2025-08-27 12:05:28,834 - INFO - Starting maelstrom
2025-08-27 12:05:28,848 - INFO - Input is not mean-centered, setting the mean of all rows to 0.
2025-08-27 12:05:28,848 - INFO - Use --nocenter if you know what you're doing and want to change this behavior.
2025-08-27 12:05:28,848 - 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 12:05:28,916 - INFO - motif scanning (counts)
2025-08-27 12:05:28,916 - INFO - reading table
2025-08-27 12:05:31,316 - INFO - setting threshold
2025-08-27 12:06:48,486 - INFO - creating count table
2025-08-27 12:07:44,618 - INFO - done
2025-08-27 12:07:44,619 - INFO - creating dataframe
2025-08-27 12:07:56,032 - INFO - motif scanning (scores)
2025-08-27 12:07:56,032 - INFO - reading table
2025-08-27 12:08:02,720 - INFO - creating score table (z-score, GC%)
2025-08-27 12:13:51,361 - INFO - done
2025-08-27 12:13:51,361 - INFO - creating dataframe
2025-08-27 12:16:11,637 - WARNING - Skipping xgboost. Reason: Optional dependency xgboost is required.
2025-08-27 12:16:15,446 - INFO - Fitting BayesianRidge

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 33%|███▎      | 1/3 [00:06<00:13,  6.87s/it]
 67%|██████▋   | 2/3 [00:13<00:06,  6.96s/it]
100%|██████████| 3/3 [00:20<00:00,  6.91s/it]
100%|██████████| 3/3 [00:20<00:00,  6.91s/it]
2025-08-27 12:16:36,811 - INFO - Done
2025-08-27 12:16:40,794 - 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: 21268.0143571198, 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: 102769.56599324942, 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: 60578.65355524421, 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: 85045.81384110451, 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: 58879.14982923865, 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: 196423.2974770069, 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: 282486.0813727975, 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: 145373.4462223649, 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: 99536.49721485376, 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: 158875.74748438597, 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: 223955.0672363937, 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: 290718.7960141301, 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: 530729.6070534587, 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: 71181.71516031027, 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: 128997.84734895825, 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: 225533.83968423307, 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: 494652.01209038496, 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: 507571.9239650667, 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: 145666.66530293226, 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: 222160.96779295802, 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: 359066.95197600126, 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: 388693.6189879775, 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: 1265696.12148498, 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: 462922.6036937237, 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: 311586.8826082051, 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: 1039576.3979814053, 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: 739213.2035396397, 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: 1049296.5417966694, 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: 612805.5994658619, 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: 812207.2407232076, 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: 820230.7587948889, 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: 193141.77427783608, 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: 1457388.4297746867, 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: 255284.03209486604, 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: 1044085.2968029082, 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: 302160.32477888465, 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: 399076.1582531929, 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: 520892.7252417803, 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: 560550.8093698919, 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: 595130.999563992, tolerance: 20859.70837740763
  _warn(*args, **kwargs)
2025-08-27 15:14:49,302 - INFO - Done
2025-08-27 15:14:53,216 - 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 15:17:08,718 - INFO - Done
2025-08-27 15:17:08,738 - INFO - Rank aggregation
2025-08-27 15:17:09,984 - INFO - Correlation
2025-08-27 15:17:17,575 - INFO - html report
2025-08-27 15:29:41,108 - INFO - out_gm/gimme.maelstrom.report.html