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comparison test-data/peakcalling_sicer/test_2/output_log_file.contains @ 0:82a8234e03f2 draft

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Imported from capsule None
author devteam
date Mon, 27 Jan 2014 09:28:33 -0500
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1 #############################################
2 ###### SICER v1.1 ######
3 #############################################
4 Input library directory:
5 ChIP library: input_bed_file.bed
6 Control library: input_control_file.bed
7 Output directory:
8 Species: mm8
9 Threshold for redundancy allowed for chip reads: 1
10 Threshold for redundancy allowed for control reads: 1
11 Window size: 200 bps
12 Fragment size: 150 bps. The shift for reads is half of 150
13 Effective genome size as a fraction of the reference genome of mm8: 0.740000
14 Gap size: 600 bps
15 Evalue for identification of candidate islands that exhibit clustering: 1000
16 False discovery rate controlling significance: 0.01
17 Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
18 chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963
19 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
20 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
21 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
22 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
23 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
24 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
25 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
26 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
27 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
28 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
29 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
30 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
31 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
32 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
33 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
34 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
35 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
36 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
37 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
38 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
39 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
40 Preprocess the raw input_control_file file to remove redundancy with threshold 1...
41 chr1 Plus reads: 4980 Retained plus reads: 4937 ; Minus reads: 5020 Retained minus reads: 4959
