2024-03-11 17:44:43,328 [INFO] Running /home/mshokrof/miniconda3/bin/truvari bench -b /home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz -c manta.HG002.vcf.gz --includebed /home/mshokrof/NistSV/HG002_SVs_Tier1_v0.6.GRCh38.bed -o truvari_output_manta --passonly -r 2000 -C 3000 --reference /group/ctbrowngrp/mshokrof/GRCh38_full_analysis_set_plus_decoy_hla.fa
2024-03-11 17:44:43,328 [INFO] Params:
{
    "base": "/home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz",
    "comp": "manta.HG002.vcf.gz",
    "output": "truvari_output_manta",
    "reference": "/group/ctbrowngrp/mshokrof/GRCh38_full_analysis_set_plus_decoy_hla.fa",
    "giabreport": false,
    "debug": false,
    "prog": false,
    "refdist": 2000,
    "unroll": false,
    "pctsim": 0.7,
    "minhaplen": 50,
    "pctsize": 0.7,
    "pctovl": 0.0,
    "typeignore": false,
    "dup_to_ins": false,
    "use_lev": false,
    "chunksize": 3000,
    "gtcomp": false,
    "bSample": null,
    "cSample": null,
    "sizemin": 50,
    "sizefilt": 30,
    "sizemax": 50000,
    "passonly": true,
    "no_ref": false,
    "includebed": "/home/mshokrof/NistSV/HG002_SVs_Tier1_v0.6.GRCh38.bed",
    "extend": 0,
    "multimatch": false
}
2024-03-11 17:44:43,328 [INFO] Truvari version: 3.5.0
2024-03-11 17:44:44,176 [INFO] Including 34811 bed regions
2024-03-11 17:44:44,602 [INFO] Found 1 chromosomes with overlapping regions
2024-03-11 17:44:58,189 [INFO] Zipped 26899 variants Counter({'base': 19922, 'comp': 6977})
2024-03-11 17:44:58,189 [INFO] 9740 chunks of 26899 variants Counter({'__filtered': 12089, 'base': 9570, 'comp': 5240})
2024-03-11 17:44:58,191 [INFO] Stats: {
    "TP-base": 3698,
    "TP-call": 3698,
    "FP": 1160,
    "FN": 5872,
    "precision": 0.7612186084808563,
    "recall": 0.3864158829676071,
    "f1": 0.5126143609647907,
    "base cnt": 9570,
    "call cnt": 4858,
    "TP-call_TP-gt": 3550,
    "TP-call_FP-gt": 148,
    "TP-base_TP-gt": 3550,
    "TP-base_FP-gt": 148,
    "gt_concordance": 0.9599783666846944,
    "gt_matrix": {
        "(0, 1)": {
            "(0, 1)": 1859,
            "(1, 1)": 108
        },
        "(1, 1)": {
            "(1, 1)": 1691,
            "(0, 1)": 40
        }
    }
}
2024-03-11 17:44:58,251 [INFO] Finished bench