2024-03-11 16:06:18,325 [INFO] Running /home/mshokrof/miniconda3/bin/truvari bench -b /home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz -c merged.3156467.vcf.gz --includebed /home/mshokrof/NistSV/HG002_SVs_Tier1_v0.6.GRCh38.bed -o truvari_output_1kg --passonly -r 2000 -C 3000 --reference /group/ctbrowngrp/mshokrof/GRCh38_full_analysis_set_plus_decoy_hla.fa
2024-03-11 16:06:18,325 [INFO] Params:
{
    "base": "/home/mshokrof/NistSV/HG002_SVs_Tier1_GRCH38.vcf.gz",
    "comp": "merged.3156467.vcf.gz",
    "output": "truvari_output_1kg",
    "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 16:06:18,325 [INFO] Truvari version: 3.5.0
2024-03-11 16:06:19,401 [INFO] Including 34811 bed regions
2024-03-11 16:06:19,910 [INFO] Found 1 chromosomes with overlapping regions
2024-03-11 16:08:18,520 [WARNING] Unable to fetch chr7_KI270803v1_alt from b'merged.3156467.vcf.gz'
2024-03-11 16:08:25,810 [WARNING] Unable to fetch chr8_KI270821v1_alt from b'merged.3156467.vcf.gz'
2024-03-11 16:08:31,350 [INFO] Zipped 3998627 variants Counter({'comp': 3978705, 'base': 19922})
2024-03-11 16:08:31,350 [INFO] 9639 chunks of 3998627 variants Counter({'__filtered': 3985936, 'base': 9570, 'comp': 3121})
2024-03-11 16:08:31,353 [INFO] Stats: {
    "TP-base": 783,
    "TP-call": 783,
    "FP": 2068,
    "FN": 8787,
    "precision": 0.27464047702560507,
    "recall": 0.08181818181818182,
    "f1": 0.1260768054101924,
    "base cnt": 9570,
    "call cnt": 2851,
    "TP-call_TP-gt": 729,
    "TP-call_FP-gt": 54,
    "TP-base_TP-gt": 729,
    "TP-base_FP-gt": 54,
    "gt_concordance": 0.9310344827586207,
    "gt_matrix": {
        "(0, 1)": {
            "(0, 1)": 273,
            "(1, 0)": 259,
            "(1, 1)": 8
        },
        "(1, 1)": {
            "(1, 1)": 197,
            "(0, 1)": 24,
            "(1, 0)": 22
        }
    }
}
2024-03-11 16:08:31,377 [INFO] Finished bench