bad_alloc

[bbimber]

Hello -

I am trying to run GLNExus to combine gVCFs produced by DeepVariant. The input is 16 single-sample gVCFs, aligned to the rhesus macaque genome. I split the job to run one contig at a time, and I find that chromosome 1 consistently gives a std::bad_alloc error. Below is the command and output. Can you suggest any debugging steps I could try?

docker run --rm=true \
-v /SequenceO.work:/work \
-w /work \
-v /mnt/scratch/prime-seq/tmp.lwcDaskfexRun_GLNexus_2024-02-12_12-17-24:/tmp \
--memory=120g \
ghcr.io/dnanexus-rnd/glnexus:v1.4.3 \
glnexus_cli --config DeepVariant \
--bed /work/contig.bed \
--trim-uncalled-alleles \
--mem-gbytes 120 \
--threads 8 \
/work/TNPRC-GR91.g.vcf.gz /work/TNPRC-HF97.g.vcf.gz /work/TNPRC-IJ90.g.vcf.gz /work/TNPRC-IP72.g.vcf.gz /work/TNPRC-GH30.g.vcf.gz /work/TNPRC-HR17.g.vcf.gz /work/TNPRC-FP85.g.vcf.gz /work/TNPRC-FP05.g.vcf.gz /work/TNPRC-EP96.g.vcf.gz /work/TNPRC-DN75.g.vcf.gz /work/TNPRC-II86.g.vcf.gz /work/TNPRC-IB18.g.vcf.gz /work/TNPRC-II50.g.vcf.gz /work/TNPRC-HR27.g.vcf.gz /work/TNPRC-HP89.g.vcf.gz /work/TNPRC-GB29.g.vcf.gz | bcftools view | bgzip -c > myFile.vcf.gz

In the command, contig.bed is a one-line bed file specifying chromosome 1.

The output is the following:

