2025-08-27 18:46:54,852 - INFO - Starting maelstrom
2025-08-27 18:46:54,867 - INFO - Input is not mean-centered, setting the mean of all rows to 0.
2025-08-27 18:46:54,867 - INFO - Use --nocenter if you know what you're doing and want to change this behavior.
2025-08-27 18:46:54,867 - INFO - Note that if you use count data (ChIP-seq, ATAC-seq) we recommend to first transform your data, for instance using log2(), and to normalize between samples. To create a table suitable for maelstrom you can use the coverage_table script included with GimmeMotifs.
2025-08-27 18:46:54,931 - INFO - motif scanning (counts)
2025-08-27 18:46:54,931 - INFO - reading table
2025-08-27 18:46:57,430 - INFO - setting threshold
2025-08-27 18:47:04,027 - INFO - creating count table
2025-08-27 18:47:58,658 - INFO - done
2025-08-27 18:47:58,658 - INFO - creating dataframe
2025-08-27 18:48:10,785 - INFO - motif scanning (scores)
2025-08-27 18:48:10,785 - INFO - reading table
2025-08-27 18:48:17,797 - INFO - creating score table (z-score, GC%)
2025-08-27 18:50:39,735 - INFO - done
2025-08-27 18:50:39,735 - INFO - creating dataframe
2025-08-27 18:53:02,000 - WARNING - Skipping xgboost. Reason: Optional dependency xgboost is required.
2025-08-27 18:53:05,807 - INFO - Fitting BayesianRidge

  0%|          | 0/3 [00:00<?, ?it/s]
 33%|███▎      | 1/3 [00:07<00:14,  7.28s/it]
 67%|██████▋   | 2/3 [00:14<00:07,  7.45s/it]
100%|██████████| 3/3 [00:21<00:00,  7.24s/it]
100%|██████████| 3/3 [00:21<00:00,  7.28s/it]
2025-08-27 18:53:28,253 - INFO - Done
2025-08-27 18:53:32,295 - INFO - Fitting MultiTaskLasso
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 126822.06003662944, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 69915.62543568015, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 88161.76619762182, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 48525.887451052666, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 164581.07203245163, tolerance: 20885.709699505893
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 318804.84412774444, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 173943.14195731282, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 94819.04921495914, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 128507.45536923409, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 164421.89697551727, tolerance: 20885.709699505893
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 285017.6429154873, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 540517.6513410509, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 95744.35261848569, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 127396.05174204707, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 506162.5488412976, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 175466.45239412785, tolerance: 20885.709699505893
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 754304.1554681659, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 182438.95061564445, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 177888.27800157666, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 514367.3248872161, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 326329.9755744785, tolerance: 20885.709699505893
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 1697039.0790516436, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 537913.2303854823, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 300326.3322197199, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 819824.2329812646, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 1038543.596134603, tolerance: 20885.709699505893
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 1295515.85895662, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 664080.5878731012, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 766386.8569367081, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 955476.9793820083, tolerance: 20885.709699505893
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 217255.23599117994, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 1373675.5055202246, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 254501.55575108528, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 266316.87851184607, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 1049513.5039641708, tolerance: 20885.709699505893
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 276779.6727272868, tolerance: 21473.875699496566
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 494423.6031034291, tolerance: 21217.314592965653
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 716062.9677188843, tolerance: 21229.273666848487
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: ConvergenceWarning: Objective did not converge. You might want to increase the number of iterations. Duality gap: 644509.6526470035, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
2025-08-27 21:37:40,133 - INFO - Done
2025-08-27 21:37:44,409 - INFO - Fitting SVR
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: FutureWarning: The default value of `dual` will change from `True` to `'auto'` in 1.5. Set the value of `dual` explicitly to suppress the warning.
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: FutureWarning: The default value of `dual` will change from `True` to `'auto'` in 1.5. Set the value of `dual` explicitly to suppress the warning.
  _warn(*args, **kwargs)
/home/siebrenf/miniconda3/envs/gimme2/lib/python3.10/site-packages/gimmemotifs/__init__.py:30: FutureWarning: The default value of `dual` will change from `True` to `'auto'` in 1.5. Set the value of `dual` explicitly to suppress the warning.
  _warn(*args, **kwargs)
2025-08-27 21:40:02,094 - INFO - Done
2025-08-27 21:40:02,120 - INFO - Rank aggregation
2025-08-27 21:40:03,255 - INFO - Correlation
2025-08-27 21:40:10,441 - INFO - html report
2025-08-27 21:52:24,781 - INFO - out_mg/gimme.maelstrom.report.html