[hongbo.liu@login01 SMART]$ lsb_release -a LSB Version: :core-4.1-amd64:core-4.1-noarch Distributor ID: CentOS Description: CentOS Linux release 7.3.1611 (Core) Release: 7.3.1611 Codename: Core Python: 2.7.12 [hongbo.liu@login01 SMART]$ pip install --user SMART-BS-Seq Collecting SMART-BS-Seq Using cached https://files.pythonhosted.org/packages/5f/66/aa5194687293a3afbed30e60a2f82d4eb85bb06b78f01201bd8a1890a3a7/SMART_BS_Seq-2.2.8-py2-none-any.whl Requirement already satisfied: pandas==0.19.2 in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages (from SMART-BS-Seq) Requirement already satisfied: statsmodels>=0.8.0 in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages (from SMART-BS-Seq) Requirement already satisfied: numpy>=1.11.2 in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages/numpy-1.14.2-py2.7-linux-x86_64.egg (from SMART-BS-Seq) Requirement already satisfied: scipy>=0.18.1 in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages (from SMART-BS-Seq) Requirement already satisfied: pytz>=2011k in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages (from pandas==0.19.2->SMART-BS-Seq) Requirement already satisfied: python-dateutil in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages (from pandas==0.19.2->SMART-BS-Seq) Requirement already satisfied: patsy in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages (from statsmodels>=0.8.0->SMART-BS-Seq) Requirement already satisfied: six>=1.5 in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages/six-1.11.0-py2.7.egg (from python-dateutil->pandas==0.19.2->SMART-BS-Seq) Installing collected packages: SMART-BS-Seq Successfully installed SMART-BS-Seq-2.2.8 You are using pip version 9.0.1, however version 10.0.0 is available. You should consider upgrading via the 'pip install --upgrade pip' command. [hongbo.liu@login01 SMART]$ SMART -v SMART 2.2.8 [hongbo.liu@login01 SMART]$ SMART -h usage: SMART [-h] [-t {DeNovoDMR,DMROI,DMC,Segment}] [-r REGION_OF_INTEREST] [-c CASE_CONTROL_MATRIX] [-n PROJECT_NAME] [-o OUTPUT_FOLDER] [-MR MISS_VALUE_REPLACE] [-AG PERCENTAGE_OF_AVAILABLE_GROUPS] [-MS METHYLATION_SPECIFICITY] [-ED EUCLIDEAN_DISTANCE] [-SM SIMILARITY_ENTROPY] [-CD CPG_DISTANCE] [-CN CPG_NUMBER] [-SL SEGMENT_LENGTH] [-PD P_DMR] [-PM P_METHYLMARK] [-PC P_DMR_CASECONTROL] [-AD ABSMEANMETHDIFFER] [-v] MethylMatrix [hongbo.liu@login01 SMART]$ cd /primary/home/hongbo.liu/.local/lib/python2.7/site-packages/SMART/Example [hongbo.liu@login01 Example]$ SMART -t DeNovoDMR -c Case_control_matrix.txt MethylMatrix_Test.txt 2018-04-20 17:36:13 ***************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 17:36:13 *****************Project SMART Start***************** 2018-04-20 17:36:13 Start to check methylation data and fill missing value... 2018-04-20 17:36:16 Start genome segmentation ... 2018-04-20 17:36:16 Finish segmentation for chrY 2018-04-20 17:36:26 Finish segmentation for chr18 2018-04-20 17:36:27 Finish segmentation for chr20 2018-04-20 17:36:27 Finish segmentation for chr14 2018-04-20 17:36:28 Finish segmentation for chr1 2018-04-20 17:36:31 Finish segmentation for chr3 2018-04-20 17:36:31 Finish segmentation for chr11 2018-04-20 17:36:31 Finish segmentation for chr8 2018-04-20 17:36:32 Finish segmentation for chr21 2018-04-20 17:36:32 Finish segmentation for chr19 2018-04-20 17:36:32 Finish segmentation for chr2 2018-04-20 17:36:32 Finish segmentation for chr16 2018-04-20 17:36:33 Finish segmentation for chr10 2018-04-20 17:36:33 Finish segmentation for chr13 2018-04-20 17:36:33 Finish segmentation for chr9 2018-04-20 17:36:33 Finish segmentation for chr15 2018-04-20 17:36:34 Finish segmentation for chr22 2018-04-20 17:36:34 Finish segmentation for chr12 2018-04-20 17:36:34 Finish segmentation for chrX 2018-04-20 17:36:34 Finish segmentation for chr6 2018-04-20 17:36:34 Finish segmentation for chr4 2018-04-20 17:36:35 Finish segmentation for chr5 2018-04-20 17:36:35 Finish segmentation for chr7 2018-04-20 17:36:35 Finish segmentation for chr17 2018-04-20 17:36:35 Start to merge small segments... 