Job ID = 2008038 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,784,016 reads read : 3,568,032 reads written : 3,568,032 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:49 1784016 reads; of these: 1784016 (100.00%) were paired; of these: 200200 (11.22%) aligned concordantly 0 times 1451892 (81.38%) aligned concordantly exactly 1 time 131924 (7.39%) aligned concordantly >1 times ---- 200200 pairs aligned concordantly 0 times; of these: 48923 (24.44%) aligned discordantly 1 time ---- 151277 pairs aligned 0 times concordantly or discordantly; of these: 302554 mates make up the pairs; of these: 267028 (88.26%) aligned 0 times 22219 (7.34%) aligned exactly 1 time 13307 (4.40%) aligned >1 times 92.52% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 101556 / 1622546 = 0.0626 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 17:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 17:23:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:23:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 17:23:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:23:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 05 Jul 2019 17:23:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:23:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:23:30: 1000000 INFO @ Fri, 05 Jul 2019 17:23:31: 1000000 INFO @ Fri, 05 Jul 2019 17:23:31: 1000000 INFO @ Fri, 05 Jul 2019 17:23:39: 2000000 INFO @ Fri, 05 Jul 2019 17:23:39: 2000000 INFO @ Fri, 05 Jul 2019 17:23:40: 2000000 INFO @ Fri, 05 Jul 2019 17:23:47: 3000000 INFO @ Fri, 05 Jul 2019 17:23:48: 3000000 INFO @ Fri, 05 Jul 2019 17:23:48: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:23:48: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:23:48: #1 total tags in treatment: 1483809 INFO @ Fri, 05 Jul 2019 17:23:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:23:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:23:48: #1 tags after filtering in treatment: 1397296 INFO @ Fri, 05 Jul 2019 17:23:48: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:23:48: #1 finished! INFO @ Fri, 05 Jul 2019 17:23:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:23:48: #2 number of paired peaks: 185 WARNING @ Fri, 05 Jul 2019 17:23:48: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 05 Jul 2019 17:23:48: start model_add_line... INFO @ Fri, 05 Jul 2019 17:23:48: start X-correlation... INFO @ Fri, 05 Jul 2019 17:23:48: end of X-cor INFO @ Fri, 05 Jul 2019 17:23:48: #2 finished! INFO @ Fri, 05 Jul 2019 17:23:48: #2 predicted fragment length is 223 bps INFO @ Fri, 05 Jul 2019 17:23:48: #2 alternative fragment length(s) may be 1,14,26,34,70,91,114,139,174,192,223,266,301,345,364,414,465,504,530,560,563,581,598 bps INFO @ Fri, 05 Jul 2019 17:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.20_model.r INFO @ Fri, 05 Jul 2019 17:23:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:23:48: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:23:48: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:23:48: #1 total tags in treatment: 1483809 INFO @ Fri, 05 Jul 2019 17:23:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:23:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:23:48: #1 tags after filtering in treatment: 1397296 INFO @ Fri, 05 Jul 2019 17:23:48: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:23:48: #1 finished! INFO @ Fri, 05 Jul 2019 17:23:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:23:49: #2 number of paired peaks: 185 WARNING @ Fri, 05 Jul 2019 17:23:49: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 05 Jul 2019 17:23:49: start model_add_line... INFO @ Fri, 05 Jul 2019 17:23:49: start X-correlation... INFO @ Fri, 05 Jul 2019 17:23:49: end of X-cor INFO @ Fri, 05 Jul 2019 17:23:49: #2 finished! INFO @ Fri, 05 Jul 2019 17:23:49: #2 predicted fragment length is 223 bps INFO @ Fri, 05 Jul 2019 17:23:49: #2 alternative fragment length(s) may be 1,14,26,34,70,91,114,139,174,192,223,266,301,345,364,414,465,504,530,560,563,581,598 bps INFO @ Fri, 05 Jul 2019 17:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.05_model.r INFO @ Fri, 05 Jul 2019 17:23:49: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:23:49: 3000000 INFO @ Fri, 05 Jul 2019 17:23:50: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:23:50: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:23:50: #1 total tags in treatment: 1483809 INFO @ Fri, 05 Jul 2019 17:23:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:23:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:23:50: #1 tags after filtering in treatment: 1397296 INFO @ Fri, 05 Jul 2019 17:23:50: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 05 Jul 2019 17:23:50: #1 finished! INFO @ Fri, 05 Jul 2019 17:23:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:23:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:23:50: #2 number of paired peaks: 185 WARNING @ Fri, 05 Jul 2019 17:23:50: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Fri, 05 Jul 2019 17:23:50: start model_add_line... INFO @ Fri, 05 Jul 2019 17:23:50: start X-correlation... INFO @ Fri, 05 Jul 2019 17:23:50: end of X-cor INFO @ Fri, 05 Jul 2019 17:23:50: #2 finished! INFO @ Fri, 05 Jul 2019 17:23:50: #2 predicted fragment length is 223 bps INFO @ Fri, 05 Jul 2019 17:23:50: #2 alternative fragment length(s) may be 1,14,26,34,70,91,114,139,174,192,223,266,301,345,364,414,465,504,530,560,563,581,598 bps INFO @ Fri, 05 Jul 2019 17:23:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.10_model.r INFO @ Fri, 05 Jul 2019 17:23:50: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:23:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:23:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:23:53: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:23:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.20_summits.bed INFO @ Fri, 05 Jul 2019 17:23:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.05_summits.bed INFO @ Fri, 05 Jul 2019 17:23:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471823/ERX471823.10_summits.bed INFO @ Fri, 05 Jul 2019 17:23:56: Done! CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。