File size: 2,381 Bytes
a4cc8bb | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 | {
"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": "/scratch/users/vhecht/chromatin-atlas-2022/ATAC/ENCSR670REK/preprocessing/bigWigs/ENCSR670REK.bigWig",
"input_fragment_file": null,
"input_tagalign_file": null,
"output_dir": "/scratch/users/vhecht/chromatin-atlas-2022/ATAC/ENCSR670REK/fold_0/model_outputs",
"data_type": "ATAC",
"peaks": "/scratch/users/vhecht/chromatin-atlas-2022/ATAC/ENCSR670REK/fold_0/model_outputs/auxiliary/filtered.peaks.bed",
"nonpeaks": "/scratch/users/vhecht/chromatin-atlas-2022/ATAC/ENCSR670REK/fold_0/model_outputs/auxiliary/filtered.nonpeaks.bed",
"chr_fold_path": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/splits/fold_0.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": "/scratch/users/vhecht/chromatin-atlas-2022/reference/ATAC/fold_0/model.bias.fold_0.ENCSR868FGK.h5",
"negative_sampling_ratio": 0.1,
"filters": 512,
"n_dilation_layers": 8,
"max_jitter": 500,
"batch_size": 64,
"output_prefix": "/scratch/users/vhecht/chromatin-atlas-2022/ATAC/ENCSR670REK/fold_0/model_outputs/models/chrombpnet",
"bigwig": "/scratch/users/vhecht/chromatin-atlas-2022/ATAC/ENCSR670REK/fold_0/model_outputs/auxiliary/data_unstranded.bw",
"plus_shift": null,
"minus_shift": null,
"chr": "chr8",
"pwm_width": 24,
"params": "/scratch/users/vhecht/chromatin-atlas-2022/ATAC/ENCSR670REK/fold_0/model_outputs/logs/chrombpnet_model_params.tsv"
} |