2018-04-20 17:36:35 Finish merging segments for chr1 2018-04-20 17:36:35 Finish merging segments for chr2 2018-04-20 17:36:36 Finish merging segments for chr3 2018-04-20 17:36:36 Finish merging segments for chr4 2018-04-20 17:36:36 Finish merging segments for chr5 2018-04-20 17:36:36 Finish merging segments for chr6 2018-04-20 17:36:36 Finish merging segments for chr7 2018-04-20 17:36:36 Finish merging segments for chr8 2018-04-20 17:36:36 Finish merging segments for chr9 2018-04-20 17:36:36 Finish merging segments for chr10 2018-04-20 17:36:36 Finish merging segments for chr11 2018-04-20 17:36:36 Finish merging segments for chr12 2018-04-20 17:36:36 Finish merging segments for chr13 2018-04-20 17:36:36 Finish merging segments for chr14 2018-04-20 17:36:36 Finish merging segments for chr15 2018-04-20 17:36:36 Finish merging segments for chr16 2018-04-20 17:36:36 Finish merging segments for chr17 2018-04-20 17:36:36 Finish merging segments for chr18 2018-04-20 17:36:36 Finish merging segments for chr19 2018-04-20 17:36:36 Finish merging segments for chr20 2018-04-20 17:36:36 Finish merging segments for chr21 2018-04-20 17:36:37 Finish merging segments for chr22 2018-04-20 17:36:37 Finish merging segments for chrX 2018-04-20 17:36:37 Finish merging segments for chrY 2018-04-20 17:36:37 Start to identify DMRs... 2018-04-20 17:36:37 Finish DMR identification for chrY 2018-04-20 17:36:39 Finish DMR identification for chr20 2018-04-20 17:36:39 Finish DMR identification for chr3 2018-04-20 17:36:39 Finish DMR identification for chr14 2018-04-20 17:36:40 Finish DMR identification for chr6 2018-04-20 17:36:40 Finish DMR identification for chr21 2018-04-20 17:36:40 Finish DMR identification for chr2 2018-04-20 17:36:40 Finish DMR identification for chr9 2018-04-20 17:36:40 Finish DMR identification for chr1 2018-04-20 17:36:40 Finish DMR identification for chr16 2018-04-20 17:36:40 Finish DMR identification for chr22 2018-04-20 17:36:40 Finish DMR identification for chr15 2018-04-20 17:36:40 Finish DMR identification for chr18 2018-04-20 17:36:40 Finish DMR identification for chr19 2018-04-20 17:36:41 Finish DMR identification for chr10 2018-04-20 17:36:41 Finish DMR identification for chrX 2018-04-20 17:36:41 Finish DMR identification for chr8 2018-04-20 17:36:41 Finish DMR identification for chr11 2018-04-20 17:36:41 Finish DMR identification for chr4 2018-04-20 17:36:41 Finish DMR identification for chr13 2018-04-20 17:36:41 Finish DMR identification for chr5 2018-04-20 17:36:41 Finish DMR identification for chr7 2018-04-20 17:36:41 Finish DMR identification for chr17 2018-04-20 17:36:41 Finish DMR identification for chr12 2018-04-20 17:36:41 Finish DMR identification for all chromesomes 2018-04-20 17:36:41 ********************Project Summary****************** 2018-04-20 17:36:41 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 17:36:41 Sample Number : 18 2018-04-20 17:36:41 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 17:36:41 Group Number : 7 2018-04-20 17:36:41 Group Names : G7,G6,G5,G4,G3,G2,G1 2018-04-20 17:36:41 Number of total CpG sites in all chromesomes :24000 2018-04-20 17:36:41 Number of CpG sites with methylation in all groups :11837 2018-04-20 17:36:41 Number of missing values that have been filled :18911 2018-04-20 17:36:41 Small Segment Number :5097 2018-04-20 17:36:41 Merged Segment Number :591 2018-04-20 17:36:41 DMR Number :329 2018-04-20 17:36:41 NonDMR Number :262 2018-04-20 17:36:41 NonDMR-UniHypo Segment Number :59 2018-04-20 17:36:41 NonDMR-UnipLow Segment Number :19 2018-04-20 17:36:41 NonDMR-UnipHigh Segment Number :70 2018-04-20 17:36:41 NonDMR-UniHyper Segment Number :114 2018-04-20 17:36:41 MethyMark Segment Number :312 2018-04-20 17:36:41 MethyMark-HypoMark Segment Number :132 2018-04-20 17:36:41 MethyMark-HyperMark Segment Number :180 2018-04-20 17:36:41 G7 HypoMark Number: 16 2018-04-20 17:36:41 G7 HyperMark Number: 2 2018-04-20 17:36:41 G6 HypoMark Number: 0 2018-04-20 17:36:41 G6 HyperMark Number: 84 2018-04-20 17:36:41 G5 HypoMark Number: 21 2018-04-20 17:36:41 G5 HyperMark Number: 7 2018-04-20 17:36:41 G4 HypoMark Number: 36 2018-04-20 17:36:41 G4 HyperMark Number: 14 2018-04-20 17:36:41 G3 HypoMark Number: 7 2018-04-20 17:36:41 G3 HyperMark Number: 43 2018-04-20 17:36:41 G2 HypoMark Number: 29 2018-04-20 17:36:41 G2 HyperMark Number: 28 2018-04-20 17:36:41 G1 HypoMark Number: 23 2018-04-20 17:36:41 G1 HyperMark Number: 2 2018-04-20 17:36:41 G3_G4 Case Hypo DMR Number: 30 2018-04-20 17:36:41 G3_G4 Case Hyper DMR Number: 141 2018-04-20 17:36:41 G1_G3 Case Hypo DMR Number: 145 2018-04-20 17:36:41 G1_G3 Case Hyper DMR Number: 27 2018-04-20 17:36:41 G1_G2 Case Hypo DMR Number: 139 2018-04-20 17:36:41 G1_G2 Case Hyper DMR Number: 54 2018-04-20 17:36:41 *********************Summary End********************* 2018-04-20 17:36:41 Detailed results in /primary/home/hongbo.liu/.local/lib/python2.7/site-packages/SMART/Example/SMART20180420173613/ 2018-04-20 17:36:41 For any questions, visit http://fame.edbc.org/smart/ or contact Hongbo Liu (hongbo919@gmail.com) 2018-04-20 17:36:41 ***************Project SMART Finished!***************