07 Mar 2024 13:43:06,239 DEBUG: 	[1] [2024-03-07 21:43:06.239] [GLnexus] [info] glnexus_cli release v1.4.3-0-gcecf42e Sep 20 2021
07 Mar 2024 13:43:06,241 DEBUG: 	[1] [2024-03-07 21:43:06.239] [GLnexus] [info] detected jemalloc 5.2.1-0-gea6b3e973b477b8061e0076bb257dbd7f3faa756
07 Mar 2024 13:43:06,243 DEBUG: 	[1] [2024-03-07 21:43:06.239] [GLnexus] [info] Loading config preset DeepVariant
07 Mar 2024 13:43:06,247 DEBUG: 	[1] [2024-03-07 21:43:06.247] [GLnexus] [info] config:
07 Mar 2024 13:43:06,249 DEBUG: 	unifier_config:
07 Mar 2024 13:43:06,250 DEBUG: 	  drop_filtered: false
07 Mar 2024 13:43:06,252 DEBUG: 	  min_allele_copy_number: 1
07 Mar 2024 13:43:06,253 DEBUG: 	  min_AQ1: 10
07 Mar 2024 13:43:06,255 DEBUG: 	  min_AQ2: 10
07 Mar 2024 13:43:06,256 DEBUG: 	  min_GQ: 0
07 Mar 2024 13:43:06,258 DEBUG: 	  max_alleles_per_site: 32
07 Mar 2024 13:43:06,259 DEBUG: 	  monoallelic_sites_for_lost_alleles: true
07 Mar 2024 13:43:06,260 DEBUG: 	  preference: common
07 Mar 2024 13:43:06,262 DEBUG: 	genotyper_config:
07 Mar 2024 13:43:06,263 DEBUG: 	  revise_genotypes: true
07 Mar 2024 13:43:06,265 DEBUG: 	  min_assumed_allele_frequency: 9.99999975e-05
07 Mar 2024 13:43:06,266 DEBUG: 	  snv_prior_calibration: 0.600000024
07 Mar 2024 13:43:06,268 DEBUG: 	  indel_prior_calibration: 0.449999988
07 Mar 2024 13:43:06,269 DEBUG: 	  required_dp: 0
07 Mar 2024 13:43:06,270 DEBUG: 	  allow_partial_data: true
07 Mar 2024 13:43:06,271 DEBUG: 	  allele_dp_format: AD
07 Mar 2024 13:43:06,273 DEBUG: 	  ref_dp_format: MIN_DP
07 Mar 2024 13:43:06,274 DEBUG: 	  output_residuals: false
07 Mar 2024 13:43:06,275 DEBUG: 	  more_PL: true
07 Mar 2024 13:43:06,276 DEBUG: 	  squeeze: false
07 Mar 2024 13:43:06,277 DEBUG: 	  trim_uncalled_alleles: true
07 Mar 2024 13:43:06,279 DEBUG: 	  top_two_half_calls: false
07 Mar 2024 13:43:06,280 DEBUG: 	  output_format: BCF
07 Mar 2024 13:43:06,281 DEBUG: 	  liftover_fields:
07 Mar 2024 13:43:06,282 DEBUG: 	    - {orig_names: [MIN_DP, DP], name: DP, description: "##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Approximate read depth (reads with MQ=255 or with bad mates are filtered)\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}
07 Mar 2024 13:43:06,284 DEBUG: 	    - {orig_names: [AD], name: AD, description: "##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths for the ref and alt alleles in the order listed\">", type: int, number: alleles, default_type: zero, count: 0, combi_method: min, ignore_non_variants: false}
07 Mar 2024 13:43:06,285 DEBUG: 	    - {orig_names: [GQ], name: GQ, description: "##FORMAT=<ID=GQ,Number=1,Type=Integer,Description=\"Genotype Quality\">", type: int, number: basic, default_type: missing, count: 1, combi_method: min, ignore_non_variants: true}
07 Mar 2024 13:43:06,286 DEBUG: 	    - {orig_names: [PL], name: PL, description: "##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred-scaled genotype Likelihoods\">", type: int, number: genotype, default_type: missing, count: 0, combi_method: missing, ignore_non_variants: true}
07 Mar 2024 13:43:06,287 DEBUG: 	[1] [2024-03-07 21:43:06.247] [GLnexus] [info] config CRC32C = 2932316105
07 Mar 2024 13:43:06,289 DEBUG: 	[1] [2024-03-07 21:43:06.248] [GLnexus] [info] init database, exemplar_vcf=/work/TNPRC-GR91.g.vcf.gz
07 Mar 2024 13:43:06,620 DEBUG: 	[1] [2024-03-07 21:43:06.620] [GLnexus] [info] Initialized GLnexus database in GLnexus.DB
07 Mar 2024 13:43:06,621 DEBUG: 	[1] [2024-03-07 21:43:06.620] [GLnexus] [info] bucket size: 30000
