HB:SMART hongbo.liu$ sw_vers ProductName: Mac OS X ProductVersion: 10.13.4 BuildVersion: 17E199 Python: 2.7.12 HB:SMART hongbo.liu$ pip install SMART-BS-Seq Collecting SMART-BS-Seq Downloading https://files.pythonhosted.org/packages/5f/66/aa5194687293a3afbed30e60a2f82d4eb85bb06b78f01201bd8a1890a3a7/SMART_BS_Seq-2.2.8-py2-none-any.whl (973kB) Requirement already satisfied: numpy>=1.11.2 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from SMART-BS-Seq) (1.12.1) Requirement already satisfied: statsmodels>=0.8.0 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from SMART-BS-Seq) (0.8.0) Requirement already satisfied: scipy>=0.18.1 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from SMART-BS-Seq) (0.19.0) Requirement already satisfied: pandas==0.19.2 in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from SMART-BS-Seq) (0.19.2) Requirement already satisfied: patsy in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages (from statsmodels>=0.8.0->SMART-BS-Seq) (0.4.1) Requirement already satisfied: python-dateutil in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from pandas==0.19.2->SMART-BS-Seq) (1.5) Requirement already satisfied: pytz>=2011k in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from pandas==0.19.2->SMART-BS-Seq) (2013.7) Requirement already satisfied: six in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from patsy->statsmodels>=0.8.0->SMART-BS-Seq) (1.4.1) Installing collected packages: SMART-BS-Seq Successfully installed SMART-BS-Seq-2.2.8 HB:SMART hongbo.liu$ cd /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/SMART/Example HB:Example hongbo.liu$ SMART -t DeNovoDMR -c Case_control_matrix.txt MethylMatrix_Test.txt 2018-04-20 18:19:57 ***************Project SMART parameters************** {'Project_Name': 'SMART', 'Euclidean_Distance': 0.2, 'CpG_Distance': 500, 'AbsMeanMethDiffer': 0.3, 'Percentage_of_Available_Groups': 1.0, 'p_DMR_CaseControl': 0.05, 'CpG_Number': 5, 'Output_Folder': '', 'Miss_Value_Replace': 0.5, 'Segment_Length': 20, 'p_DMR': 0.05, 'Project_Type': 'DeNovoDMR', 'p_MethylMark': 0.05, 'Similarity_Entropy': 0.6, 'MethylMatrix': 'MethylMatrix_Test.txt', 'Region_of_interest': '', 'Case_control_matrix': 'Case_control_matrix.txt', 'Methylation_Specificity': 0.5} 2018-04-20 18:19:57 *****************Project SMART Start***************** 2018-04-20 18:19:57 Start to check methylation data and fill missing value... 2018-04-20 18:20:00 Start genome segmentation ... 2018-04-20 18:20:00 Finish segmentation for chrY 2018-04-20 18:20:04 Finish segmentation for chr20 2018-04-20 18:20:05 Finish segmentation for chr14 2018-04-20 18:20:05 Finish segmentation for chr18 2018-04-20 18:20:06 Finish segmentation for chr1 2018-04-20 18:20:06 Finish segmentation for chr11 2018-04-20 18:20:06 Finish segmentation for chr21 2018-04-20 18:20:06 Finish segmentation for chr16 2018-04-20 18:20:07 Finish segmentation for chr3 2018-04-20 18:20:07 Finish segmentation for chr9 2018-04-20 18:20:07 Finish segmentation for chr19 2018-04-20 18:20:07 Finish segmentation for chr10 2018-04-20 18:20:07 Finish segmentation for chr2 2018-04-20 18:20:07 Finish segmentation for chr8 2018-04-20 18:20:07 Finish segmentation for chr15 2018-04-20 18:20:08 Finish segmentation for chr22 2018-04-20 18:20:08 Finish segmentation for chr6 2018-04-20 18:20:08 Finish segmentation for chrX 2018-04-20 18:20:08 Finish segmentation for chr12 2018-04-20 18:20:08 Finish segmentation for chr4 2018-04-20 18:20:08 Finish segmentation for chr13 2018-04-20 18:20:08 Finish segmentation for chr5 2018-04-20 18:20:09 Finish segmentation for chr7 2018-04-20 18:20:09 Finish segmentation for chr17 2018-04-20 18:20:09 Start to merge small segments... 2018-04-20 18:20:09 Finish merging segments for chr1 2018-04-20 18:20:09 Finish merging segments for chr2 2018-04-20 18:20:10 Finish merging segments for chr3 2018-04-20 18:20:10 Finish merging segments for chr4 2018-04-20 18:20:10 Finish merging segments for chr5 2018-04-20 18:20:10 Finish merging segments for chr6 2018-04-20 18:20:10 Finish merging segments for chr7 2018-04-20 18:20:10 Finish merging segments for chr8 2018-04-20 18:20:10 Finish merging segments for chr9 2018-04-20 18:20:10 Finish merging segments for chr10 2018-04-20 18:20:10 Finish merging segments for chr11 2018-04-20 18:20:10 Finish merging segments for chr12 2018-04-20 18:20:10 Finish merging segments for chr13 2018-04-20 18:20:11 Finish merging segments for chr14 2018-04-20 18:20:11 