Job ID = 2003637 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,197,295 reads read : 34,197,295 reads written : 34,197,295 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:30:09 34197295 reads; of these: 34197295 (100.00%) were unpaired; of these: 5254735 (15.37%) aligned 0 times 20128017 (58.86%) aligned exactly 1 time 8814543 (25.78%) aligned >1 times 84.63% overall alignment rate Time searching: 00:30:15 Overall time: 00:30:15 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 12 files... [bam_rmdupse_core] 1651778 / 28942560 = 0.0571 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 13:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.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 13:36:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:36:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.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 13:36:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:36:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.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 13:36:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:36:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:36:32: 1000000 INFO @ Fri, 05 Jul 2019 13:36:34: 1000000 INFO @ Fri, 05 Jul 2019 13:36:35: 1000000 INFO @ Fri, 05 Jul 2019 13:36:40: 2000000 INFO @ Fri, 05 Jul 2019 13:36:44: 2000000 INFO @ Fri, 05 Jul 2019 13:36:44: 2000000 INFO @ Fri, 05 Jul 2019 13:36:48: 3000000 INFO @ Fri, 05 Jul 2019 13:36:53: 3000000 INFO @ Fri, 05 Jul 2019 13:36:53: 3000000 INFO @ Fri, 05 Jul 2019 13:36:56: 4000000 INFO @ Fri, 05 Jul 2019 13:37:02: 4000000 INFO @ Fri, 05 Jul 2019 13:37:03: 4000000 INFO @ Fri, 05 Jul 2019 13:37:04: 5000000 INFO @ Fri, 05 Jul 2019 13:37:11: 5000000 INFO @ Fri, 05 Jul 2019 13:37:12: 6000000 INFO @ Fri, 05 Jul 2019 13:37:12: 5000000 INFO @ Fri, 05 Jul 2019 13:37:19: 7000000 INFO @ Fri, 05 Jul 2019 13:37:20: 6000000 INFO @ Fri, 05 Jul 2019 13:37:22: 6000000 INFO @ Fri, 05 Jul 2019 13:37:27: 8000000 INFO @ Fri, 05 Jul 2019 13:37:29: 7000000 INFO @ Fri, 05 Jul 2019 13:37:31: 7000000 INFO @ Fri, 05 Jul 2019 13:37:35: 9000000 INFO @ Fri, 05 Jul 2019 13:37:38: 8000000 INFO @ Fri, 05 Jul 2019 13:37:40: 8000000 INFO @ Fri, 05 Jul 2019 13:37:43: 10000000 INFO @ Fri, 05 Jul 2019 13:37:47: 9000000 INFO @ Fri, 05 Jul 2019 13:37:50: 9000000 INFO @ Fri, 05 Jul 2019 13:37:50: 11000000 INFO @ Fri, 05 Jul 2019 13:37:56: 10000000 INFO @ Fri, 05 Jul 2019 13:37:58: 12000000 INFO @ Fri, 05 Jul 2019 13:38:00: 10000000 INFO @ Fri, 05 Jul 2019 13:38:05: 11000000 INFO @ Fri, 05 Jul 2019 13:38:06: 13000000 INFO @ Fri, 05 Jul 2019 13:38:09: 11000000 INFO @ Fri, 05 Jul 2019 13:38:13: 14000000 INFO @ Fri, 05 Jul 2019 13:38:13: 12000000 INFO @ Fri, 05 Jul 2019 13:38:18: 12000000 INFO @ Fri, 05 Jul 2019 13:38:21: 15000000 INFO @ Fri, 05 Jul 2019 13:38:22: 13000000 INFO @ Fri, 05 Jul 2019 13:38:27: 13000000 INFO @ Fri, 05 Jul 2019 13:38:29: 16000000 INFO @ Fri, 05 Jul 2019 13:38:31: 14000000 INFO @ Fri, 05 Jul 2019 13:38:36: 14000000 INFO @ Fri, 05 Jul 2019 13:38:37: 17000000 INFO @ Fri, 05 Jul 2019 13:38:40: 15000000 INFO @ Fri, 05 Jul 2019 13:38:44: 18000000 INFO @ Fri, 05 Jul 2019 13:38:46: 15000000 INFO @ Fri, 05 Jul 2019 13:38:49: 16000000 INFO @ Fri, 05 Jul 2019 13:38:52: 19000000 INFO @ Fri, 05 Jul 2019 13:38:55: 16000000 INFO @ Fri, 05 Jul 2019 13:38:57: 17000000 INFO @ Fri, 05 Jul 2019 13:39:00: 20000000 INFO @ Fri, 05 Jul 2019 13:39:03: 17000000 INFO @ Fri, 05 Jul 2019 13:39:06: 18000000 INFO @ Fri, 05 Jul 2019 13:39:07: 21000000 INFO @ Fri, 05 Jul 2019 13:39:13: 18000000 INFO @ Fri, 05 Jul 2019 13:39:15: 19000000 INFO @ Fri, 05 Jul 2019 13:39:15: 22000000 INFO @ Fri, 05 Jul 2019 13:39:22: 19000000 INFO @ Fri, 05 Jul 2019 13:39:22: 23000000 INFO @ Fri, 05 Jul 2019 13:39:23: 20000000 INFO @ Fri, 05 Jul 2019 13:39:30: 24000000 INFO @ Fri, 05 Jul 2019 13:39:31: 20000000 INFO @ Fri, 05 Jul 2019 13:39:32: 21000000 INFO @ Fri, 05 Jul 2019 13:39:38: 25000000 INFO @ Fri, 05 Jul 2019 13:39:40: 22000000 INFO @ Fri, 05 Jul 2019 13:39:41: 21000000 INFO @ Fri, 05 Jul 2019 13:39:45: 26000000 INFO @ Fri, 05 Jul 2019 13:39:49: 23000000 INFO @ Fri, 05 Jul 2019 13:39:50: 22000000 INFO @ Fri, 05 Jul 2019 13:39:53: 27000000 INFO @ Fri, 05 Jul 2019 13:39:56: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:39:56: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:39:56: #1 total tags in treatment: 27290782 INFO @ Fri, 05 Jul 2019 13:39:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:39:56: #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 13:39:57: #1 tags after filtering in treatment: 27290689 INFO @ Fri, 05 Jul 2019 13:39:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:39:57: #1 finished! INFO @ Fri, 05 Jul 2019 13:39:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:39:58: 24000000 INFO @ Fri, 05 Jul 2019 13:39:59: 23000000 INFO @ Fri, 05 Jul 2019 13:40:01: #2 number of paired peaks: 27667 INFO @ Fri, 05 Jul 2019 13:40:01: start model_add_line... INFO @ Fri, 05 Jul 2019 13:40:01: start X-correlation... INFO @ Fri, 05 Jul 2019 13:40:01: end of X-cor INFO @ Fri, 05 Jul 2019 13:40:01: #2 finished! INFO @ Fri, 05 Jul 2019 13:40:01: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 13:40:01: #2 alternative fragment length(s) may be 249 bps INFO @ Fri, 05 Jul 2019 13:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.20_model.r INFO @ Fri, 05 Jul 2019 13:40:01: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:40:07: 25000000 INFO @ Fri, 05 Jul 2019 13:40:08: 24000000 INFO @ Fri, 05 Jul 2019 13:40:15: 26000000 INFO @ Fri, 05 Jul 2019 13:40:16: 25000000 INFO @ Fri, 05 Jul 2019 13:40:24: 27000000 INFO @ Fri, 05 Jul 2019 13:40:25: 26000000 INFO @ Fri, 05 Jul 2019 13:40:27: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:40:27: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:40:27: #1 total tags in treatment: 27290782 INFO @ Fri, 05 Jul 2019 13:40:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:40:27: #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 13:40:28: #1 tags after filtering in treatment: 27290689 INFO @ Fri, 05 Jul 2019 13:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:40:28: #1 finished! INFO @ Fri, 05 Jul 2019 13:40:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:40:32: #2 number of paired peaks: 27667 INFO @ Fri, 05 Jul 2019 13:40:32: start model_add_line... INFO @ Fri, 05 Jul 2019 13:40:32: start X-correlation... INFO @ Fri, 05 Jul 2019 13:40:32: end of X-cor INFO @ Fri, 05 Jul 2019 13:40:32: #2 finished! INFO @ Fri, 05 Jul 2019 13:40:32: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 13:40:32: #2 alternative fragment length(s) may be 249 bps INFO @ Fri, 05 Jul 2019 13:40:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.05_model.r INFO @ Fri, 05 Jul 2019 13:40:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:40:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:40:35: 27000000 INFO @ Fri, 05 Jul 2019 13:40:38: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 13:40:38: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 13:40:38: #1 total tags in treatment: 27290782 INFO @ Fri, 05 Jul 2019 13:40:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:40:38: #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 13:40:39: #1 tags after filtering in treatment: 27290689 INFO @ Fri, 05 Jul 2019 13:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:40:39: #1 finished! INFO @ Fri, 05 Jul 2019 13:40:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:40:43: #2 number of paired peaks: 27667 INFO @ Fri, 05 Jul 2019 13:40:43: start model_add_line... INFO @ Fri, 05 Jul 2019 13:40:43: start X-correlation... INFO @ Fri, 05 Jul 2019 13:40:43: end of X-cor INFO @ Fri, 05 Jul 2019 13:40:43: #2 finished! INFO @ Fri, 05 Jul 2019 13:40:43: #2 predicted fragment length is 249 bps INFO @ Fri, 05 Jul 2019 13:40:43: #2 alternative fragment length(s) may be 249 bps INFO @ Fri, 05 Jul 2019 13:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.10_model.r INFO @ Fri, 05 Jul 2019 13:40:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:41:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:42:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.20_summits.bed INFO @ Fri, 05 Jul 2019 13:42:13: Done! pass1 - making usageList (52 chroms): 3 millis pass2 - checking and writing primary data (3142 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:42:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.05_summits.bed INFO @ Fri, 05 Jul 2019 13:42:45: Done! pass1 - making usageList (87 chroms): 5 millis pass2 - checking and writing primary data (12189 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:43:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:43:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:43:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX278552/SRX278552.10_summits.bed INFO @ Fri, 05 Jul 2019 13:43:02: Done! pass1 - making usageList (72 chroms): 5 millis pass2 - checking and writing primary data (7616 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。