Job ID = 2003641 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 50,173,372 reads read : 50,173,372 reads written : 50,173,372 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: 00:00:01 Multiseed full-index search: 00:22:52 50173372 reads; of these: 50173372 (100.00%) were unpaired; of these: 2523575 (5.03%) aligned 0 times 32970459 (65.71%) aligned exactly 1 time 14679338 (29.26%) aligned >1 times 94.97% overall alignment rate Time searching: 00:22:55 Overall time: 00:22:55 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 16 files... [bam_rmdupse_core] 5835045 / 47649797 = 0.1225 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 13:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.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 13:44:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:44:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.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 13:44:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:44:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.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 13:44:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:44:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:44:11: 1000000 INFO @ Fri, 05 Jul 2019 13:44:13: 1000000 INFO @ Fri, 05 Jul 2019 13:44:13: 1000000 INFO @ Fri, 05 Jul 2019 13:44:18: 2000000 INFO @ Fri, 05 Jul 2019 13:44:22: 2000000 INFO @ Fri, 05 Jul 2019 13:44:23: 2000000 INFO @ Fri, 05 Jul 2019 13:44:25: 3000000 INFO @ Fri, 05 Jul 2019 13:44:31: 4000000 INFO @ Fri, 05 Jul 2019 13:44:31: 3000000 INFO @ Fri, 05 Jul 2019 13:44:32: 3000000 INFO @ Fri, 05 Jul 2019 13:44:37: 5000000 INFO @ Fri, 05 Jul 2019 13:44:40: 4000000 INFO @ Fri, 05 Jul 2019 13:44:40: 4000000 INFO @ Fri, 05 Jul 2019 13:44:44: 6000000 INFO @ Fri, 05 Jul 2019 13:44:48: 5000000 INFO @ Fri, 05 Jul 2019 13:44:49: 5000000 INFO @ Fri, 05 Jul 2019 13:44:50: 7000000 INFO @ Fri, 05 Jul 2019 13:44:56: 6000000 INFO @ Fri, 05 Jul 2019 13:44:57: 6000000 INFO @ Fri, 05 Jul 2019 13:44:57: 8000000 INFO @ Fri, 05 Jul 2019 13:45:03: 9000000 INFO @ Fri, 05 Jul 2019 13:45:04: 7000000 INFO @ Fri, 05 Jul 2019 13:45:05: 7000000 INFO @ Fri, 05 Jul 2019 13:45:10: 10000000 INFO @ Fri, 05 Jul 2019 13:45:13: 8000000 INFO @ Fri, 05 Jul 2019 13:45:13: 8000000 INFO @ Fri, 05 Jul 2019 13:45:16: 11000000 INFO @ Fri, 05 Jul 2019 13:45:21: 9000000 INFO @ Fri, 05 Jul 2019 13:45:21: 9000000 INFO @ Fri, 05 Jul 2019 13:45:22: 12000000 INFO @ Fri, 05 Jul 2019 13:45:29: 13000000 INFO @ Fri, 05 Jul 2019 13:45:29: 10000000 INFO @ Fri, 05 Jul 2019 13:45:29: 10000000 INFO @ Fri, 05 Jul 2019 13:45:35: 14000000 INFO @ Fri, 05 Jul 2019 13:45:37: 11000000 INFO @ Fri, 05 Jul 2019 13:45:37: 11000000 INFO @ Fri, 05 Jul 2019 13:45:41: 15000000 INFO @ Fri, 05 Jul 2019 13:45:45: 12000000 INFO @ Fri, 05 Jul 2019 13:45:46: 12000000 INFO @ Fri, 05 Jul 2019 13:45:48: 16000000 INFO @ Fri, 05 Jul 2019 13:45:54: 13000000 INFO @ Fri, 05 Jul 2019 13:45:54: 17000000 INFO @ Fri, 05 Jul 2019 13:45:54: 13000000 INFO @ Fri, 05 Jul 2019 13:46:00: 18000000 INFO @ Fri, 05 Jul 2019 13:46:02: 14000000 INFO @ Fri, 05 Jul 2019 13:46:02: 14000000 INFO @ Fri, 05 Jul 2019 13:46:07: 19000000 INFO @ Fri, 05 Jul 2019 13:46:10: 15000000 INFO @ Fri, 05 Jul 2019 13:46:10: 15000000 INFO @ Fri, 05 Jul 2019 13:46:16: 20000000 INFO @ Fri, 05 Jul 2019 13:46:18: 16000000 INFO @ Fri, 05 Jul 2019 13:46:18: 16000000 INFO @ Fri, 05 Jul 2019 13:46:22: 21000000 INFO @ Fri, 05 Jul 2019 13:46:26: 17000000 INFO @ Fri, 05 Jul 2019 13:46:26: 17000000 INFO @ Fri, 05 Jul 2019 13:46:28: 22000000 INFO @ Fri, 05 Jul 2019 13:46:34: 18000000 INFO @ Fri, 05 Jul 2019 13:46:34: 18000000 INFO @ Fri, 05 Jul 2019 13:46:35: 23000000 INFO @ Fri, 05 Jul 2019 13:46:41: 24000000 INFO @ Fri, 