/test-data/peakcalling_sicer/test_1/output_log_file.contains
https://bitbucket.org/cistrome/cistrome-harvard/ · Unknown · 190 lines · 190 code · 0 blank · 0 comment · 0 complexity · 6c634e618a1e1227946f68b58b81a15a MD5 · raw file
- #############################################
- ###### SICER v1.1 ######
- #############################################
- Input library directory:
- ChIP library:
- Output directory:
- Species: mm8
- Threshold for redundancy allowed for reads: 1
- Window size: 200 bps
- Fragment size: 150 bps. The shift for reads is half of 150
- Effective genome size as a fraction of the reference genome of mm8: 0.740000
- Gap size: 600 bps
- Evalue for identification of significant islands: 0.01
- Preprocess the raw input_bed_file file to remove redundancy with threshold 1...
- chr1 Plus reads: 4989 Retained plus reads: 4935 ; Minus reads: 5011 Retained minus reads: 4963
- chr2 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr3 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr4 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr5 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr6 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr7 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr8 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr9 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr10 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr11 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr12 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr13 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr14 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr15 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr16 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr17 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr18 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chr19 Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chrX Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chrY Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- chrM Plus reads: 0 Retained plus reads: 0 ; Minus reads: 0 Retained minus reads: 0
- Partion the genome in windows ...
- Generate summary files for input_bed_file...
- total tag count in chr1.bed is: 9898.0 = 4935.0+4963.0
- total tag count in chr2.bed is: 0.0 = 0.0+0.0
- total tag count in chr3.bed is: 0.0 = 0.0+0.0
- total tag count in chr4.bed is: 0.0 = 0.0+0.0
- total tag count in chr5.bed is: 0.0 = 0.0+0.0
- total tag count in chr6.bed is: 0.0 = 0.0+0.0
- total tag count in chr7.bed is: 0.0 = 0.0+0.0
- total tag count in chr8.bed is: 0.0 = 0.0+0.0
- total tag count in chr9.bed is: 0.0 = 0.0+0.0
- total tag count in chr10.bed is: 0.0 = 0.0+0.0
- total tag count in chr11.bed is: 0.0 = 0.0+0.0
- total tag count in chr12.bed is: 0.0 = 0.0+0.0
- total tag count in chr13.bed is: 0.0 = 0.0+0.0
- total tag count in chr14.bed is: 0.0 = 0.0+0.0
- total tag count in chr15.bed is: 0.0 = 0.0+0.0
- total tag count in chr16.bed is: 0.0 = 0.0+0.0
- total tag count in chr17.bed is: 0.0 = 0.0+0.0
- total tag count in chr18.bed is: 0.0 = 0.0+0.0
- total tag count in chr19.bed is: 0.0 = 0.0+0.0
- total tag count in chrX.bed is: 0.0 = 0.0+0.0
- total tag count in chrY.bed is: 0.0 = 0.0+0.0
- total tag count in chrM.bed is: 0.0 = 0.0+0.0
- Normalize summary graph by total redundancy-removed reads per million for input_bed_file ...
- Convert the normalized summary graph into wig vstep format...
- Find significant islands with E-value 0.01 for input_bed_file...
- Species: mm8
- Window_size: 200
- Gap size: 600
- E value is: 0.01
- Total read count: 9898.0
- Genome Length: 2644093988
- Effective genome Length: 1956629551
- Window average: 0.0010117398048
- Window pvalue: 0.2
- Minimum num of tags in a qualified window: 1
- Generate the enriched probscore summary graph and filter the summary graph to get rid of ineligible windows
- Determine the score threshold from random background
- The score threshold is: 21.384
- Make and write islands
- Total number of islands: 352
- Filter reads with identified significant islands for input_bed_file...
- Make summary graph with filtered reads for input_bed_file...