42 chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
43 chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
44 chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
45 chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
46 chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
47 chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
48 chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
49 chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
50 chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
51 chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
52 chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
53 chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
54 chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
55 chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
56 chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
57 chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
58 chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
59 chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
60 chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
61 chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
62 chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
63 Partion the genome in windows ...
64 Generate summary files ...
65 total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
66 total tag count in chr2.bed is: 0.0 = 0.0+0.0
67 total tag count in chr3.bed is: 0.0 = 0.0+0.0
68 total tag count in chr4.bed is: 0.0 = 0.0+0.0
69 total tag count in chr5.bed is: 0.0 = 0.0+0.0
70 total tag count in chr6.bed is: 0.0 = 0.0+0.0
71 total tag count in chr7.bed is: 0.0 = 0.0+0.0
72 total tag count in chr8.bed is: 0.0 = 0.0+0.0
73 total tag count in chr9.bed is: 0.0 = 0.0+0.0
74 total tag count in chr10.bed is: 0.0 = 0.0+0.0
75 total tag count in chr11.bed is: 0.0 = 0.0+0.0
76 total tag count in chr12.bed is: 0.0 = 0.0+0.0
77 total tag count in chr13.bed is: 0.0 = 0.0+0.0
78 total tag count in chr14.bed is: 0.0 = 0.0+0.0
79 total tag count in chr15.bed is: 0.0 = 0.0+0.0
80 total tag count in chr16.bed is: 0.0 = 0.0+0.0
81 total tag count in chr17.bed is: 0.0 = 0.0+0.0
82 total tag count in chr18.bed is: 0.0 = 0.0+0.0
83 total tag count in chr19.bed is: 0.0 = 0.0+0.0
84 total tag count in chrX.bed is: 0.0 = 0.0+0.0
85 total tag count in chrY.bed is: 0.0 = 0.0+0.0
86 total tag count in chrM.bed is: 0.0 = 0.0+0.0
87 Normalize summary graph by total island filtered reads per million for input_bed_file ...
88 Convert the normalized summary graph into wig vstep format...
89 Find candidate islands exhibiting clustering ...
90 Species: mm8
91 Window_size: 200
92 Gap size: 600
93 E value is: 1000.0
94 Total read count: 9898.0
95 Genome Length: 2644093988
96 Effective genome Length: 1956629551
97 Window average: 0.0010117398048
98 Window pvalue: 0.2
99 Minimum num of tags in a qualified window: 1
100 Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows
101 Determine the score threshold from random background
102 The score threshold is: 6.898
103 Make and write islands
104 Total number of islands: 417
105 Calculate significance of candidate islands using the control library ...
106 chip library size 9898.0
107 control library size 9896.0
108 Total number of chip reads on islands is: 9811
109 Total number of control reads on islands is: 8514
110 Identify significant islands using FDR criterion ...
111 Given significance 0.01 , there are 184 significant islands
112 Convert island summary to island bed file of format chr start end ChIP-read-count
113 Filter reads with identified significant islands...
114 Make summary graph with filtered reads...
115 total tag count in chr1.bed is: 4303.0 = 2148.0+2155.0
116 total tag count in chr2.bed is: 0.0 = 0.0+0.0
117 total tag count in chr3.bed is: 0.0 = 0.0+0.0
118 total tag count in chr4.bed is: 0.0 = 0.0+0.0
119 total tag count in chr5.bed is: 0.0 = 0.0+0.0
120 total tag count in chr6.bed is: 0.0 = 0.0+0.0
121 total tag count in chr7.bed is: 0.0 = 0.0+0.0
122 total tag count in chr8.bed is: 0.0 = 0.0+0.0
123 total tag count in chr9.bed is: 0.0 = 0.0+0.0
124 total tag count in chr10.bed is: 0.0 = 0.0+0.0
125 total tag count in chr11.bed is: 0.0 = 0.0+0.0
126 total tag count in chr12.bed is: 0.0 = 0.0+0.0
127 total tag count in chr13.bed is: 0.0 = 0.0+0.0
128 total tag count in chr14.bed is: 0.0 = 0.0+0.0
129 total tag count in chr15.bed is: 0.0 = 0.0+0.0
130 total tag count in chr16.bed is: 0.0 = 0.0+0.0
131 total tag count in chr17.bed is: 0.0 = 0.0+0.0
132 total tag count in chr18.bed is: 0.0 = 0.0+0.0
133 total tag count in chr19.bed is: 0.0 = 0.0+0.0
134 total tag count in chrX.bed is: 0.0 = 0.0+0.0
135 total tag count in chrY.bed is: 0.0 = 0.0+0.0
136 total tag count in chrM.bed is: 0.0 = 0.0+0.0
137 Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
138 Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...
139 Done!
140 Additionally, these warnings were reported:
141 Warning: chr2 reads do not exist in
142 Warning: chr3 reads do not exist in
143 Warning: chr4 reads do not exist in
144 Warning: chr5 reads do not exist in
145 Warning: chr6 reads do not exist in
146 Warning: chr7 reads do not exist in
147 Warning: chr8 reads do not exist in
148 Warning: chr9 reads do not exist in
149 Warning: chr10 reads do not exist in
150 Warning: chr11 reads do not exist in
151 Warning: chr12 reads do not exist in
152 Warning: chr13 reads do not exist in
