chang-m-yun's picture
Upload folder using huggingface_hub
9b92b61 verified
Raw
History Blame Contribute Delete
2.51 kB
{
"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/ENCSR362JSZ/preprocessing/bigWigs/ENCSR362JSZ.bigWig",
"input_fragment_file": null,
"input_tagalign_file": null,
"output_dir": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR362JSZ/fold_2",
"data_type": "DNASE",
"peaks": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR362JSZ/fold_2/auxiliary/filtered.peaks.bed",
"nonpeaks": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR362JSZ/fold_2/auxiliary/filtered.nonpeaks.bed",
"chr_fold_path": "/oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/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/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/projects/chromatin-atlas-2022/reference/ENCSR146KFX/fold_2/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/ENCSR362JSZ/fold_2/models/chrombpnet",
"bigwig": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR362JSZ/fold_2/auxiliary/data_unstranded.bw",
"plus_shift": null,
"minus_shift": null,
"chr": "chr22",
"pwm_width": 24,
"params": "/oak/stanford/groups/akundaje/vhecht/chromatin_atlas_bias_corrected/DNASE_model/ENCSR362JSZ/fold_2/logs/chrombpnet_model_params.tsv"
}