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/test-data/peakcalling_sicer/test_1/output_log_file.contains

https://bitbucket.org/cistrome/cistrome-harvard/
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  1#############################################
  2######           SICER v1.1            ######
  3#############################################
  4Input library directory:
  5ChIP library:
  6Output directory:
  7Species: mm8
  8Threshold for redundancy allowed for reads: 1
  9Window size: 200 bps
 10Fragment size: 150 bps. The shift for reads is half of 150
 11Effective genome size as a fraction of the reference genome of mm8: 0.740000
 12Gap size: 600 bps
 13Evalue for identification of significant islands: 0.01
 14Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
 15chr1 	Plus reads: 4989 	Retained plus reads: 4935 ;	Minus reads: 5011 	Retained minus reads: 4963
 16chr2 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 17chr3 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 18chr4 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 19chr5 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 20chr6 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 21chr7 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 22chr8 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 23chr9 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 24chr10 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 25chr11 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 26chr12 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 27chr13 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 28chr14 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 29chr15 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 30chr16 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 31chr17 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 32chr18 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 33chr19 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 34chrX 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 35chrY 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 36chrM 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 37Partion the genome in windows ...
 38Generate summary files for input_bed_file...
 39total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
 40total tag count in chr2.bed is: 0.0 = 0.0+0.0
 41total tag count in chr3.bed is: 0.0 = 0.0+0.0
 42total tag count in chr4.bed is: 0.0 = 0.0+0.0
 43total tag count in chr5.bed is: 0.0 = 0.0+0.0
 44total tag count in chr6.bed is: 0.0 = 0.0+0.0
 45total tag count in chr7.bed is: 0.0 = 0.0+0.0
 46total tag count in chr8.bed is: 0.0 = 0.0+0.0
 47total tag count in chr9.bed is: 0.0 = 0.0+0.0
 48total tag count in chr10.bed is: 0.0 = 0.0+0.0
 49total tag count in chr11.bed is: 0.0 = 0.0+0.0
 50total tag count in chr12.bed is: 0.0 = 0.0+0.0
 51total tag count in chr13.bed is: 0.0 = 0.0+0.0
 52total tag count in chr14.bed is: 0.0 = 0.0+0.0
 53total tag count in chr15.bed is: 0.0 = 0.0+0.0
 54total tag count in chr16.bed is: 0.0 = 0.0+0.0
 55total tag count in chr17.bed is: 0.0 = 0.0+0.0
 56total tag count in chr18.bed is: 0.0 = 0.0+0.0
 57total tag count in chr19.bed is: 0.0 = 0.0+0.0
 58total tag count in chrX.bed is: 0.0 = 0.0+0.0
 59total tag count in chrY.bed is: 0.0 = 0.0+0.0
 60total tag count in chrM.bed is: 0.0 = 0.0+0.0
 61Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...
 62Convert the normalized summary graph into wig vstep format...
 63Find significant islands with E-value 0.01 for input_bed_file...
 64Species:  mm8
 65Window_size:  200
 66Gap size:  600
 67E value is: 0.01
 68Total read count: 9898.0
 69Genome Length:  2644093988
 70Effective genome Length:  1956629551
 71Window average: 0.0010117398048
 72Window pvalue: 0.2
 73Minimum num of tags in a qualified window:  1
 74Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows 
 75Determine the score threshold from random background
 76The score threshold is:  21.384
 77Make and write islands
 78Total number of islands:  352
 79Filter reads with identified significant islands for input_bed_file...
 80Make summary graph with filtered reads for input_bed_file...
 81total tag count in chr1.bed is: 9654.0 = 4808.0+4846.0
 82total tag count in chr2.bed is: 0.0 = 0.0+0.0
 83total tag count in chr3.bed is: 0.0 = 0.0+0.0
 84total tag count in chr4.bed is: 0.0 = 0.0+0.0
 85total tag count in chr5.bed is: 0.0 = 0.0+0.0
 86total tag count in chr6.bed is: 0.0 = 0.0+0.0
 87total tag count in chr7.bed is: 0.0 = 0.0+0.0
 88total tag count in chr8.bed is: 0.0 = 0.0+0.0
 89total tag count in chr9.bed is: 0.0 = 0.0+0.0
 90total tag count in chr10.bed is: 0.0 = 0.0+0.0
 91total tag count in chr11.bed is: 0.0 = 0.0+0.0
 92total tag count in chr12.bed is: 0.0 = 0.0+0.0
 93total tag count in chr13.bed is: 0.0 = 0.0+0.0
 94total tag count in chr14.bed is: 0.0 = 0.0+0.0
 95total tag count in chr15.bed is: 0.0 = 0.0+0.0
 96total tag count in chr16.bed is: 0.0 = 0.0+0.0
 97total tag count in chr17.bed is: 0.0 = 0.0+0.0
 98total tag count in chr18.bed is: 0.0 = 0.0+0.0
 99total tag count in chr19.bed is: 0.0 = 0.0+0.0
100total tag count in chrX.bed is: 0.0 = 0.0+0.0
101total tag count in chrY.bed is: 0.0 = 0.0+0.0
102total tag count in chrM.bed is: 0.0 = 0.0+0.0
103Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
104Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...
