fold_4/logs.models.fold_4.ENCSR398JUP/logfile.modelling.fold_4.ENCSR398JUP.args.json

{
    "cmd": "pipeline",
    "genome": "/oak/stanford/groups/akundaje/ziwei75/atac_seq_pipeline/hg38/GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta",
    "chrom_sizes": "/oak/stanford/groups/akundaje/ziwei75/atac_seq_pipeline/hg38/GRCh38_EBV.chrom.sizes.tsv",
    "input_bam_file": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/DNASE/ENCSR398JUP/preprocessing/bigWigs/ENCSR398JUP.bigWig",
    "input_fragment_file": null,
    "input_tagalign_file": null,
    "output_dir": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR398JUP/fold_4",
    "data_type": "DNASE",
    "peaks": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR398JUP/fold_4/auxiliary/filtered.peaks.bed",
    "nonpeaks": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR398JUP/fold_4/auxiliary/filtered.nonpeaks.bed",
    "chr_fold_path": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/splits/fold_4.json",
    "outlier_threshold": 0.9999,
    "ATAC_ref_path": null,
    "DNASE_ref_path": null,
    "num_samples": 10000,
    "inputlen": 2114,
    "outputlen": 1000,
    "seed": 1234,
    "epochs": 50,
    "early_stop": 5,
    "learning_rate": 0.001,
    "trackables": [
        "logcount_predictions_loss",
        "loss",
        "logits_profile_predictions_loss",
        "val_logcount_predictions_loss",
        "val_loss",
        "val_logits_profile_predictions_loss"
    ],
    "architecture_from_file": "/home/users/vhecht/chrombpnet/chrombpnet/chrombpnet/training/models/chrombpnet_with_bias_model.py",
    "file_prefix": null,
    "html_prefix": "./",
    "bsort": false,
    "tmpdir": null,
    "no_st": false,
    "bias_model_path": "/oak/stanford/groups/akundaje/ziwei75/chromatin_atlas_bias/DNase_bias_model/bias_threshold_0.8/ENCSR398JUP/models/bias.h5",
    "negative_sampling_ratio": 0.1,
    "filters": 512,
    "n_dilation_layers": 8,
    "max_jitter": 500,
    "batch_size": 64,
    "output_prefix": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR398JUP/fold_4/models/chrombpnet",
    "bigwig": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR398JUP/fold_4/auxiliary/data_unstranded.bw",
    "plus_shift": null,
    "minus_shift": null,
    "chr": "chr10",
    "pwm_width": 24,
    "params": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR398JUP/fold_4/logs/chrombpnet_model_params.tsv"
}