encode-chrombpnet-ATAC-ENCSR382LBS-ENCSR546DOB / fold_2 /logs.models.fold_2.ENCSR382LBS /logfile.modelling.fold_2.ENCSR382LBS.args.json
| { | |
| "cmd": "pipeline", | |
| "genome": "/oak/stanford/groups/akundaje/cmyun/chromatlas/reference/hg38.fa", | |
| "chrom_sizes": "/oak/stanford/groups/akundaje/cmyun/chromatlas/reference/hg38.chrom.sizes", | |
| "input_bam_file": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/ATAC/ENCSR382LBS/preprocessing/bigWigs/ENCSR382LBS.bigWig", | |
| "input_fragment_file": null, | |
| "input_tagalign_file": null, | |
| "output_dir": "/oak/stanford/groups/akundaje/cmyun/chromatlas/ATAC/ENCSR382LBS/chrombpnet_model_fold_2/", | |
| "data_type": "ATAC", | |
| "peaks": "/oak/stanford/groups/akundaje/cmyun/chromatlas/ATAC/ENCSR382LBS/chrombpnet_model_fold_2/auxiliary/filtered.peaks.bed", | |
| "nonpeaks": "/oak/stanford/groups/akundaje/cmyun/chromatlas/ATAC/ENCSR382LBS/chrombpnet_model_fold_2/auxiliary/filtered.nonpeaks.bed", | |
| "chr_fold_path": "/oak/stanford/groups/akundaje/cmyun/chromatlas/reference/splits/fold_2.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/cmyun/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/cmyun/chromatlas/bias_model/ENCFF881REW/fold_2/model.bias.fold_2.ENCSR868FGK.h5", | |
| "negative_sampling_ratio": 0.1, | |
| "filters": 512, | |
| "n_dilation_layers": 8, | |
| "max_jitter": 500, | |
| "batch_size": 64, | |
| "output_prefix": "/oak/stanford/groups/akundaje/cmyun/chromatlas/ATAC/ENCSR382LBS/chrombpnet_model_fold_2/models/chrombpnet", | |
| "bigwig": "/oak/stanford/groups/akundaje/cmyun/chromatlas/ATAC/ENCSR382LBS/chrombpnet_model_fold_2/auxiliary/data_unstranded.bw", | |
| "plus_shift": null, | |
| "minus_shift": null, | |
| "chr": "chr22", | |
| "pwm_width": 24, | |
| "params": "/oak/stanford/groups/akundaje/cmyun/chromatlas/ATAC/ENCSR382LBS/chrombpnet_model_fold_2/logs/chrombpnet_model_params.tsv" | |
| } |