2024-01-16 14:29:52,064 [INFO] Truvari v4.1.0
2024-01-16 14:29:52,064 [INFO] Command /home/tigem/h.poddar/anaconda3/envs/truvari/bin/truvari bench -b HG002_insertions.vcf.gz -c diploid_insertion.vcf.gz -o diploid_insertion --includebed HG002_SVs.bed -f /home/tigem/h.poddar/short_reads_pipeline/reference_genome/GRCh37/GRCh37.p13.genome.fa --pctseq 0 -C 1000 -P 0 -s 50 --sizemax 260000000 -S 50 -r 1000 --pick multi --passonly
2024-01-16 14:29:52,064 [INFO] Params:
{
    "base": "/home/tigem/h.poddar/new_bench/dragen/HG002_insertions.vcf.gz",
    "comp": "/home/tigem/h.poddar/new_bench/dragen/diploid_insertion.vcf.gz",
    "output": "diploid_insertion",
    "includebed": "/home/tigem/h.poddar/new_bench/dragen/HG002_SVs.bed",
    "extend": 0,
    "debug": false,
    "reference": "/home/tigem/h.poddar/short_reads_pipeline/reference_genome/GRCh37/GRCh37.p13.genome.fa",
    "refdist": 1000,
    "pctseq": 0.0,
    "minhaplen": 50,
    "pctsize": 0.0,
    "pctovl": 0.0,
    "typeignore": false,
    "chunksize": 1000,
    "bSample": "HG002",
    "cSample": "none",
    "dup_to_ins": false,
    "sizemin": 50,
    "sizefilt": 50,
    "sizemax": 260000000,
    "passonly": true,
    "no_ref": false,
    "pick": "multi",
    "check_monref": true,
    "check_multi": true
}
2024-01-16 14:29:52,442 [INFO] Including 34830 bed regions
2024-01-16 14:29:54,265 [INFO] Zipped 10849 variants Counter({'base': 9882, 'comp': 967})
2024-01-16 14:29:54,265 [INFO] 5459 chunks of 10849 variants Counter({'base': 5443, '__filtered': 4754, 'comp': 652})
2024-01-16 14:29:54,701 [INFO] Stats: {
    "TP-base": 645,
    "TP-comp": 647,
    "FP": 5,
    "FN": 4798,
    "precision": 0.9923312883435583,
    "recall": 0.11850082674995407,
    "f1": 0.21171890239896343,
    "base cnt": 5443,
    "comp cnt": 652,
    "TP-comp_TP-gt": 586,
    "TP-comp_FP-gt": 61,
    "TP-base_TP-gt": 584,
    "TP-base_FP-gt": 61,
    "gt_concordance": 0.9057187017001546,
    "gt_matrix": {
        "(1, 1)": {
            "(1, 1)": 384,
            "(0, 1)": 29
        },
        "(0, 1)": {
            "(0, 1)": 200,
            "(1, 1)": 32
        }
    },
    "weighted": {
        "sequence": {
            "TP": 0.0,
            "FP": 652.0,
            "FN": 5443.0,
            "precision": 0.0,
            "recall": 0.0,
            "f1": null,
            "total": 6095
        },
        "size": {
            "TP": 1258.170499816537,
            "FP": 22.413300089538097,
            "FN": 4814.416200093925,
            "precision": 0.9824975920426433,
            "recall": 0.20718856098589555,
            "f1": 0.34221170306004156,
            "total": 6095
        }
    }
}
2024-01-16 14:29:54,701 [INFO] Finished bench