annotate test-data/test_2_output_log_file.contains @ 3:5c2cc3b58c7d draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/sicer commit 0cbb1b33c232da498a31902aa5afcdc97971a74b"

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######           SICER v1.1            ######
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Input library directory:
ChIP library: input_bed_file.bed
Control library: input_control_file.bed
Output directory:
Species: mm8
Threshold for redundancy allowed for chip reads: 1
Threshold for redundancy allowed for control 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 candidate islands that exhibit clustering: 1000
False discovery rate controlling significance: 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
Preprocess the raw input_control_file file to remove redundancy with threshold 1...
chr1 	Plus reads: 4980 	Retained plus reads: 4937 ;	Minus reads: 5020 	Retained minus reads: 4959
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 ...
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 island filtered reads per million for input_bed_file ...
Convert the normalized summary graph into wig vstep format...
Find candidate islands exhibiting clustering ...
Species:  mm8
Window_size:  200
Gap size:  600
E value is: 1000.0
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:  6.898
Make and write islands
Total number of islands:  417
Calculate significance of candidate islands using the control library ...
chip library size   9898.0
control library size   9896.0
Total number of chip reads on islands is:  9811
Total number of control reads on islands is:  8514
Identify significant islands using FDR criterion ...
Given significance 0.01 ,  there are 184 significant islands
Convert island summary to island bed file of format chr start end ChIP-read-count
Filter reads with identified significant islands...
Make summary graph with filtered reads...
total tag count in chr1.bed is: 4303.0 = 2148.0+2155.0
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
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