Loading anaconda3/gpu/new
  Loading requirement: cuda/11.8
started
Tue Apr  7 10:31:21 AM EDT 2026
started for KG1

============================================================
Processing UPREGULATED data...
============================================================
Loading dataset from /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s4_data_matrices/KG1/upregulated_data.npy...
Computing log2 fold change differential...
Generating histogram after differential computation...
Saved differential histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_histogram_1_differential.png
Applying variance filtering: top 2000 genes, top 500 CAPs...
Generating histogram after variance filtering...
Saved variance filtered histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_histogram_2_variance_filtered.png
Saved variability plot to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_variability.png
Generating ChIP-seq tracks before noise removal...
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep1_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep1_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep1 tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep2_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep2_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep2 tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_differential_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_differential_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved Differential tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated
Removing noise (keeping top 10.0% extreme values)...
Generating histogram after noise removal...
Saved noise removed histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_histogram_3_noise_removed.png
Generating ChIP-seq tracks AFTER noise removal...
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep1_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep1_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep1 tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep2_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_kg1_rep2_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep2 tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_differential_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated/upregulated_differential_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved Differential tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated
Saving processed dataset...
Saved dataset to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/upregulated
Dataset summary:
ChromnitronDataset Summary:
  Shape: (2000, 23) (2000 genes × 23 CAPs)
  Conditions: KG1_rep1, KG1_rep2
  Filtered: 2000 genes × 23 CAPs
  Available matrices: ['KG1_rep1', 'KG1_rep2', 'differential']
    KG1_rep1: range [0.000, 24.308]
    KG1_rep2: range [0.000, 29.215]
    differential: range [-1.925, 3.635]

============================================================
Processing DOWNREGULATED data...
============================================================
Loading dataset from /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s4_data_matrices/KG1/downregulated_data.npy...
Computing log2 fold change differential...
Generating histogram after differential computation...
Saved differential histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_histogram_1_differential.png
Applying variance filtering: top 2000 genes, top 500 CAPs...
Generating histogram after variance filtering...
Saved variance filtered histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_histogram_2_variance_filtered.png
Saved variability plot to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_variability.png
Generating ChIP-seq tracks before noise removal...
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep1_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep1_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep1 tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep2_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep2_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep2 tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_differential_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_differential_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved Differential tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated
Removing noise (keeping top 10.0% extreme values)...
Generating histogram after noise removal...
Saved noise removed histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_histogram_3_noise_removed.png
Generating ChIP-seq tracks AFTER noise removal...
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep1_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep1_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep1 tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep2_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_kg1_rep2_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep2 tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_differential_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated/downregulated_differential_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved Differential tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated
Saving processed dataset...
Saved dataset to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/downregulated
Dataset summary:
ChromnitronDataset Summary:
  Shape: (2000, 23) (2000 genes × 23 CAPs)
  Conditions: KG1_rep1, KG1_rep2
  Filtered: 2000 genes × 23 CAPs
  Available matrices: ['KG1_rep1', 'KG1_rep2', 'differential']
    KG1_rep1: range [0.000, 50.137]
    KG1_rep2: range [0.000, 46.614]
    differential: range [-3.158, 2.727]

============================================================
Processing CONSERVED data...
============================================================
Loading dataset from /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s4_data_matrices/KG1/conserved_data.npy...
Computing log2 fold change differential...
Generating histogram after differential computation...
Saved differential histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_histogram_1_differential.png
Applying variance filtering: top 2000 genes, top 500 CAPs...
Generating histogram after variance filtering...
Saved variance filtered histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_histogram_2_variance_filtered.png
Saved variability plot to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_variability.png
Generating ChIP-seq tracks before noise removal...
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep1_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep1_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep1 tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep2_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep2_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep2 tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_differential_before_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_differential_before_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved Differential tracks (before noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved
Removing noise (keeping top 10.0% extreme values)...
Generating histogram after noise removal...
Saved noise removed histogram to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_histogram_3_noise_removed.png
Generating ChIP-seq tracks AFTER noise removal...
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep1_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep1_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep1 tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep2_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_kg1_rep2_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved KG1_rep2 tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved
Creating multipage PDF: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_differential_after_noise_removal.pdf
Added page 1/1 to PDF
Multipage PDF saved: /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved/conserved_differential_after_noise_removal.pdf
Total pages: 1
Total TFs: 23
Saved Differential tracks (after noise removal) to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved
Saving processed dataset...
Saved dataset to /gpfs/data/aifantislab/home/zhouh05/genomics/dimitris/chromnitron/run_202603/downstream/results/KG1/s5_postprocessing/KG1/conserved
Dataset summary:
ChromnitronDataset Summary:
  Shape: (2000, 23) (2000 genes × 23 CAPs)
  Conditions: KG1_rep1, KG1_rep2
  Filtered: 2000 genes × 23 CAPs
  Available matrices: ['KG1_rep1', 'KG1_rep2', 'differential']
    KG1_rep1: range [0.000, 48.601]
    KG1_rep2: range [0.000, 48.214]
    differential: range [-2.327, 2.535]
Done for KG1
Tue Apr  7 10:31:56 AM EDT 2026
Done
/cm/local/apps/slurm/var/spoold/slurmd.cl40s-8004/job20206299/slurm_script: line 25: /gpfs/home/zhouh05: Is a directory