2025-05-26 20:44:11,731 [INFO] Running /home/mshokrof/miniconda3/envs/cattle_sv/bin/truvari bench -b /home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz -c merged.2982624.vcf.gz --includebed /home/mshokrof/NistSV/HG002_SVs_Tier1_v0.6.GRCh38.chr20.bed -o truvari_output_1kg_chr20 --passonly -r 2000 -C 3000 --reference /group/ctbrowngrp/mshokrof/GRCh38_full_analysis_set_plus_decoy_hla.fa
2025-05-26 20:44:11,733 [INFO] Params:
{
    "base": "/home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz",
    "comp": "merged.2982624.vcf.gz",
    "output": "truvari_output_1kg_chr20",
    "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.chr20.bed",
    "extend": 0,
    "multimatch": false
}
2025-05-26 20:44:11,733 [INFO] Truvari version: 3.5.0
2025-05-26 20:44:11,914 [INFO] Including 873 bed regions
2025-05-26 20:44:15,554 [INFO] Zipped 86184 variants Counter({'comp': 85692, 'base': 492})
2025-05-26 20:44:15,554 [INFO] 275 chunks of 86184 variants Counter({'__filtered': 85833, 'base': 266, 'comp': 85})
2025-05-26 20:44:15,557 [INFO] Stats: {
    "TP-base": 25,
    "TP-call": 25,
    "FP": 48,
    "FN": 241,
    "precision": 0.3424657534246575,
    "recall": 0.09398496240601503,
    "f1": 0.14749262536873156,
    "base cnt": 266,
    "call cnt": 73,
    "TP-call_TP-gt": 23,
    "TP-call_FP-gt": 2,
    "TP-base_TP-gt": 23,
    "TP-base_FP-gt": 2,
    "gt_concordance": 0.92,
    "gt_matrix": {
        "(1, 1)": {
            "(1, 1)": 6,
            "(1, 0)": 2
        },
        "(0, 1)": {
            "(1, 0)": 11,
            "(0, 1)": 6
        }
    }
}
2025-05-26 20:44:15,578 [INFO] Finished bench