05 Jul 2019 13:46:42: 19000000 INFO @ Fri, 05 Jul 2019 13:46:42: 19000000 INFO @ Fri, 05 Jul 2019 13:46:48: 25000000 INFO @ Fri, 05 Jul 2019 13:46:50: 20000000 INFO @ Fri, 05 Jul 2019 13:46:50: 20000000 INFO @ Fri, 05 Jul 2019 13:46:54: 26000000 INFO @ Fri, 05 Jul 2019 13:46:58: 21000000 INFO @ Fri, 05 Jul 2019 13:46:58: 21000000 INFO @ Fri, 05 Jul 2019 13:47:01: 27000000 INFO @ Fri, 05 Jul 2019 13:47:06: 22000000 INFO @ Fri, 05 Jul 2019 13:47:06: 22000000 INFO @ Fri, 05 Jul 2019 13:47:07: 28000000 INFO @ Fri, 05 Jul 2019 13:47:14: 29000000 INFO @ Fri, 05 Jul 2019 13:47:14: 23000000 INFO @ Fri, 05 Jul 2019 13:47:14: 23000000 INFO @ Fri, 05 Jul 2019 13:47:20: 30000000 INFO @ Fri, 05 Jul 2019 13:47:21: 24000000 INFO @ Fri, 05 Jul 2019 13:47:22: 24000000 INFO @ Fri, 05 Jul 2019 13:47:27: 31000000 INFO @ Fri, 05 Jul 2019 13:47:29: 25000000 INFO @ Fri, 05 Jul 2019 13:47:30: 25000000 INFO @ Fri, 05 Jul 2019 13:47:34: 32000000 INFO @ Fri, 05 Jul 2019 13:47:36: 26000000 INFO @ Fri, 05 Jul 2019 13:47:38: 26000000 INFO @ Fri, 05 Jul 2019 13:47:40: 33000000 INFO @ Fri, 05 Jul 2019 13:47:45: 27000000 INFO @ Fri, 05 Jul 2019 13:47:47: 27000000 INFO @ Fri, 05 Jul 2019 13:47:47: 34000000 INFO @ Fri, 05 Jul 2019 13:47:54: 35000000 INFO @ Fri, 05 Jul 2019 13:47:54: 28000000 INFO @ Fri, 05 Jul 2019 13:47:55: 28000000 INFO @ Fri, 05 Jul 2019 13:48:00: 36000000 INFO @ Fri, 05 Jul 2019 13:48:02: 29000000 INFO @ Fri, 05 Jul 2019 13:48:04: 29000000 INFO @ Fri, 05 Jul 2019 13:48:07: 37000000 INFO @ Fri, 05 Jul 2019 13:48:11: 30000000 INFO @ Fri, 05 Jul 2019 13:48:13: 30000000 INFO @ Fri, 05 Jul 2019 13:48:14: 38000000 INFO @ Fri, 05 Jul 2019 13:48:20: 39000000 INFO @ Fri, 05 Jul 2019 13:48:21: 31000000 INFO @ Fri, 05 Jul 2019 13:48:23: 31000000 INFO @ Fri, 05 Jul 2019 13:48:27: 40000000 INFO @ Fri, 05 Jul 2019 13:48:31: 32000000 INFO @ Fri, 05 Jul 2019 13:48:33: 32000000 INFO @ Fri, 05 Jul 2019 13:48:34: 41000000 INFO @ Fri, 05 Jul 2019 13:48:40: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:48:40: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:48:40: #1 total tags in treatment: 41814752 INFO @ Fri, 05 Jul 2019 13:48:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:48:40: #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 13:48:41: 33000000 INFO @ Fri, 05 Jul 2019 13:48:41: #1 tags after filtering in treatment: 41814688 INFO @ Fri, 05 Jul 2019 13:48:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:48:41: #1 finished! INFO @ Fri, 05 Jul 2019 13:48:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:48:42: 33000000 INFO @ Fri, 05 Jul 2019 13:48:47: #2 number of paired peaks: 29986 INFO @ Fri, 05 Jul 2019 13:48:47: start model_add_line... INFO @ Fri, 05 Jul 2019 13:48:47: start X-correlation... INFO @ Fri, 05 Jul 2019 13:48:47: end of X-cor INFO @ Fri, 05 Jul 2019 13:48:47: #2 finished! INFO @ Fri, 05 Jul 2019 13:48:47: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 13:48:47: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 05 Jul 2019 13:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.20_model.r INFO @ Fri, 05 Jul 2019 13:48:50: 34000000 INFO @ Fri, 05 Jul 2019 13:48:52: 34000000 INFO @ Fri, 05 Jul 2019 13:48:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:49:00: 35000000 INFO @ Fri, 05 Jul 2019 13:49:02: 35000000 INFO @ Fri, 05 Jul 2019 13:49:10: 36000000 INFO @ Fri, 05 Jul 2019 13:49:12: 36000000 INFO @ Fri, 05 Jul 2019 13:49:19: 37000000 INFO @ Fri, 05 Jul 2019 13:49:22: 37000000 INFO @ Fri, 05 Jul 2019 13:49:28: 38000000 INFO @ Fri, 05 Jul 2019 13:49:31: 38000000 INFO @ Fri, 05 Jul 2019 13:49:37: 39000000 INFO @ Fri, 05 Jul 2019 13:49:39: 39000000 INFO @ Fri, 05 Jul 2019 13:49:46: 40000000 INFO @ Fri, 05 Jul 2019 13:49:48: 40000000 INFO @ Fri, 05 Jul 2019 13:49:54: 