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/test-data/peakcalling_sicer/test_2/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: input_bed_file.bed
  6Control library: input_control_file.bed
  7Output directory:
  8Species: mm8
  9Threshold for redundancy allowed for chip reads: 1
 10Threshold for redundancy allowed for control reads: 1
 11Window size: 200 bps
 12Fragment size: 150 bps. The shift for reads is half of 150
 13Effective genome size as a fraction of the reference genome of mm8: 0.740000
 14Gap size: 600 bps
 15Evalue for identification of candidate islands that exhibit clustering: 1000
 16False discovery rate controlling significance: 0.01
 17Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
 18chr1 	Plus reads: 4989 	Retained plus reads: 4935 ;	Minus reads: 5011 	Retained minus reads: 4963
 19chr2 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 20chr3 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 21chr4 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 22chr5 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 23chr6 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 24chr7 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 25chr8 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 26chr9 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 27chr10 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 28chr11 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 29chr12 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 30chr13 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 31chr14 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 32chr15 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 33chr16 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 34chr17 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 35chr18 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 36chr19 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 37chrX 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 38chrY 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 39chrM 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 40Preprocess the raw input_control_file file to remove redundancy with threshold 1...
 41chr1 	Plus reads: 4980 	Retained plus reads: 4937 ;	Minus reads: 5020 	Retained minus reads: 4959
 42chr2 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 43chr3 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 44chr4 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 45chr5 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 46chr6 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 47chr7 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 48chr8 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 49chr9 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 50chr10 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 51chr11 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 52chr12 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 53chr13 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 54chr14 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 55chr15 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 56chr16 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 57chr17 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 58chr18 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 59chr19 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 60chrX 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 61chrY 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 62chrM 	Plus reads: 0 	Retained plus reads: 0 ;	Minus reads: 0 	Retained minus reads: 0
 63Partion the genome in windows ...
 64Generate summary files ...
 65total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
 66total tag count in chr2.bed is: 0.0 = 0.0+0.0
 67total tag count in chr3.bed is: 0.0 = 0.0+0.0
 68total tag count in chr4.bed is: 0.0 = 0.0+0.0
 69total tag count in chr5.bed is: 0.0 = 0.0+0.0
 70total tag count in chr6.bed is: 0.0 = 0.0+0.0
 71total tag count in chr7.bed is: 0.0 = 0.0+0.0
 72total tag count in chr8.bed is: 0.0 = 0.0+0.0
 73total tag count in chr9.bed is: 0.0 = 0.0+0.0
 74total tag count in chr10.bed is: 0.0 = 0.0+0.0
 75total tag count in chr11.bed is: 0.0 = 0.0+0.0
 76total tag count in chr12.bed is: 0.0 = 0.0+0.0
 77total tag count in chr13.bed is: 0.0 = 0.0+0.0
 78total tag count in chr14.bed is: 0.0 = 0.0+0.0
 79total tag count in chr15.bed is: 0.0 = 0.0+0.0
 80total tag count in chr16.bed is: 0.0 = 0.0+0.0
 81total tag count in chr17.bed is: 0.0 = 0.0+0.0
 82total tag count in chr18.bed is: 0.0 = 0.0+0.0
 83total tag count in chr19.bed is: 0.0 = 0.0+0.0
 84total tag count in chrX.bed is: 0.0 = 0.0+0.0
 85total tag count in chrY.bed is: 0.0 = 0.0+0.0
 86total tag count in chrM.bed is: 0.0 = 0.0+0.0
 87Normalize summary graph by total island filtered reads per million for input_bed_file ...
 88Convert the normalized summary graph into wig vstep format...
 89Find candidate islands exhibiting clustering ...
 90Species:  mm8
 91Window_size:  200
 92Gap size:  600
 93E value is: 1000.0
 94Total read count: 9898.0
 95Genome Length:  2644093988
 96Effective genome Length:  1956629551
 97Window average: 0.0010117398048
 98Window pvalue: 0.2
 99Minimum num of tags in a qualified window:  1
100Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows 
101Determine the score threshold from random background
102The score threshold is:  6.898
103Make and write islands
104Total number of islands:  417
105Calculate significance of candidate islands using the control library ...
