2023-06-21 16:26:35,331 [INFO] Running /home/mshokrof/miniconda3/bin/truvari bench --includebed /home/mshokrof/deepvariantTest/HG002_SVs_Tier1_v0.6.chr20.GRCh38.bed -b /home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz -c manta.HG002.chr20.vcf.gz -o bencmakrk_manta --passonly -r 2000 -C 3000 --reference /group/ctbrowngrp/mshokrof/GRCh38_full_analysis_set_plus_decoy_hla.fa
2023-06-21 16:26:35,332 [INFO] Params:
{
    "base": "/home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz",
    "comp": "manta.HG002.chr20.vcf.gz",
    "output": "bencmakrk_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/deepvariantTest/HG002_SVs_Tier1_v0.6.chr20.GRCh38.bed",
    "extend": 0,
    "multimatch": false
}
2023-06-21 16:26:35,332 [INFO] Truvari version: 3.5.0
2023-06-21 16:26:35,531 [INFO] Including 873 bed regions
2023-06-21 16:26:36,002 [INFO] Zipped 658 variants Counter({'base': 492, 'comp': 166})
2023-06-21 16:26:36,002 [INFO] 271 chunks of 658 variants Counter({'base': 266, '__filtered': 266, 'comp': 126})
2023-06-21 16:26:36,003 [INFO] Stats: {
    "TP-base": 84,
    "TP-call": 84,
    "FP": 25,
    "FN": 182,
    "precision": 0.7706422018348624,
    "recall": 0.3157894736842105,
    "f1": 0.448,
    "base cnt": 266,
    "call cnt": 109,
    "TP-call_TP-gt": 80,
    "TP-call_FP-gt": 4,
    "TP-base_TP-gt": 80,
    "TP-base_FP-gt": 4,
    "gt_concordance": 0.9523809523809523,
    "gt_matrix": {
        "(1, 1)": {
            "(1, 1)": 40,
            "(0, 1)": 1
        },
        "(0, 1)": {
            "(0, 1)": 40,
            "(1, 1)": 3
        }
    }
}
2023-06-21 16:26:36,015 [INFO] Finished bench