07 Mar 2024 13:43:06,623 DEBUG: 	[1] [2024-03-07 21:43:06.620] [GLnexus] [info] contigs: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 ML143117.1 ML143118.1 ML143119.1 ML143120.1 ML143121.1 ML143122.1 ML143123.1 ML143124.1 MT QNVO02000039.1 QNVO02000040.1 QNVO02000041.1 QNVO02000042.1 QNVO02000043.1 QNVO02000044.1 QNVO02000045.1 QNVO02000046.1 QNVO02000047.1 QNVO02000048.1 QNVO02000049.1 QNVO02000050.1 QNVO02000051.1 QNVO02000052.1 QNVO02000061.1 QNVO02000062.1 QNVO02000063.1 QNVO02000064.1 QNVO02000065.1 QNVO02000066.1 QNVO02000067.1 QNVO02000068.1 QNVO02000069.1 QNVO02000070.1 QNVO02000071.1 QNVO02000072.1 QNVO02000073.1 QNVO02000074.1 QNVO02000082.1 QNVO02000083.1 QNVO02000084.1 QNVO02000085.1 QNVO02000086.1 QNVO02000087.1 QNVO02000088.1 QNVO02000096.1 QNVO02000097.1 QNVO02000098.1 QNVO02000099.1 QNVO02000100.1 QNVO02000101.1 QNVO02000102.1 QNVO02000113.1 QNVO02000114.1 QNVO02000115.1 QNVO02000116.1 QNVO02000117.1 QNVO02000118.1 QNVO02000119.1 QNVO02000120.1 QNVO02000121.1 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QNVO02000328.1 QNVO02000329.1 QNVO02000330.1 QNVO02000331.1 QNVO02000332.1 QNVO02000333.1 QNVO02000334.1 QNVO02000347.1 QNVO02000348.1 QNVO02000349.1 QNVO02000350.1 QNVO02000351.1 QNVO02000352.1 QNVO02000353.1 QNVO02000354.1 QNVO02000355.1 QNVO02000356.1 QNVO02000357.1 QNVO02000358.1 QNVO02000359.1 QNVO02000360.1 QNVO02000361.1 QNVO02000362.1 QNVO02000371.1 QNVO02000372.1 QNVO02000373.1 QNVO02000374.1 QNVO02000375.1 QNVO02000376.1 QNVO02000377.1 QNVO02000378.1 QNVO02000379.1 QNVO02000380.1 QNVO02000381.1 QNVO02000382.1 QNVO02000383.1 QNVO02000384.1 QNVO02000385.1 QNVO02000393.1 QNVO02000394.1 QNVO02000395.1 QNVO02000396.1 QNVO02000397.1 QNVO02000398.1 QNVO02000399.1 QNVO02000400.1 QNVO02000401.1 QNVO02000402.1 QNVO02000403.1 QNVO02000404.1 QNVO02000405.1 QNVO02000406.1 QNVO02000424.1 QNVO02000425.1 QNVO02000426.1 QNVO02000427.1 QNVO02000428.1 QNVO02000429.1 QNVO02000430.1 QNVO02000431.1 QNVO02000432.1 QNVO02000433.1 QNVO02000434.1 QNVO02000435.1 QNVO02000436.1 QNVO02000437.1 QNVO02000438.1 QNVO02000439.1 QNVO02000440.1 QNVO02000441.1 QNVO02000458.1 QNVO02000459.1 QNVO02000460.1 QNVO02000461.1 QNVO02000462.1 QNVO02000463.1 QNVO02000464.1 QNVO02000465.1 QNVO02000466.1 QNVO02000467.1 QNVO02000468.1 QNVO02000469.1 QNVO02000470.1 QNVO02000471.1 QNVO02000472.1 QNVO02000473.1 QNVO02000504.1 QNVO02000505.1 QNVO02000506.1 QNVO02000507.1 QNVO02000508.1 QNVO02000509.1 QNVO02000510.1 QNVO02000511.1 QNVO02000512.1 QNVO02000513.1 QNVO02000514.1 QNVO02000515.1 QNVO02000516.1 QNVO02000517.1 QNVO02000518.1 QNVO02000519.1 QNVO02000520.1 QNVO02000521.1 QNVO02000522.1 QNVO02000523.1 QNVO02000524.1 QNVO02000525.1 QNVO02000526.1 QNVO02000527.1 QNVO02000528.1 QNVO02000529.1 QNVO02000530.1 QNVO02000531.1 QNVO02000532.1 QNVO02000533.1 QNVO02000534.1 QNVO02000535.1 QNVO02000536.1 QNVO02000537.1 QNVO02000538.1 QNVO02000539.1 QNVO02000540.1 QNVO02000541.1 QNVO02000542.1 QNVO02000543.1 QNVO02000544.1 QNVO02000545.1 QNVO02000546.1 QNVO02000547.1 QNVO02000548.1 QNVO02000549.1 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QNVO02000616.1 QNVO02000617.1 QNVO02000618.1 QNVO02000619.1 QNVO02000620.1 QNVO02000621.1 QNVO02000622.1 QNVO02000623.1 QNVO02000624.1 QNVO02000625.1 QNVO02000626.1 QNVO02000627.1 QNVO02000628.1 QNVO02000632.1 QNVO02000633.1 QNVO02000634.1 QNVO02000635.1 QNVO02000636.1 QNVO02000637.1 QNVO02000638.1 QNVO02000639.1 QNVO02000640.1 QNVO02000641.1 QNVO02000642.1 QNVO02000643.1 QNVO02000644.1 QNVO02000645.1 QNVO02000646.1 QNVO02000647.1 QNVO02000648.1 QNVO02000649.1 QNVO02000650.1 QNVO02000651.1 QNVO02000652.1 QNVO02000653.1 QNVO02000654.1 QNVO02000655.1 QNVO02000656.1 QNVO02000657.1 QNVO02000658.1 QNVO02000659.1 QNVO02000660.1 QNVO02000661.1 QNVO02000662.1 QNVO02000663.1 QNVO02000664.1 QNVO02000665.1 QNVO02000666.1 QNVO02000667.1 QNVO02000668.1 QNVO02000669.1 QNVO02000670.1 QNVO02000671.1 QNVO02000672.1 