python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr10 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr10
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr10_GL383545v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr10_GL383545v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr10_GL383546v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr10_GL383546v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr10_KI270824v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr10_KI270824v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr10_KI270825v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr10_KI270825v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_GL383547v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_GL383547v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_JH159136v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_JH159136v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_JH159137v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_JH159137v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270721v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270721v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270826v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270826v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270827v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270827v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270829v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270829v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270830v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270830v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270831v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270831v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270832v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270832v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270902v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270902v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270903v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270903v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr11_KI270927v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr11_KI270927v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_GL383549v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_GL383549v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_GL383550v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_GL383550v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_GL383551v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_GL383551v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_GL383552v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_GL383552v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_GL383553v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_GL383553v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_GL877875v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_GL877875v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_GL877876v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_GL877876v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_KI270833v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_KI270833v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_KI270834v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_KI270834v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_KI270835v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_KI270835v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_KI270836v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_KI270836v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_KI270837v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_KI270837v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr12_KI270904v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr12_KI270904v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr13 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr13
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr13_KI270838v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr13_KI270838v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr13_KI270839v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr13_KI270839v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr13_KI270840v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr13_KI270840v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr13_KI270841v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr13_KI270841v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr13_KI270842v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr13_KI270842v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr13_KI270843v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr13_KI270843v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_GL000009v2_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_GL000009v2_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_GL000194v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_GL000194v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_GL000225v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_GL000225v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270722v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270722v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270723v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270723v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270724v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270724v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270725v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270725v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270726v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270726v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270844v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270844v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270845v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270845v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270846v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270846v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr14_KI270847v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr14_KI270847v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_GL383554v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_GL383554v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_GL383555v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_GL383555v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270727v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270727v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270848v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270848v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270849v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270849v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270850v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270850v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270851v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270851v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270852v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270852v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270905v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270905v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr15_KI270906v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr15_KI270906v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16_GL383556v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16_GL383556v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16_GL383557v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16_GL383557v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16_KI270728v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16_KI270728v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16_KI270853v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16_KI270853v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16_KI270854v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16_KI270854v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16_KI270855v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16_KI270855v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr16_KI270856v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr16_KI270856v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_GL000205v2_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_GL000205v2_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_GL000258v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_GL000258v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_GL383563v3_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_GL383563v3_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_GL383564v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_GL383564v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_GL383565v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_GL383565v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_GL383566v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_GL383566v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_JH159146v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_JH159146v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_JH159147v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_JH159147v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_JH159148v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_JH159148v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270729v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270729v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270730v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270730v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270857v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270857v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270858v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270858v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270859v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270859v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270860v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270860v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270861v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270861v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270862v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270862v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270907v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270907v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270908v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270908v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270909v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270909v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr17_KI270910v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr17_KI270910v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_GL383567v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_GL383567v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_GL383568v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_GL383568v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_GL383569v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_GL383569v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_GL383570v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_GL383570v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_GL383571v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_GL383571v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_GL383572v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_GL383572v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_KI270863v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_KI270863v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_KI270864v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_KI270864v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_KI270911v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_KI270911v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr18_KI270912v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr18_KI270912v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL000209v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL000209v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL383573v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL383573v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL383574v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL383574v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL383575v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL383575v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL383576v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL383576v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949746v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949746v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949747v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949747v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949748v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949748v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949749v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949749v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949750v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949750v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949751v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949751v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949752v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949752v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_GL949753v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_GL949753v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270865v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270865v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270866v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270866v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270867v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270867v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270868v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270868v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270882v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270882v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270883v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270883v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270884v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270884v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270885v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270885v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270886v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270886v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270887v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270887v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270888v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270888v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270889v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270889v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270890v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270890v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270891v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270891v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270914v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270914v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270915v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270915v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270916v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270916v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270917v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270917v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270918v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270918v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270919v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270919v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270920v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270920v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270921v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270921v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270922v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270922v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270923v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270923v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270929v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270929v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270930v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270930v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270931v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270931v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270932v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270932v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270933v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270933v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr19_KI270938v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr19_KI270938v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_GL383518v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_GL383518v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_GL383519v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_GL383519v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_GL383520v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_GL383520v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270706v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270706v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270707v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270707v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270708v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270708v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270709v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270709v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270710v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270710v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270711v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270711v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270712v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270712v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270713v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270713v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270714v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270714v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270759v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270759v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270760v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270760v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270761v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270761v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270762v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270762v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270763v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270763v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270764v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270764v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270765v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270765v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270766v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270766v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr1_KI270892v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr1_KI270892v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr20 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr20
