff_to_CollapseUltraRare = opt$MACCutoff_to_CollapseUltraRare, cateVarRatioMinMACVecExclude = cateVarRatioMinMACVecExclude, cateVarRatioMaxMACVecInclude = cateVarRatioMaxMACVecInclude, weights.beta = weights.beta, r.corr = opt$r.corr, condition = opt$condition, weights_for_condition = weights_for_condition, SPAcutoff = opt$SPAcutoff, dosage_zerod_cutoff = opt$dosage_zerod_cutoff, dosage_zerod_MAC_cutoff = opt$dosage_zerod_MAC_cutoff, is_Firth_beta = opt$is_Firth_beta, pCutoffforFirth = opt$pCutoffforFirth, is_single_in_groupTest = opt$is_single_in_groupTest, is_no_weight_in_groupTest = opt$is_no_weight_in_groupTest, is_output_markerList_in_groupTest = opt$is_output_markerList_in_groupTest, is_fastTest = opt$is_fastTest, max_MAC_use_ER = opt$max_MAC_for_ER, subSampleFile = opt$subSampleFile) An irrecoverable exception occurred. R is aborting now ... Segmentation fault