Job ID = 2001702 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,128,610 reads read : 22,128,610 reads written : 22,128,610 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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:38 22128610 reads; of these: 22128610 (100.00%) were unpaired; of these: 423163 (1.91%) aligned 0 times 19523934 (88.23%) aligned exactly 1 time 2181513 (9.86%) aligned >1 times 98.09% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 11135027 / 21705447 = 0.5130 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 09:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.bam'] # control file = None # effective genome size = 2.15e+09 # 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 09:20:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:20:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.bam'] # control file = None # effective genome size = 2.15e+09 # 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 09:20:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:20:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:20:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.bam'] # control file = None # effective genome size = 2.15e+09 # 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 09:20:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:20:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:20:58: 1000000 INFO @ Fri, 05 Jul 2019 09:21:00: 1000000 INFO @ Fri, 05 Jul 2019 09:21:00: 1000000 INFO @ Fri, 05 Jul 2019 09:21:04: 2000000 INFO @ Fri, 05 Jul 2019 09:21:06: 2000000 INFO @ Fri, 05 Jul 2019 09:21:08: 2000000 INFO @ Fri, 05 Jul 2019 09:21:10: 3000000 INFO @ Fri, 05 Jul 2019 09:21:13: 3000000 INFO @ Fri, 05 Jul 2019 09:21:15: 3000000 INFO @ Fri, 05 Jul 2019 09:21:16: 4000000 INFO @ Fri, 05 Jul 2019 09:21:19: 4000000 INFO @ Fri, 05 Jul 2019 09:21:22: 5000000 INFO @ Fri, 05 Jul 2019 09:21:22: 4000000 INFO @ Fri, 05 Jul 2019 09:21:25: 5000000 INFO @ Fri, 05 Jul 2019 09:21:28: 6000000 INFO @ Fri, 05 Jul 2019 09:21:30: 5000000 INFO @ Fri, 05 Jul 2019 09:21:32: 6000000 INFO @ Fri, 05 Jul 2019 09:21:34: 7000000 INFO @ Fri, 05 Jul 2019 09:21:37: 6000000 INFO @ Fri, 05 Jul 2019 09:21:38: 7000000 INFO @ Fri, 05 Jul 2019 09:21:40: 8000000 INFO @ Fri, 05 Jul 2019 09:21:44: 7000000 INFO @ Fri, 05 Jul 2019 09:21:45: 8000000 INFO @ Fri, 05 Jul 2019 09:21:46: 9000000 INFO @ Fri, 05 Jul 2019 09:21:51: 9000000 INFO @ Fri, 05 Jul 2019 09:21:51: 8000000 INFO @ Fri, 05 Jul 2019 09:21:52: 10000000 INFO @ Fri, 05 Jul 2019 09:21:56: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:21:56: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:21:56: #1 total tags in treatment: 10570420 INFO @ Fri, 05 Jul 2019 09:21:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:21:56: #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 09:21:56: #1 tags after filtering in treatment: 10570145 INFO @ Fri, 05 Jul 2019 09:21:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:21:56: #1 finished! INFO @ Fri, 05 Jul 2019 09:21:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:21:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:21:57: 10000000 INFO @ Fri, 05 Jul 2019 09:21:59: 9000000 INFO @ Fri, 05 Jul 2019 09:21:59: #2 number of paired peaks: 49588 INFO @ Fri, 05 Jul 2019 09:21:59: start model_add_line... INFO @ Fri, 05 Jul 2019 09:21:59: start X-correlation... INFO @ Fri, 05 Jul 2019 09:22:00: end of X-cor INFO @ Fri, 05 Jul 2019 09:22:00: #2 finished! INFO @ Fri, 05 Jul 2019 09:22:00: #2 predicted fragment length is 145 bps INFO @ Fri, 05 Jul 2019 09:22:00: #2 alternative fragment length(s) may be 4,145 bps INFO @ Fri, 05 Jul 2019 09:22:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.05_model.r INFO @ Fri, 05 Jul 2019 09:22:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:22:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:22:01: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:22:01: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:22:01: #1 total tags in treatment: 10570420 INFO @ Fri, 05 Jul 2019 09:22:01: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:22:01: #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 09:22:01: #1 tags after filtering in treatment: 10570145 INFO @ Fri, 05 Jul 2019 09:22:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:22:01: #1 finished! INFO @ Fri, 05 Jul 2019 09:22:01: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:22:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:22:05: #2 number of paired peaks: 49588 INFO @ Fri, 05 Jul 2019 09:22:05: start model_add_line... INFO @ Fri, 05 Jul 2019 09:22:05: start X-correlation... INFO @ Fri, 05 Jul 2019 09:22:05: end of X-cor INFO @ Fri, 05 Jul 2019 09:22:05: #2 finished! INFO @ Fri, 05 Jul 2019 09:22:05: #2 predicted fragment length is 145 bps INFO @ Fri, 05 Jul 2019 09:22:05: #2 alternative fragment length(s) may be 4,145 bps INFO @ Fri, 05 Jul 2019 09:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.20_model.r INFO @ Fri, 05 Jul 2019 09:22:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:22:06: 10000000 INFO @ Fri, 05 Jul 2019 09:22:10: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:22:10: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:22:10: #1 total tags in treatment: 10570420 INFO @ Fri, 05 Jul 2019 09:22:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:22:10: #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 09:22:11: #1 tags after filtering in treatment: 10570145 INFO @ Fri, 05 Jul 2019 09:22:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:22:11: #1 finished! INFO @ Fri, 05 Jul 2019 09:22:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:22:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:22:14: #2 number of paired peaks: 49588 INFO @ Fri, 05 Jul 2019 09:22:14: start model_add_line... INFO @ Fri, 05 Jul 2019 09:22:14: start X-correlation... INFO @ Fri, 05 Jul 2019 09:22:14: end of X-cor INFO @ Fri, 05 Jul 2019 09:22:14: #2 finished! INFO @ Fri, 05 Jul 2019 09:22:14: #2 predicted fragment length is 145 bps INFO @ Fri, 05 Jul 2019 09:22:14: #2 alternative fragment length(s) may be 4,145 bps INFO @ Fri, 05 Jul 2019 09:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.10_model.r INFO @ Fri, 05 Jul 2019 09:22:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:22:31: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:22:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:22:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:22:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:22:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.05_summits.bed INFO @ Fri, 05 Jul 2019 09:22:49: Done! pass1 - making usageList (132 chroms): 14 millis pass2 - checking and writing primary data (40637 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:22:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:22:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:22:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.20_summits.bed INFO @ Fri, 05 Jul 2019 09:22:55: Done! pass1 - making usageList (73 chroms): 7 millis pass2 - checking and writing primary data (19157 records, 4 fields): 422 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:23:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102012/ERX102012.10_summits.bed INFO @ Fri, 05 Jul 2019 09:23:02: Done! pass1 - making usageList (109 chroms): 9 millis pass2 - checking and writing primary data (31489 records, 4 fields): 44 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。