- total tag count in chr1.bed is: 9654.0 = 4808.0+4846.0
- total tag count in chr2.bed is: 0.0 = 0.0+0.0
- total tag count in chr3.bed is: 0.0 = 0.0+0.0
- total tag count in chr4.bed is: 0.0 = 0.0+0.0
- total tag count in chr5.bed is: 0.0 = 0.0+0.0
- total tag count in chr6.bed is: 0.0 = 0.0+0.0
- total tag count in chr7.bed is: 0.0 = 0.0+0.0
- total tag count in chr8.bed is: 0.0 = 0.0+0.0
- total tag count in chr9.bed is: 0.0 = 0.0+0.0
- total tag count in chr10.bed is: 0.0 = 0.0+0.0
- total tag count in chr11.bed is: 0.0 = 0.0+0.0
- total tag count in chr12.bed is: 0.0 = 0.0+0.0
- total tag count in chr13.bed is: 0.0 = 0.0+0.0
- total tag count in chr14.bed is: 0.0 = 0.0+0.0
- total tag count in chr15.bed is: 0.0 = 0.0+0.0
- total tag count in chr16.bed is: 0.0 = 0.0+0.0
- total tag count in chr17.bed is: 0.0 = 0.0+0.0
- total tag count in chr18.bed is: 0.0 = 0.0+0.0
- total tag count in chr19.bed is: 0.0 = 0.0+0.0
- total tag count in chrX.bed is: 0.0 = 0.0+0.0
- total tag count in chrY.bed is: 0.0 = 0.0+0.0
- total tag count in chrM.bed is: 0.0 = 0.0+0.0
- Normalize summary graph with filtered reads for input_bed_file by total island filtered reads per million...
- Convert the summary graph made with the filtered reads into wig vstep format and normalize by total island-filtered read count per million...
- Done!
- Additionally, these warnings were reported:
- Warning: chr2 reads do not exist in
- Warning: chr3 reads do not exist in
- Warning: chr4 reads do not exist in
- Warning: chr5 reads do not exist in
- Warning: chr6 reads do not exist in
- Warning: chr7 reads do not exist in
- Warning: chr8 reads do not exist in
- Warning: chr9 reads do not exist in
- Warning: chr10 reads do not exist in
- Warning: chr11 reads do not exist in
- Warning: chr12 reads do not exist in
- Warning: chr13 reads do not exist in
- Warning: chr14 reads do not exist in
- Warning: chr15 reads do not exist in
- Warning: chr16 reads do not exist in
- Warning: chr17 reads do not exist in
- Warning: chr18 reads do not exist in
- Warning: chr19 reads do not exist in
- Warning: chrX reads do not exist in
- Warning: chrY reads do not exist in
- Warning: chrM reads do not exist in
- Warning: chr2 reads do not exist in
- Warning: chr3 reads do not exist in
- Warning: chr4 reads do not exist in
- Warning: chr5 reads do not exist in
- Warning: chr6 reads do not exist in
- Warning: chr7 reads do not exist in
- Warning: chr8 reads do not exist in
- Warning: chr9 reads do not exist in
- Warning: chr10 reads do not exist in
- Warning: chr11 reads do not exist in
- Warning: chr12 reads do not exist in
- Warning: chr13 reads do not exist in
- Warning: chr14 reads do not exist in
- Warning: chr15 reads do not exist in
- Warning: chr16 reads do not exist in
- Warning: chr17 reads do not exist in
- Warning: chr18 reads do not exist in
- Warning: chr19 reads do not exist in
- Warning: chrX reads do not exist in
- Warning: chrY reads do not exist in
- Warning: chrM reads do not exist in
- Warning: chr2 reads do not exist in
- Warning: chr3 reads do not exist in
- Warning: chr4 reads do not exist in
- Warning: chr5 reads do not exist in
- Warning: chr6 reads do not exist in
- Warning: chr7 reads do not exist in
- Warning: chr8 reads do not exist in
- Warning: chr9 reads do not exist in
- Warning: chr10 reads do not exist in
- Warning: chr11 reads do not exist in
- Warning: chr12 reads do not exist in
- Warning: chr13 reads do not exist in
- Warning: chr14 reads do not exist in
- Warning: chr15 reads do not exist in
- Warning: chr16 reads do not exist in
- Warning: chr17 reads do not exist in
- Warning: chr18 reads do not exist in
- Warning: chr19 reads do not exist in
- Warning: chrX reads do not exist in
- Warning: chrY reads do not exist in
- Warning: chrM reads do not exist in
- Warning: chr2 reads do not exist in
- Warning: chr3 reads do not exist in
- Warning: chr4 reads do not exist in
- Warning: chr5 reads do not exist in
- Warning: chr6 reads do not exist in
- Warning: chr7 reads do not exist in
- Warning: chr8 reads do not exist in
- Warning: chr9 reads do not exist in
- Warning: chr10 reads do not exist in
- Warning: chr11 reads do not exist in
- Warning: chr12 reads do not exist in
- Warning: chr13 reads do not exist in
- Warning: chr14 reads do not exist in
- Warning: chr15 reads do not exist in
- Warning: chr16 reads do not exist in
- Warning: chr17 reads do not exist in
- Warning: chr18 reads do not exist in
- Warning: chr19 reads do not exist in
- Warning: chrX reads do not exist in
- Warning: chrY reads do not exist in
- Warning: chrM reads do not exist in