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr20_GL383577v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr20_GL383577v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr20_KI270869v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr20_KI270869v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr20_KI270870v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr20_KI270870v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr20_KI270871v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr20_KI270871v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21_GL383578v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21_GL383578v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21_GL383579v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21_GL383579v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21_GL383580v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21_GL383580v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21_GL383581v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21_GL383581v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21_KI270872v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21_KI270872v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21_KI270873v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21_KI270873v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr21_KI270874v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr21_KI270874v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_GL383582v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_GL383582v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_GL383583v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_GL383583v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KB663609v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KB663609v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270731v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270731v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270732v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270732v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270733v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270733v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270734v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270734v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270735v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270735v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270736v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270736v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270737v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270737v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270738v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270738v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270739v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270739v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270875v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270875v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270876v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270876v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270877v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270877v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270878v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270878v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270879v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270879v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr22_KI270928v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr22_KI270928v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_GL383521v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_GL383521v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_GL383522v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_GL383522v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_GL582966v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_GL582966v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270715v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270715v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270716v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270716v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270767v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270767v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270768v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270768v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270769v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270769v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270770v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270770v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270771v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270771v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270772v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270772v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270773v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270773v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270774v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270774v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270775v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270775v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270776v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270776v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270893v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270893v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr2_KI270894v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr2_KI270894v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_GL000221v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_GL000221v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_GL383526v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_GL383526v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_JH636055v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_JH636055v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270777v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270777v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270778v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270778v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270779v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270779v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270780v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270780v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270781v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270781v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270782v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270782v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270783v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270783v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270784v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270784v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270895v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270895v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270924v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270924v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270934v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270934v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270935v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270935v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270936v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270936v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr3_KI270937v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr3_KI270937v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_GL000008v2_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_GL000008v2_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_GL000257v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_GL000257v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_GL383527v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_GL383527v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_GL383528v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_GL383528v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270785v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270785v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270786v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270786v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270787v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270787v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270788v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270788v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270789v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270789v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270790v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270790v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270896v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270896v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr4_KI270925v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr4_KI270925v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_GL000208v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_GL000208v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_GL339449v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_GL339449v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_GL383530v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_GL383530v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_GL383531v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_GL383531v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_GL383532v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_GL383532v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_GL949742v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_GL949742v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270791v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270791v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270792v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270792v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270793v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270793v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270794v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270794v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270795v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270795v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270796v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270796v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270897v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270897v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr5_KI270898v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr5_KI270898v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL000250v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL000250v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL000251v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL000251v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL000252v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL000252v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL000253v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL000253v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL000254v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL000254v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL000255v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL000255v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL000256v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL000256v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_GL383533v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_GL383533v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KB021644v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KB021644v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KI270758v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KI270758v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KI270797v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KI270797v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KI270798v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KI270798v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KI270799v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KI270799v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KI270800v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KI270800v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KI270801v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KI270801v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr6_KI270802v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr6_KI270802v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_GL383534v2_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_GL383534v2_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270803v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270803v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270804v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270804v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270805v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270805v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270806v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270806v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270807v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270807v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270808v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270808v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270809v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270809v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr7_KI270899v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr7_KI270899v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270810v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270810v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270811v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270811v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270812v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270812v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270813v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270813v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270814v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270814v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270815v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270815v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270816v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270816v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270817v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270817v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270818v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270818v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270819v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270819v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270820v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270820v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270821v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270821v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270822v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270822v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270900v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270900v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270901v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270901v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr8_KI270926v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr8_KI270926v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_GL383539v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_GL383539v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_GL383540v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_GL383540v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_GL383541v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_GL383541v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_GL383542v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_GL383542v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_KI270717v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_KI270717v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_KI270718v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_KI270718v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_KI270719v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_KI270719v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_KI270720v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_KI270720v1_random