41000000 INFO @ Fri, 05 Jul 2019 13:49:57: 41000000 INFO @ Fri, 05 Jul 2019 13:50:02: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:50:02: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:50:02: #1 total tags in treatment: 41814752 INFO @ Fri, 05 Jul 2019 13:50:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:02: #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 13:50:03: #1 tags after filtering in treatment: 41814688 INFO @ Fri, 05 Jul 2019 13:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:03: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:05: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 13:50:05: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 13:50:05: #1 total tags in treatment: 41814752 INFO @ Fri, 05 Jul 2019 13:50:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 13:50:05: #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 13:50:06: #1 tags after filtering in treatment: 41814688 INFO @ Fri, 05 Jul 2019 13:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 13:50:06: #1 finished! INFO @ Fri, 05 Jul 2019 13:50:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 13:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 13:50:09: #2 number of paired peaks: 29986 INFO @ Fri, 05 Jul 2019 13:50:09: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:09: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:09: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:09: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:09: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 13:50:09: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 05 Jul 2019 13:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.10_model.r INFO @ Fri, 05 Jul 2019 13:50:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:50:11: #2 number of paired peaks: 29986 INFO @ Fri, 05 Jul 2019 13:50:13: start model_add_line... INFO @ Fri, 05 Jul 2019 13:50:14: start X-correlation... INFO @ Fri, 05 Jul 2019 13:50:14: end of X-cor INFO @ Fri, 05 Jul 2019 13:50:14: #2 finished! INFO @ Fri, 05 Jul 2019 13:50:14: #2 predicted fragment length is 136 bps INFO @ Fri, 05 Jul 2019 13:50:14: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 05 Jul 2019 13:50:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.05_model.r INFO @ Fri, 05 Jul 2019 13:50:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 13:50:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 13:51:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.20_peaks.xls INFO @ Fri, 05 Jul 2019 13:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.20_summits.bed INFO @ Fri, 05 Jul 2019 13:52:17: Done! pass1 - making usageList (51 chroms): 4 millis pass2 - checking and writing primary data (4733 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 13:52:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:52:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 13:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.10_peaks.xls INFO @ Fri, 05 Jul 2019 13:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:53:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.10_summits.bed INFO @ Fri, 05 Jul 2019 13:53:34: Done! pass1 - making usageList (89 chroms): 3 millis pass2 - checking and writing primary data (13541 records, 4 fields): 21 millis INFO @ Fri, 05 Jul 2019 13:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.05_peaks.xls INFO @ Fri, 05 Jul 2019 13:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 13:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX330073/SRX330073.05_summits.bed INFO @ Fri, 05 Jul 2019 13:53:36: Done! pass1 - making usageList (112 chroms): 4 millis pass2 - checking and writing primary data (20236 records, 4 fields): 31 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。