Finish merging segments for chr15 2018-04-20 18:20:11 Finish merging segments for chr16 2018-04-20 18:20:11 Finish merging segments for chr17 2018-04-20 18:20:11 Finish merging segments for chr18 2018-04-20 18:20:11 Finish merging segments for chr19 2018-04-20 18:20:11 Finish merging segments for chr20 2018-04-20 18:20:11 Finish merging segments for chr21 2018-04-20 18:20:11 Finish merging segments for chr22 2018-04-20 18:20:11 Finish merging segments for chrX 2018-04-20 18:20:11 Finish merging segments for chrY 2018-04-20 18:20:11 Start to identify DMRs... 2018-04-20 18:20:11 Finish DMR identification for chrY 2018-04-20 18:20:12 Finish DMR identification for chr14 2018-04-20 18:20:12 Finish DMR identification for chr3 2018-04-20 18:20:12 Finish DMR identification for chr20 2018-04-20 18:20:12 Finish DMR identification for chr9 2018-04-20 18:20:13 Finish DMR identification for chr21 2018-04-20 18:20:13 Finish DMR identification for chr18 2018-04-20 18:20:13 Finish DMR identification for chr16 2018-04-20 18:20:13 Finish DMR identification for chr11 2018-04-20 18:20:13 Finish DMR identification for chr15 2018-04-20 18:20:13 Finish DMR identification for chr8 2018-04-20 18:20:13 Finish DMR identification for chr1 2018-04-20 18:20:13 Finish DMR identification for chr2 2018-04-20 18:20:13 Finish DMR identification for chr13 2018-04-20 18:20:13 Finish DMR identification for chr5 2018-04-20 18:20:13 Finish DMR identification for chr6 2018-04-20 18:20:13 Finish DMR identification for chr22 2018-04-20 18:20:13 Finish DMR identification for chr10 2018-04-20 18:20:13 Finish DMR identification for chr4 2018-04-20 18:20:13 Finish DMR identification for chrX 2018-04-20 18:20:13 Finish DMR identification for chr19 2018-04-20 18:20:13 Finish DMR identification for chr12 2018-04-20 18:20:13 Finish DMR identification for chr7 2018-04-20 18:20:13 Finish DMR identification for chr17 2018-04-20 18:20:13 Finish DMR identification for all chromesomes 2018-04-20 18:20:13 ********************Project Summary****************** 2018-04-20 18:20:13 Chromesomes : chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY 2018-04-20 18:20:13 Sample Number : 18 2018-04-20 18:20:13 Sample Names : G1_1,G1_2,G2_1,G2_2,G3_1,G3_2,G3_3,G4_1,G4_2,G4_3,G5_1,G5_2,G6_1,G6_2,G7_1,G7_2,G7_3,G7_4 2018-04-20 18:20:13 Group Number : 7 2018-04-20 18:20:13 Group Names : G7,G6,G5,G4,G3,G2,G1 2018-04-20 18:20:13 Number of total CpG sites in all chromesomes :24000 2018-04-20 18:20:13 Number of CpG sites with methylation in all groups :11837 2018-04-20 18:20:13 Number of missing values that have been filled :18911 2018-04-20 18:20:13 Small Segment Number :5097 2018-04-20 18:20:13 Merged Segment Number :591 2018-04-20 18:20:13 DMR Number :329 2018-04-20 18:20:13 NonDMR Number :262 2018-04-20 18:20:13 NonDMR-UniHypo Segment Number :59 2018-04-20 18:20:13 NonDMR-UnipLow Segment Number :19 2018-04-20 18:20:13 NonDMR-UnipHigh Segment Number :70 2018-04-20 18:20:13 NonDMR-UniHyper Segment Number :114 2018-04-20 18:20:13 MethyMark Segment Number :312 2018-04-20 18:20:13 MethyMark-HypoMark Segment Number :132 2018-04-20 18:20:13 MethyMark-HyperMark Segment Number :180 2018-04-20 18:20:13 G7 HypoMark Number: 16 2018-04-20 18:20:13 G7 HyperMark Number: 2 2018-04-20 18:20:13 G6 HypoMark Number: 0 2018-04-20 18:20:13 G6 HyperMark Number: 84 2018-04-20 18:20:13 G5 HypoMark Number: 21 2018-04-20 18:20:13 G5 HyperMark Number: 7 2018-04-20 18:20:13 G4 HypoMark Number: 36 2018-04-20 18:20:13 G4 HyperMark Number: 14 2018-04-20 18:20:13 G3 HypoMark Number: 7 2018-04-20 18:20:13 G3 HyperMark Number: 43 2018-04-20 18:20:13 G2 HypoMark Number: 29 2018-04-20 18:20:13 G2 HyperMark Number: 28 2018-04-20 18:20:13 G1 HypoMark Number: 23 2018-04-20 18:20:13 G1 HyperMark Number: 2 2018-04-20 18:20:13 G3_G4 Case Hypo DMR Number: 30 2018-04-20 18:20:13 G3_G4 Case Hyper DMR Number: 141 2018-04-20 18:20:13 G1_G3 Case Hypo DMR Number: 145 2018-04-20 18:20:13 G1_G3 Case Hyper DMR Number: 27 2018-04-20 18:20:13 G1_G2 Case Hypo DMR Number: 139 2018-04-20 18:20:13 G1_G2 Case Hyper DMR Number: 54 2018-04-20 18:20:13 *********************Summary End********************* 2018-04-20 18:20:13 Detailed results in /Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/SMART/Example/SMART20180420181957/ 2018-04-20 18:20:13 For any questions, visit http://fame.edbc.org/smart/ or contact Hongbo Liu (hongbo919@gmail.com) 2018-04-20 18:20:13 ***************Project SMART Finished!***************