Job ID = 2001522 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,039,875 reads read : 34,039,875 reads written : 34,039,875 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:30 34039875 reads; of these: 34039875 (100.00%) were unpaired; of these: 849787 (2.50%) aligned 0 times 25320509 (74.38%) aligned exactly 1 time 7869579 (23.12%) aligned >1 times 97.50% overall alignment rate Time searching: 00:15:31 Overall time: 00:15:31 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] 2862378 / 33190088 = 0.0862 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 04:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.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 04:49:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:49:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.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 04:49:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:49:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:49:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.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 04:49:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:49:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:49:30: 1000000 INFO @ Fri, 05 Jul 2019 04:49:31: 1000000 INFO @ Fri, 05 Jul 2019 04:49:31: 1000000 INFO @ Fri, 05 Jul 2019 04:49:39: 2000000 INFO @ Fri, 05 Jul 2019 04:49:40: 2000000 INFO @ Fri, 05 Jul 2019 04:49:40: 2000000 INFO @ Fri, 05 Jul 2019 04:49:48: 3000000 INFO @ Fri, 05 Jul 2019 04:49:49: 3000000 INFO @ Fri, 05 Jul 2019 04:49:50: 3000000 INFO @ Fri, 05 Jul 2019 04:49:56: 4000000 INFO @ Fri, 05 Jul 2019 04:49:59: 4000000 INFO @ Fri, 05 Jul 2019 04:49:59: 4000000 INFO @ Fri, 05 Jul 2019 04:50:05: 5000000 INFO @ Fri, 05 Jul 2019 04:50:08: 5000000 INFO @ Fri, 05 Jul 2019 04:50:09: 5000000 INFO @ Fri, 05 Jul 2019 04:50:13: 6000000 INFO @ Fri, 05 Jul 2019 04:50:17: 6000000 INFO @ Fri, 05 Jul 2019 04:50:18: 6000000 INFO @ Fri, 05 Jul 2019 04:50:22: 7000000 INFO @ Fri, 05 Jul 2019 04:50:26: 7000000 INFO @ Fri, 05 Jul 2019 04:50:27: 7000000 INFO @ Fri, 05 Jul 2019 04:50:30: 8000000 INFO @ Fri, 05 Jul 2019 04:50:35: 8000000 INFO @ Fri, 05 Jul 2019 04:50:37: 8000000 INFO @ Fri, 05 Jul 2019 04:50:38: 9000000 INFO @ Fri, 05 Jul 2019 04:50:44: 9000000 INFO @ Fri, 05 Jul 2019 04:50:46: 9000000 INFO @ Fri, 05 Jul 2019 04:50:47: 10000000 INFO @ Fri, 05 Jul 2019 04:50:53: 10000000 INFO @ Fri, 05 Jul 2019 04:50:55: 11000000 INFO @ Fri, 05 Jul 2019 04:50:56: 10000000 INFO @ Fri, 05 Jul 2019 04:51:02: 11000000 INFO @ Fri, 05 Jul 2019 04:51:03: 12000000 INFO @ Fri, 05 Jul 2019 04:51:05: 11000000 INFO @ Fri, 05 Jul 2019 04:51:11: 12000000 INFO @ Fri, 05 Jul 2019 04:51:12: 13000000 INFO @ Fri, 05 Jul 2019 04:51:14: 12000000 INFO @ Fri, 05 Jul 2019 04:51:20: 14000000 INFO @ Fri, 05 Jul 2019 04:51:20: 13000000 INFO @ Fri, 05 Jul 2019 04:51:24: 13000000 INFO @ Fri, 05 Jul 2019 04:51:28: 15000000 INFO @ Fri, 05 Jul 2019 04:51:29: 14000000 INFO @ Fri, 05 Jul 2019 04:51:33: 14000000 INFO @ Fri, 05 Jul 2019 04:51:37: 16000000 INFO @ Fri, 05 Jul 2019 04:51:38: 15000000 INFO @ Fri, 05 Jul 2019 04:51:42: 15000000 INFO @ Fri, 05 Jul 2019 04:51:45: 17000000 INFO @ Fri, 05 Jul 2019 04:51:47: 16000000 INFO @ Fri, 05 Jul 2019 04:51:52: 16000000 INFO @ Fri, 05 Jul 2019 04:51:54: 18000000 INFO @ Fri, 05 Jul 2019 04:51:57: 17000000 INFO @ Fri, 05 Jul 2019 04:52:02: 17000000 INFO @ Fri, 05 Jul 2019 04:52:03: 19000000 INFO @ Fri, 05 Jul 2019 04:52:06: 18000000 INFO @ Fri, 05 Jul 2019 04:52:11: 20000000 INFO @ Fri, 05 Jul 2019 04:52:12: 18000000 INFO @ Fri, 05 Jul 2019 04:52:15: 19000000 INFO @ Fri, 05 Jul 2019 04:52:20: 21000000 INFO @ Fri, 05 Jul 2019 04:52:21: 19000000 INFO @ Fri, 05 Jul 2019 04:52:24: 20000000 INFO @ Fri, 05 Jul 2019 04:52:28: 22000000 INFO @ Fri, 05 Jul 2019 04:52:31: 20000000 INFO @ Fri, 05 Jul 2019 04:52:33: 21000000 INFO @ Fri, 05 Jul 2019 04:52:36: 23000000 INFO @ Fri, 05 Jul 2019 04:52:40: 21000000 INFO @ Fri, 05 Jul 2019 04:52:42: 22000000 INFO @ Fri, 05 Jul 2019 04:52:45: 24000000 INFO @ Fri, 05 Jul 2019 04:52:49: 22000000 INFO @ Fri, 05 Jul 2019 04:52:50: 23000000 INFO @ Fri, 05 Jul 2019 04:52:53: 25000000 INFO @ Fri, 05 Jul 2019 04:52:58: 23000000 INFO @ Fri, 05 Jul 2019 04:52:59: 24000000 INFO @ Fri, 05 Jul 2019 04:53:00: 26000000 INFO @ Fri, 05 Jul 2019 04:53:07: 24000000 INFO @ Fri, 05 Jul 2019 04:53:07: 25000000 INFO @ Fri, 05 Jul 2019 04:53:08: 27000000 INFO @ Fri, 05 Jul 2019 04:53:16: 25000000 INFO @ Fri, 05 Jul 2019 04:53:16: 26000000 INFO @ Fri, 05 Jul 2019 04:53:16: 28000000 INFO @ Fri, 05 Jul 2019 04:53:24: 29000000 INFO @ Fri, 05 Jul 2019 04:53:24: 26000000 INFO @ Fri, 05 Jul 2019 04:53:25: 27000000 INFO @ Fri, 05 Jul 2019 04:53:33: 30000000 INFO @ Fri, 05 Jul 2019 04:53:34: 28000000 INFO @ Fri, 05 Jul 2019 04:53:34: 