105Done!
106Additionally, these warnings were reported:
107Warning: chr2 reads do not exist in
108Warning: chr3 reads do not exist in
109Warning: chr4 reads do not exist in
110Warning: chr5 reads do not exist in
111Warning: chr6 reads do not exist in
112Warning: chr7 reads do not exist in
113Warning: chr8 reads do not exist in
114Warning: chr9 reads do not exist in
115Warning: chr10 reads do not exist in
116Warning: chr11 reads do not exist in
117Warning: chr12 reads do not exist in
118Warning: chr13 reads do not exist in
119Warning: chr14 reads do not exist in
120Warning: chr15 reads do not exist in
121Warning: chr16 reads do not exist in
122Warning: chr17 reads do not exist in
123Warning: chr18 reads do not exist in
124Warning: chr19 reads do not exist in
125Warning: chrX reads do not exist in
126Warning: chrY reads do not exist in
127Warning: chrM reads do not exist in
128Warning: chr2 reads do not exist in
129Warning: chr3 reads do not exist in
130Warning: chr4 reads do not exist in
131Warning: chr5 reads do not exist in
132Warning: chr6 reads do not exist in
133Warning: chr7 reads do not exist in
134Warning: chr8 reads do not exist in
135Warning: chr9 reads do not exist in
136Warning: chr10 reads do not exist in
137Warning: chr11 reads do not exist in
138Warning: chr12 reads do not exist in
139Warning: chr13 reads do not exist in
140Warning: chr14 reads do not exist in
141Warning: chr15 reads do not exist in
142Warning: chr16 reads do not exist in
143Warning: chr17 reads do not exist in
144Warning: chr18 reads do not exist in
145Warning: chr19 reads do not exist in
146Warning: chrX reads do not exist in
147Warning: chrY reads do not exist in
148Warning: chrM reads do not exist in
149Warning: chr2 reads do not exist in
150Warning: chr3 reads do not exist in
151Warning: chr4 reads do not exist in
152Warning: chr5 reads do not exist in
153Warning: chr6 reads do not exist in
154Warning: chr7 reads do not exist in
155Warning: chr8 reads do not exist in
156Warning: chr9 reads do not exist in
157Warning: chr10 reads do not exist in
158Warning: chr11 reads do not exist in
159Warning: chr12 reads do not exist in
160Warning: chr13 reads do not exist in
161Warning: chr14 reads do not exist in
162Warning: chr15 reads do not exist in
163Warning: chr16 reads do not exist in
164Warning: chr17 reads do not exist in
165Warning: chr18 reads do not exist in
166Warning: chr19 reads do not exist in
167Warning: chrX reads do not exist in
168Warning: chrY reads do not exist in
169Warning: chrM reads do not exist in
170Warning: chr2 reads do not exist in
171Warning: chr3 reads do not exist in
172Warning: chr4 reads do not exist in
173Warning: chr5 reads do not exist in
174Warning: chr6 reads do not exist in
175Warning: chr7 reads do not exist in
176Warning: chr8 reads do not exist in
177Warning: chr9 reads do not exist in
178Warning: chr10 reads do not exist in
179Warning: chr11 reads do not exist in
180Warning: chr12 reads do not exist in
181Warning: chr13 reads do not exist in
182Warning: chr14 reads do not exist in
183Warning: chr15 reads do not exist in
184Warning: chr16 reads do not exist in
185Warning: chr17 reads do not exist in
186Warning: chr18 reads do not exist in
187Warning: chr19 reads do not exist in
188Warning: chrX reads do not exist in
189Warning: chrY reads do not exist in
190Warning: chrM reads do not exist in