Memory issue in step2_SPAtests.R in version 0.44 but not in 0.42

Hi there,

I am getting a memory error in step2, in the newest version. When I download an older version (0.42) it works fine. I note that there are a few memory error issues open already but I couldn't tell if they were actually the same error or not.

Here is the backtrace for the error, hopefully it will give you an indication of what might be the issue:

*** Error in `/usr/local/lib/R/bin/exec/R': double free or corruption (!prev): 0x00000000096af310 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f9c13ebb7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f9c13ec437a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f9c13ec853c]
/usr/local/lib/R/library/SAIGE/libs/SAIGE.so(_ZN5savvy7variant15deserialize_vcfERS0_RSiRKNS_10dictionaryEmNS_7phasingE+0x5e)[0x7f9b7075249e]
/usr/local/lib/R/library/SAIGE/libs/SAIGE.so(_ZN5savvy6reader11read_recordERNS_7variantE+0x31b)[0x7f9b7075dc9b]
/usr/local/lib/R/library/SAIGE/libs/SAIGE.so(_ZN22variant_group_iterator9incrementEv+0x5f1)[0x7f9b70766ab1]
/usr/local/lib/R/library/SAIGE/libs/SAIGE.so(_ZN22variant_group_iterator4initEv+0x4f6)[0x7f9b70767226]
/usr/local/lib/R/library/SAIGE/libs/SAIGE.so(_Z17getGenoOfGene_vcfNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEf+0x780)[0x7f9b70761cf0]
/usr/local/lib/R/library/SAIGE/libs/SAIGE.so(_SAIGE_getGenoOfGene_vcf+0x96)[0x7f9b706bcbc6]
/usr/local/lib/R/bin/exec/R[0x499802]
/usr/local/lib/R/bin/exec/R[0x4d088a]
/usr/local/lib/R/bin/exec/R(Rf_eval+0x330)[0x4da0c0]
/usr/local/lib/R/bin/exec/R[0x4db843]
/usr/local/lib/R/bin/exec/R[0x4d153f]
/usr/local/lib/R/bin/exec/R(Rf_eval+0x330)[0x4da0c0]
/usr/local/lib/R/bin/exec/R[0x4db843]
/usr/local/lib/R/bin/exec/R(Rf_eval+0x2e2)[0x4da072]
/usr/local/lib/R/bin/exec/R(Rf_ReplIteration+0x209)[0x507b39]
/usr/local/lib/R/bin/exec/R[0x507f18]
/usr/local/lib/R/bin/exec/R(run_Rmainloop+0x45)[0x507fc5]
/usr/local/lib/R/bin/exec/R(main+0x18)[0x41ab58]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f9c13e64830]
/usr/local/lib/R/bin/exec/R(_start+0x29)[0x41ab89]

I will also attach the exact commands I was running here in case there is some issue with them:

This one has the memory error

singularity exec saige_0.44.6.5.sif step2_SPAtests.R \
    --vcfFile=chr1_230837119_236502915.vcf.gz \
    --vcfFileIndex=chr1_230837119_236502915.vcf.gz.csi \
    --vcfField=GT \
    --GMMATmodelFile=null_glmm.rda \
    --varianceRatioFile=null_glmm_var_ratio.varianceRatio.txt \
    --SAIGEOutputFile=chr1_230837119_236502915.output \
    --minMAF=0.0 \
    --minMAC=0.0 \
    --groupFile=chr1_230837119_236502915.regions.tsv \
    --sparseSigmaFile=null_glmm_var_ratio.varianceRatio.txt_relatednessCutoff_0.125_2000_randomMarkersUsed.sparseSigma.mtx \
    --LOCO=FALSE \

This one works

singularity exec saige_0.42.1.sif step2_SPAtests.R \
    --vcfFile=chr1_230837119_236502915.vcf.gz \
    --vcfFileIndex=chr1_230837119_236502915.vcf.gz.csi \
    --vcfField=GT \
    --GMMATmodelFile=null_glmm.rda \
    --varianceRatioFile=null_glmm_var_ratio.varianceRatio.txt \
    --SAIGEOutputFile=chr1_230837119_236502915.output \
    --minMAF=0.0 \
    --minMAC=0.0 \
    --groupFile=chr1_230837119_236502915.regions.tsv \
    --sparseSigmaFile=null_glmm_var_ratio.varianceRatio.txt_relatednessCutoff_0.125_2000_randomMarkersUsed.sparseSigma.mtx \
    --LOCO=FALSE \

Please let me know if there is any other info that you might need.

Kind regards //Adrian

weizhouUMICH / SAIGE

Memory issue in step2_SPAtests.R in version 0.44 but not in 0.42 #382