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chr9_KI270823v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chr9_KI270823v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrM -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrM
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000195v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000195v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000213v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000213v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000214v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000214v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000216v2 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000216v2
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000218v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000218v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000219v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000219v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000220v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000220v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000224v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000224v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_GL000226v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_GL000226v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270302v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270302v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270303v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270303v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270304v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270304v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270305v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270305v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270310v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270310v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270311v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270311v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270312v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270312v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270315v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270315v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270316v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270316v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270317v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270317v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270320v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270320v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270322v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270322v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270329v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270329v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270330v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270330v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270333v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270333v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270334v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270334v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270335v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270335v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270336v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270336v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270337v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270337v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270338v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270338v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270340v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270340v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270362v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270362v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270363v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270363v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270364v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270364v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270366v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270366v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270371v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270371v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270372v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270372v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270373v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270373v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270374v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270374v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270375v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270375v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270376v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270376v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270378v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270378v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270379v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270379v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270381v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270381v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270382v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270382v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270383v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270383v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270384v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270384v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270385v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270385v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270386v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270386v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270387v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270387v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270388v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270388v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270389v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270389v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270390v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270390v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270391v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270391v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270392v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270392v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270393v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270393v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270394v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270394v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270395v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270395v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270396v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270396v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270411v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270411v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270412v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270412v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270414v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270414v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270417v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270417v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270418v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270418v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270419v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270419v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270420v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270420v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270422v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270422v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270423v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270423v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270424v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270424v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270425v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270425v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270429v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270429v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270435v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270435v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270438v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270438v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270442v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270442v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270448v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270448v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270465v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270465v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270466v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270466v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270467v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270467v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270468v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270468v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270507v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270507v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270508v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270508v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270509v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270509v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270510v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270510v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270511v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270511v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270512v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270512v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270515v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270515v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270516v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270516v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270517v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270517v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270518v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270518v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270519v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270519v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270521v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270521v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270522v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270522v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270528v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270528v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270529v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270529v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270530v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270530v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270538v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270538v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270539v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270539v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270544v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270544v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270548v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270548v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270579v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270579v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270580v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270580v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270581v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270581v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270582v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270582v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270583v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270583v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270584v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270584v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270587v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270587v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270588v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270588v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270589v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270589v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270590v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270590v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270591v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270591v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270593v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270593v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270741v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270741v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270742v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270742v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270743v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270743v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270744v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270744v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270745v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270745v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270746v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270746v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270747v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270747v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270748v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270748v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270749v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270749v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270750v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270750v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270751v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270751v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270752v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270752v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270753v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270753v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270754v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270754v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270755v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270755v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270756v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270756v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrUn_KI270757v1 -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrUn_KI270757v1
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrX -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrX
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrX_KI270880v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrX_KI270880v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrX_KI270881v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrX_KI270881v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrX_KI270913v1_alt -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrX_KI270913v1_alt
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrY -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrY
python /oak/stanford/groups/akundaje/marinovg/programs/chrombpnet/CHROMBPNET.py pred_bw -cm /oak/stanford/groups/akundaje/projects/chromatin-atlas-2022/chrombpnet/folds/ATAC/GM12878/GM12878_07.08.2022_bias_128_4_1234_0.4_fold_1_data_type_ATAC_PE/bias_model/bias.h5 -r hg38.500bp-step.1000bp-width.bed.chrY_KI270740v1_random -g /oak/stanford/groups/akundaje/marinovg/genomes/hg38/bowtie-indexes/hg38.fa -c /oak/stanford/groups/akundaje/marinovg/genomes/hg38/hg38.chrom.sizes -op chromBPNet-bias.chrY_KI270740v1_random