106chip library size   9898.0
107control library size   9896.0
108Total number of chip reads on islands is:  9811
109Total number of control reads on islands is:  8514
110Identify significant islands using FDR criterion ...
111Given significance 0.01 ,  there are 184 significant islands
112Convert island summary to island bed file of format chr start end ChIP-read-count
113Filter reads with identified significant islands...
114Make summary graph with filtered reads...
115total tag count in chr1.bed is: 4303.0 = 2148.0+2155.0
116total tag count in chr2.bed is: 0.0 = 0.0+0.0
117total tag count in chr3.bed is: 0.0 = 0.0+0.0
118total tag count in chr4.bed is: 0.0 = 0.0+0.0
119total tag count in chr5.bed is: 0.0 = 0.0+0.0
120total tag count in chr6.bed is: 0.0 = 0.0+0.0
121total tag count in chr7.bed is: 0.0 = 0.0+0.0
122total tag count in chr8.bed is: 0.0 = 0.0+0.0
123total tag count in chr9.bed is: 0.0 = 0.0+0.0
124total tag count in chr10.bed is: 0.0 = 0.0+0.0
125total tag count in chr11.bed is: 0.0 = 0.0+0.0
126total tag count in chr12.bed is: 0.0 = 0.0+0.0
127total tag count in chr13.bed is: 0.0 = 0.0+0.0
128total tag count in chr14.bed is: 0.0 = 0.0+0.0
129total tag count in chr15.bed is: 0.0 = 0.0+0.0
130total tag count in chr16.bed is: 0.0 = 0.0+0.0
131total tag count in chr17.bed is: 0.0 = 0.0+0.0
132total tag count in chr18.bed is: 0.0 = 0.0+0.0
133total tag count in chr19.bed is: 0.0 = 0.0+0.0
134total tag count in chrX.bed is: 0.0 = 0.0+0.0
135total tag count in chrY.bed is: 0.0 = 0.0+0.0
136total tag count in chrM.bed is: 0.0 = 0.0+0.0
137Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
138Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...
139Done!
140Additionally, these warnings were reported:
141Warning: chr2 reads do not exist in
142Warning: chr3 reads do not exist in
143Warning: chr4 reads do not exist in
144Warning: chr5 reads do not exist in
145Warning: chr6 reads do not exist in
146Warning: chr7 reads do not exist in
147Warning: chr8 reads do not exist in
148Warning: chr9 reads do not exist in
149Warning: chr10 reads do not exist in
150Warning: chr11 reads do not exist in
151Warning: chr12 reads do not exist in
152Warning: chr13 reads do not exist in
153Warning: chr14 reads do not exist in
154Warning: chr15 reads do not exist in
155Warning: chr16 reads do not exist in
156Warning: chr17 reads do not exist in
157Warning: chr18 reads do not exist in
158Warning: chr19 reads do not exist in
159Warning: chrX reads do not exist in
160Warning: chrY reads do not exist in
161Warning: chrM reads do not exist in
162Warning: chr2 reads do not exist in
163Warning: chr3 reads do not exist in
164Warning: chr4 reads do not exist in
165Warning: chr5 reads do not exist in
166Warning: chr6 reads do not exist in
167Warning: chr7 reads do not exist in
168Warning: chr8 reads do not exist in
169Warning: chr9 reads do not exist in
170Warning: chr10 reads do not exist in
171Warning: chr11 reads do not exist in
172Warning: chr12 reads do not exist in
173Warning: chr13 reads do not exist in
174Warning: chr14 reads do not exist in
175Warning: chr15 reads do not exist in
176Warning: chr16 reads do not exist in
177Warning: chr17 reads do not exist in
178Warning: chr18 reads do not exist in
179Warning: chr19 reads do not exist in
180Warning: chrX reads do not exist in
181Warning: chrY reads do not exist in
182Warning: chrM reads do not exist in
183Warning: chr2 reads do not exist in
184Warning: chr3 reads do not exist in
185Warning: chr4 reads do not exist in
186Warning: chr5 reads do not exist in
187Warning: chr6 reads do not exist in
188Warning: chr7 reads do not exist in
189Warning: chr8 reads do not exist in
190Warning: chr9 reads do not exist in
191Warning: chr10 reads do not exist in