153 Warning: chr14 reads do not exist in
154 Warning: chr15 reads do not exist in
155 Warning: chr16 reads do not exist in
156 Warning: chr17 reads do not exist in
157 Warning: chr18 reads do not exist in
158 Warning: chr19 reads do not exist in
159 Warning: chrX reads do not exist in
160 Warning: chrY reads do not exist in
161 Warning: chrM reads do not exist in
162 Warning: chr2 reads do not exist in
163 Warning: chr3 reads do not exist in
164 Warning: chr4 reads do not exist in
165 Warning: chr5 reads do not exist in
166 Warning: chr6 reads do not exist in
167 Warning: chr7 reads do not exist in
168 Warning: chr8 reads do not exist in
169 Warning: chr9 reads do not exist in
170 Warning: chr10 reads do not exist in
171 Warning: chr11 reads do not exist in
172 Warning: chr12 reads do not exist in
173 Warning: chr13 reads do not exist in
174 Warning: chr14 reads do not exist in
175 Warning: chr15 reads do not exist in
176 Warning: chr16 reads do not exist in
177 Warning: chr17 reads do not exist in
178 Warning: chr18 reads do not exist in
179 Warning: chr19 reads do not exist in
180 Warning: chrX reads do not exist in
181 Warning: chrY reads do not exist in
182 Warning: chrM reads do not exist in
183 Warning: chr2 reads do not exist in
184 Warning: chr3 reads do not exist in
185 Warning: chr4 reads do not exist in
186 Warning: chr5 reads do not exist in
187 Warning: chr6 reads do not exist in
188 Warning: chr7 reads do not exist in
189 Warning: chr8 reads do not exist in
190 Warning: chr9 reads do not exist in
191 Warning: chr10 reads do not exist in
192 Warning: chr11 reads do not exist in
193 Warning: chr12 reads do not exist in
194 Warning: chr13 reads do not exist in
195 Warning: chr14 reads do not exist in
196 Warning: chr15 reads do not exist in
197 Warning: chr16 reads do not exist in
198 Warning: chr17 reads do not exist in
199 Warning: chr18 reads do not exist in
200 Warning: chr19 reads do not exist in
201 Warning: chrX reads do not exist in
202 Warning: chrY reads do not exist in
203 Warning: chrM reads do not exist in
204 Warning: chr2 reads do not exist in
205 Warning: chr3 reads do not exist in
206 Warning: chr4 reads do not exist in
207 Warning: chr5 reads do not exist in
208 Warning: chr6 reads do not exist in
209 Warning: chr7 reads do not exist in
210 Warning: chr8 reads do not exist in
211 Warning: chr9 reads do not exist in
212 Warning: chr10 reads do not exist in
213 Warning: chr11 reads do not exist in
214 Warning: chr12 reads do not exist in
215 Warning: chr13 reads do not exist in
216 Warning: chr14 reads do not exist in
217 Warning: chr15 reads do not exist in
218 Warning: chr16 reads do not exist in
219 Warning: chr17 reads do not exist in
220 Warning: chr18 reads do not exist in
221 Warning: chr19 reads do not exist in
222 Warning: chrX reads do not exist in
223 Warning: chrY reads do not exist in
224 Warning: chrM reads do not exist in
225 Warning: chr2 reads do not exist in
226 Warning: chr3 reads do not exist in
227 Warning: chr4 reads do not exist in
228 Warning: chr5 reads do not exist in
229 Warning: chr6 reads do not exist in
230 Warning: chr7 reads do not exist in
231 Warning: chr8 reads do not exist in
232 Warning: chr9 reads do not exist in
233 Warning: chr10 reads do not exist in
234 Warning: chr11 reads do not exist in
235 Warning: chr12 reads do not exist in
236 Warning: chr13 reads do not exist in
237 Warning: chr14 reads do not exist in
238 Warning: chr15 reads do not exist in
239 Warning: chr16 reads do not exist in
240 Warning: chr17 reads do not exist in
241 Warning: chr18 reads do not exist in
242 Warning: chr19 reads do not exist in
243 Warning: chrX reads do not exist in
244 Warning: chrY reads do not exist in
245 Warning: chrM reads do not exist in
246 Warning: chr2 reads do not exist in
247 Warning: chr3 reads do not exist in
248 Warning: chr4 reads do not exist in
249 Warning: chr5 reads do not exist in
250 Warning: chr6 reads do not exist in
251 Warning: chr7 reads do not exist in
252 Warning: chr8 reads do not exist in
253 Warning: chr9 reads do not exist in
254 Warning: chr10 reads do not exist in
255 Warning: chr11 reads do not exist in
256 Warning: chr12 reads do not exist in
257 Warning: chr13 reads do not exist in
258 Warning: chr14 reads do not exist in
259 Warning: chr15 reads do not exist in
260 Warning: chr16 reads do not exist in
261 Warning: chr17 reads do not exist in
262 Warning: chr18 reads do not exist in
263 Warning: chr19 reads do not exist in
264 Warning: chrX reads do not exist in
265 Warning: chrY reads do not exist in
266 Warning: chrM reads do not exist in
267 Warning: chr2 reads do not exist in
268 Warning: chr3 reads do not exist in
269 Warning: chr4 reads do not exist in
270 Warning: chr5 reads do not exist in
271 Warning: chr6 reads do not exist in
272 Warning: chr7 reads do not exist in
273 Warning: chr8 reads do not exist in
274 Warning: chr9 reads do not exist in
275 Warning: chr10 reads do not exist in
276 Warning: chr11 reads do not exist in
277 Warning: chr12 reads do not exist in
278 Warning: chr13 reads do not exist in
279 Warning: chr14 reads do not exist in
280 Warning: chr15 reads do not exist in
281 Warning: chr16 reads do not exist in
282 Warning: chr17 reads do not exist in
283 Warning: chr18 reads do not exist in
284 Warning: chr19 reads do not exist in
285 Warning: chrX reads do not exist in
286 Warning: chrY reads do not exist in
287 Warning: chrM reads do not exist in