27000000 INFO @ Fri, 05 Jul 2019 04:53:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:53:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:53:36: #1 total tags in treatment: 30327710 INFO @ Fri, 05 Jul 2019 04:53:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:53:36: #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 04:53:37: #1 tags after filtering in treatment: 30327573 INFO @ Fri, 05 Jul 2019 04:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:53:37: #1 finished! INFO @ Fri, 05 Jul 2019 04:53:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:53:43: 29000000 INFO @ Fri, 05 Jul 2019 04:53:43: #2 number of paired peaks: 57197 INFO @ Fri, 05 Jul 2019 04:53:43: start model_add_line... INFO @ Fri, 05 Jul 2019 04:53:43: 28000000 INFO @ Fri, 05 Jul 2019 04:53:43: start X-correlation... INFO @ Fri, 05 Jul 2019 04:53:43: end of X-cor INFO @ Fri, 05 Jul 2019 04:53:43: #2 finished! INFO @ Fri, 05 Jul 2019 04:53:43: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 04:53:43: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 04:53:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.05_model.r INFO @ Fri, 05 Jul 2019 04:53:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:53:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:53:52: 30000000 INFO @ Fri, 05 Jul 2019 04:53:53: 29000000 INFO @ Fri, 05 Jul 2019 04:53:55: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:53:55: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:53:55: #1 total tags in treatment: 30327710 INFO @ Fri, 05 Jul 2019 04:53:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:53:55: #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 04:53:56: #1 tags after filtering in treatment: 30327573 INFO @ Fri, 05 Jul 2019 04:53:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:53:56: #1 finished! INFO @ Fri, 05 Jul 2019 04:53:56: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:54:02: 30000000 INFO @ Fri, 05 Jul 2019 04:54:02: #2 number of paired peaks: 57197 INFO @ Fri, 05 Jul 2019 04:54:02: start model_add_line... INFO @ Fri, 05 Jul 2019 04:54:02: start X-correlation... INFO @ Fri, 05 Jul 2019 04:54:02: end of X-cor INFO @ Fri, 05 Jul 2019 04:54:02: #2 finished! INFO @ Fri, 05 Jul 2019 04:54:02: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 04:54:02: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 04:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.20_model.r INFO @ Fri, 05 Jul 2019 04:54:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:54:05: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:54:05: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:54:05: #1 total tags in treatment: 30327710 INFO @ Fri, 05 Jul 2019 04:54:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:54:05: #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 04:54:06: #1 tags after filtering in treatment: 30327573 INFO @ Fri, 05 Jul 2019 04:54:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:54:06: #1 finished! INFO @ Fri, 05 Jul 2019 04:54:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:54:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:54:12: #2 number of paired peaks: 57197 INFO @ Fri, 05 Jul 2019 04:54:12: start model_add_line... INFO @ Fri, 05 Jul 2019 04:54:12: start X-correlation... INFO @ Fri, 05 Jul 2019 04:54:12: end of X-cor INFO @ Fri, 05 Jul 2019 04:54:12: #2 finished! INFO @ Fri, 05 Jul 2019 04:54:12: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 04:54:12: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 05 Jul 2019 04:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.10_model.r INFO @ Fri, 05 Jul 2019 04:54:12: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:55:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:55:48: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:55:54: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:56:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:56:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:56:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.05_summits.bed INFO @ Fri, 05 Jul 2019 04:56:24: Done! pass1 - making usageList (91 chroms): 6 millis pass2 - checking and writing primary data (10413 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:56:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:56:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:56:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.20_summits.bed INFO @ Fri, 05 Jul 2019 04:56:44: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (332 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101868/ERX101868.10_summits.bed INFO @ Fri, 05 Jul 2019 04:56:50: Done! pass1 - making usageList (48 chroms): 2 millis pass2 - checking and writing primary data (2805 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。