192Warning: chr11 reads do not exist in
193Warning: chr12 reads do not exist in
194Warning: chr13 reads do not exist in
195Warning: chr14 reads do not exist in
196Warning: chr15 reads do not exist in
197Warning: chr16 reads do not exist in
198Warning: chr17 reads do not exist in
199Warning: chr18 reads do not exist in
200Warning: chr19 reads do not exist in
201Warning: chrX reads do not exist in
202Warning: chrY reads do not exist in
203Warning: chrM reads do not exist in
204Warning: chr2 reads do not exist in
205Warning: chr3 reads do not exist in
206Warning: chr4 reads do not exist in
207Warning: chr5 reads do not exist in
208Warning: chr6 reads do not exist in
209Warning: chr7 reads do not exist in
210Warning: chr8 reads do not exist in
211Warning: chr9 reads do not exist in
212Warning: chr10 reads do not exist in
213Warning: chr11 reads do not exist in
214Warning: chr12 reads do not exist in
215Warning: chr13 reads do not exist in
216Warning: chr14 reads do not exist in
217Warning: chr15 reads do not exist in
218Warning: chr16 reads do not exist in
219Warning: chr17 reads do not exist in
220Warning: chr18 reads do not exist in
221Warning: chr19 reads do not exist in
222Warning: chrX reads do not exist in
223Warning: chrY reads do not exist in
224Warning: chrM reads do not exist in
225Warning: chr2 reads do not exist in
226Warning: chr3 reads do not exist in
227Warning: chr4 reads do not exist in
228Warning: chr5 reads do not exist in
229Warning: chr6 reads do not exist in
230Warning: chr7 reads do not exist in
231Warning: chr8 reads do not exist in
232Warning: chr9 reads do not exist in
233Warning: chr10 reads do not exist in
234Warning: chr11 reads do not exist in
235Warning: chr12 reads do not exist in
236Warning: chr13 reads do not exist in
237Warning: chr14 reads do not exist in
238Warning: chr15 reads do not exist in
239Warning: chr16 reads do not exist in
240Warning: chr17 reads do not exist in
241Warning: chr18 reads do not exist in
242Warning: chr19 reads do not exist in
243Warning: chrX reads do not exist in
244Warning: chrY reads do not exist in
245Warning: chrM reads do not exist in
246Warning: chr2 reads do not exist in
247Warning: chr3 reads do not exist in
248Warning: chr4 reads do not exist in
249Warning: chr5 reads do not exist in
250Warning: chr6 reads do not exist in
251Warning: chr7 reads do not exist in
252Warning: chr8 reads do not exist in
253Warning: chr9 reads do not exist in
254Warning: chr10 reads do not exist in
255Warning: chr11 reads do not exist in
256Warning: chr12 reads do not exist in
257Warning: chr13 reads do not exist in
258Warning: chr14 reads do not exist in
259Warning: chr15 reads do not exist in
260Warning: chr16 reads do not exist in
261Warning: chr17 reads do not exist in
262Warning: chr18 reads do not exist in
263Warning: chr19 reads do not exist in
264Warning: chrX reads do not exist in
265Warning: chrY reads do not exist in
266Warning: chrM reads do not exist in
267Warning: chr2 reads do not exist in
268Warning: chr3 reads do not exist in
269Warning: chr4 reads do not exist in
270Warning: chr5 reads do not exist in
271Warning: chr6 reads do not exist in
272Warning: chr7 reads do not exist in
273Warning: chr8 reads do not exist in
274Warning: chr9 reads do not exist in
275Warning: chr10 reads do not exist in
276Warning: chr11 reads do not exist in
277Warning: chr12 reads do not exist in
278Warning: chr13 reads do not exist in
279Warning: chr14 reads do not exist in
280Warning: chr15 reads do not exist in
281Warning: chr16 reads do not exist in
282Warning: chr17 reads do not exist in
283Warning: chr18 reads do not exist in
284Warning: chr19 reads do not exist in
285Warning: chrX reads do not exist in
286Warning: chrY reads do not exist in
287Warning: chrM reads do not exist in