Job ID = 2001577 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,204,517 reads read : 28,204,517 reads written : 28,204,517 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: 00:00:01 Multiseed full-index search: 00:11:48 28204517 reads; of these: 28204517 (100.00%) were unpaired; of these: 607193 (2.15%) aligned 0 times 21108414 (74.84%) aligned exactly 1 time 6488910 (23.01%) aligned >1 times 97.85% overall alignment rate Time searching: 00:11:50 Overall time: 00:11:50 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] 2147398 / 27597324 = 0.0778 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 05:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.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 05:48:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:48:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.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 05:48:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:48:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.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 05:48:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:48:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:48:37: 1000000 INFO @ Fri, 05 Jul 2019 05:48:38: 1000000 INFO @ Fri, 05 Jul 2019 05:48:38: 1000000 INFO @ Fri, 05 Jul 2019 05:48:44: 2000000 INFO @ Fri, 05 Jul 2019 05:48:45: 2000000 INFO @ Fri, 05 Jul 2019 05:48:45: 2000000 INFO @ Fri, 05 Jul 2019 05:48:51: 3000000 INFO @ Fri, 05 Jul 2019 05:48:51: 3000000 INFO @ Fri, 05 Jul 2019 05:48:52: 3000000 INFO @ Fri, 05 Jul 2019 05:48:58: 4000000 INFO @ Fri, 05 Jul 2019 05:48:58: 4000000 INFO @ Fri, 05 Jul 2019 05:49:00: 4000000 INFO @ Fri, 05 Jul 2019 05:49:05: 5000000 INFO @ Fri, 05 Jul 2019 05:49:06: 5000000 INFO @ Fri, 05 Jul 2019 05:49:07: 5000000 INFO @ Fri, 05 Jul 2019 05:49:11: 6000000 INFO @ Fri, 05 Jul 2019 05:49:13: 6000000 INFO @ Fri, 05 Jul 2019 05:49:14: 6000000 INFO @ Fri, 05 Jul 2019 05:49:18: 7000000 INFO @ Fri, 05 Jul 2019 05:49:20: 7000000 INFO @ Fri, 05 Jul 2019 05:49:22: 7000000 INFO @ Fri, 05 Jul 2019 05:49:26: 8000000 INFO @ Fri, 05 Jul 2019 05:49:28: 8000000 INFO @ Fri, 05 Jul 2019 05:49:29: 8000000 INFO @ Fri, 05 Jul 2019 05:49:33: 9000000 INFO @ Fri, 05 Jul 2019 05:49:35: 9000000 INFO @ Fri, 05 Jul 2019 05:49:36: 9000000 INFO @ Fri, 05 Jul 2019 05:49:39: 10000000 INFO @ Fri, 05 Jul 2019 05:49:43: 10000000 INFO @ Fri, 05 Jul 2019 05:49:44: 10000000 INFO @ Fri, 05 Jul 2019 05:49:46: 11000000 INFO @ Fri, 05 Jul 2019 05:49:50: 11000000 INFO @ Fri, 05 Jul 2019 05:49:51: 11000000 INFO @ Fri, 05 Jul 2019 05:49:54: 12000000 INFO @ Fri, 05 Jul 2019 05:49:58: 12000000 INFO @ Fri, 05 Jul 2019 05:49:59: 12000000 INFO @ Fri, 05 Jul 2019 05:50:02: 13000000 INFO @ Fri, 05 Jul 2019 05:50:05: 13000000 INFO @ Fri, 05 Jul 2019 05:50:07: 13000000 INFO @ Fri, 05 Jul 2019 05:50:09: 14000000 INFO @ Fri, 05 Jul 2019 05:50:14: 14000000 INFO @ Fri, 05 Jul 2019 05:50:14: 14000000 INFO @ Fri, 05 Jul 2019 05:50:18: 15000000 INFO @ Fri, 05 Jul 2019 05:50:22: 15000000 INFO @ Fri, 05 Jul 2019 05:50:22: 15000000 INFO @ Fri, 05 Jul 2019 05:50:26: 16000000 INFO @ Fri, 05 Jul 2019 05:50:30: 16000000 INFO @ Fri, 05 Jul 2019 05:50:31: 16000000 INFO @ Fri, 05 Jul 2019 05:50:35: 17000000 INFO @ Fri, 05 Jul 2019 05:50:37: 17000000 INFO @ Fri, 05 Jul 2019 05:50:39: 17000000 INFO @ Fri, 05 Jul 2019 05:50:44: 18000000 INFO @ Fri, 05 Jul 2019 05:50:45: 18000000 INFO @ Fri, 05 Jul 2019 05:50:48: 18000000 INFO @ Fri, 05 Jul 2019 05:50:52: 19000000 INFO @ Fri, 05 Jul 2019 05:50:53: 19000000 INFO @ Fri, 05 Jul 2019 05:50:56: 19000000 INFO @ Fri, 05 Jul 2019 05:51:00: 20000000 INFO @ Fri, 05 Jul 2019 05:51:00: 20000000 INFO @ Fri, 05 Jul 2019 05:51:03: 20000000 INFO @ Fri, 05 Jul 2019 05:51:08: 21000000 INFO @ Fri, 05 Jul 2019 05:51:08: 21000000 INFO @ Fri, 05 Jul 2019 05:51:11: 21000000 INFO @ Fri, 05 Jul 2019 05:51:15: 22000000 INFO @ Fri, 05 Jul 2019 05:51:15: 22000000 INFO @ Fri, 05 Jul 2019 05:51:17: 22000000 INFO @ Fri, 05 Jul 2019 05:51:22: 23000000 INFO @ Fri, 05 Jul 2019 05:51:22: 23000000 INFO @ Fri, 05 Jul 2019 05:51:24: 23000000 INFO @ Fri, 05 Jul 2019 05:51:29: 24000000 INFO @ Fri, 05 Jul 2019 05:51:29: 24000000 INFO @ Fri, 05 Jul 2019 05:51:31: 24000000 INFO @ Fri, 05 Jul 2019 05:51:37: 25000000 INFO @ Fri, 05 Jul 2019 05:51:37: 25000000 INFO @ Fri, 05 Jul 2019 05:51:38: 25000000 INFO @ Fri, 05 Jul 2019 05:51:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:51:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:51:40: #1 total tags in treatment: 25449926 INFO @ Fri, 05 Jul 2019 05:51:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:51:40: #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 05:51:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:51:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:51:40: #1 total tags in treatment: 25449926 INFO @ Fri, 05 Jul 2019 05:51:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:51:40: #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 05:51:41: #1 tags after filtering in treatment: 25449747 INFO @ Fri, 05 Jul 2019 05:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:51:41: #1 finished! INFO @ Fri, 05 Jul 2019 05:51:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:51:41: #1 tags after filtering in treatment: 25449747 INFO @ Fri, 05 Jul 2019 05:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:51:41: #1 finished! INFO @ Fri, 05 Jul 2019 05:51:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:51:41: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:51:41: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:51:41: #1 total tags in treatment: 25449926 INFO @ Fri, 05 Jul 2019 05:51:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:51:41: #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 05:51:42: #1 tags after filtering in treatment: 25449747 INFO @ Fri, 05 Jul 2019 05:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:51:42: #1 finished! INFO @ Fri, 05 Jul 2019 05:51:42: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:51:46: #2 number of paired peaks: 64162 INFO @ Fri, 05 Jul 2019 05:51:46: start model_add_line... INFO @ Fri, 05 Jul 2019 05:51:46: #2 number of paired peaks: 64162 INFO @ Fri, 05 Jul 2019 05:51:46: start model_add_line... INFO @ Fri, 05 Jul 2019 05:51:47: start X-correlation... INFO @ Fri, 05 Jul 2019 05:51:47: start X-correlation... INFO @ Fri, 05 Jul 2019 05:51:47: end of X-cor INFO @ Fri, 05 Jul 2019 05:51:47: #2 finished! INFO @ Fri, 05 Jul 2019 05:51:47: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 05:51:47: #2 alternative fragment length(s) may be 1,137,508 bps INFO @ Fri, 05 Jul 2019 05:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.10_model.r INFO @ Fri, 05 Jul 2019 05:51:47: end of X-cor INFO @ Fri, 05 Jul 2019 05:51:47: #2 finished! INFO @ Fri, 05 Jul 2019 05:51:47: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 05:51:47: #2 alternative fragment length(s) may be 1,137,508 bps INFO @ Fri, 05 Jul 2019 05:51:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.20_model.r INFO @ Fri, 05 Jul 2019 05:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:51:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:51:47: #2 number of paired peaks: 64162 INFO @ Fri, 05 Jul 2019 05:51:47: start model_add_line... INFO @ Fri, 05 Jul 2019 05:51:48: start X-correlation... INFO @ Fri, 05 Jul 2019 05:51:48: end of X-cor INFO @ Fri, 05 Jul 2019 05:51:48: #2 finished! INFO @ Fri, 05 Jul 2019 05:51:48: #2 predicted fragment length is 137 bps INFO @ Fri, 05 Jul 2019 05:51:48: #2 alternative fragment length(s) may be 1,137,508 bps INFO @ Fri, 05 Jul 2019 05:51:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.05_model.r INFO @ Fri, 05 Jul 2019 05:51:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:51:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:53:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:53:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:53:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:53:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:53:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:53:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.10_summits.bed INFO @ Fri, 05 Jul 2019 05:53:54: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (1401 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:53:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:53:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:53:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.20_summits.bed INFO @ Fri, 05 Jul 2019 05:53:54: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:53:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:53:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:53:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101920/ERX101920.05_summits.bed INFO @ Fri, 05 Jul 2019 05:53:57: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (5914 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。