QNVO02000673.1 QNVO02000674.1 QNVO02000675.1 QNVO02000676.1 QNVO02000677.1 QNVO02000678.1 QNVO02000679.1 QNVO02000680.1 QNVO02000681.1 QNVO02000682.1 QNVO02000683.1 QNVO02000684.1 QNVO02000685.1 QNVO02000686.1 QNVO02000687.1 QNVO02000688.1 QNVO02000689.1 QNVO02000690.1 QNVO02000691.1 QNVO02000692.1 QNVO02000693.1 QNVO02000694.1 QNVO02000695.1 QNVO02000696.1 QNVO02000697.1 QNVO02000698.1 QNVO02000699.1 QNVO02000700.1 QNVO02000701.1 QNVO02000702.1 QNVO02000703.1 QNVO02000704.1 QNVO02000705.1 QNVO02000706.1 QNVO02000707.1 QNVO02000708.1 QNVO02000709.1 QNVO02000710.1 QNVO02000711.1 QNVO02000712.1 QNVO02000713.1 QNVO02000714.1 QNVO02000715.1 QNVO02000716.1 QNVO02000717.1 QNVO02000718.1 QNVO02000719.1 QNVO02000720.1 QNVO02000721.1 QNVO02000722.1 QNVO02000723.1 QNVO02000724.1 QNVO02000725.1 QNVO02000726.1 QNVO02000727.1 QNVO02000728.1 QNVO02000729.1 QNVO02000730.1 QNVO02000731.1 QNVO02000732.1 QNVO02000733.1 QNVO02000734.1 QNVO02000735.1 QNVO02000736.1 QNVO02000737.1 QNVO02000738.1 QNVO02000739.1 QNVO02000740.1 QNVO02000741.1 QNVO02000746.1 QNVO02000747.1 QNVO02000748.1 QNVO02000749.1 QNVO02000750.1 QNVO02000751.1 QNVO02000752.1 QNVO02000753.1 QNVO02000754.1 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07 Mar 2024 13:43:06,643 DEBUG: 	[1] [2024-03-07 21:43:06.643] [GLnexus] [info] db_get_contigs GLnexus.DB
07 Mar 2024 13:43:06,787 DEBUG: 	[1] [2024-03-07 21:43:06.786] [GLnexus] [info] Beginning bulk load with no range filter.
07 Mar 2024 13:52:07,720 DEBUG: 	[1] [2024-03-07 21:52:07.720] [GLnexus] [info] Loaded 16 datasets with 16 samples; 137157658272 bytes in 1295984971 BCF records (1497160 duplicate) in 1587535 buckets. Bucket max 734504 bytes, 6860 records. 2260 BCF records skipped due to caller-specific exceptions
07 Mar 2024 13:52:07,736 DEBUG: 	[1] [2024-03-07 21:52:07.736] [GLnexus] [info] Created sample set *@16
07 Mar 2024 13:52:07,738 DEBUG: 	[1] [2024-03-07 21:52:07.736] [GLnexus] [info] Flushing database...
07 Mar 2024 13:53:12,910 DEBUG: 	[1] [2024-03-07 21:53:12.906] [GLnexus] [info] Bulk load complete!
07 Mar 2024 13:53:13,736 DEBUG: 	[1] [2024-03-07 21:53:13.735] [GLnexus] [info] found sample set *@16
07 Mar 2024 13:53:13,738 DEBUG: 	[1] [2024-03-07 21:53:13.735] [GLnexus] [info] discovering alleles in 1 range(s) on 6 threads
07 Mar 2024 13:53:50,417 DEBUG: 	[1] [2024-03-07 21:53:50.416] [GLnexus] [info] discovered 6125193 alleles
07 Mar 2024 13:54:07,986 DEBUG: 	terminate called after throwing an instance of 'std::bad_alloc'
07 Mar 2024 13:54:07,988 DEBUG: 	  what():  std::bad_alloc

When I run this same pattern for any of the other contigs the tool runs fine. Any help would be appreciated.

[yeyy404]

I have also encountered such a problem！Have you solved this problem? Does this mean there is not enough memory?

[bbimber]

Honestly we gave up on GLNexus. We ended up taking the per-sample VCFs produced by DeepVariant (VCF, not gVCF), and merged them directly.

[finkbine]

@bbimber We also encountered a GLNexus memory error. How did you directly merge VCFs? Thanks a lot!

[bbimber]

@finkbine: we gave up on GLnexus - it doesnt appear to have much active support. We have been taking the VCF (not gVCF) outputs from DeepVariant and merging them directly.

[finkbine]

@bbimber Dear bbimber,
Could you share the tool/package/pipeline you use for merging all VCFs? It seems that all missing entries after merging need to be treated as 0/0. Thanks a lot!

[bbimber]

we've used either bcftools or DISCVseq MergeVariantsAndGenotypes (which is a port from GATK). I dont know how it would handle the wild type genotype issue, but I would be a little concerned about assuming they're wild-type as opposed to no-call/filtered.