Job ID = 2001555 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,852,054 reads read : 28,852,054 reads written : 28,852,054 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: 00:11:30 28852054 reads; of these: 28852054 (100.00%) were unpaired; of these: 722565 (2.50%) aligned 0 times 21553457 (74.70%) aligned exactly 1 time 6576032 (22.79%) aligned >1 times 97.50% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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] 1917158 / 28129489 = 0.0682 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 05:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.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 05:11:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:11:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.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 05:11:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:11:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.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 05:11:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:11:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:11:40: 1000000 INFO @ Fri, 05 Jul 2019 05:11:41: 1000000 INFO @ Fri, 05 Jul 2019 05:11:44: 1000000 INFO @ Fri, 05 Jul 2019 05:11:47: 2000000 INFO @ Fri, 05 Jul 2019 05:11:48: 2000000 INFO @ Fri, 05 Jul 2019 05:11:53: 2000000 INFO @ Fri, 05 Jul 2019 05:11:54: 3000000 INFO @ Fri, 05 Jul 2019 05:11:55: 3000000 INFO @ Fri, 05 Jul 2019 05:12:01: 4000000 INFO @ Fri, 05 Jul 2019 05:12:01: 3000000 INFO @ Fri, 05 Jul 2019 05:12:01: 4000000 INFO @ Fri, 05 Jul 2019 05:12:07: 5000000 INFO @ Fri, 05 Jul 2019 05:12:08: 5000000 INFO @ Fri, 05 Jul 2019 05:12:10: 4000000 INFO @ Fri, 05 Jul 2019 05:12:14: 6000000 INFO @ Fri, 05 Jul 2019 05:12:15: 6000000 INFO @ Fri, 05 Jul 2019 05:12:18: 5000000 INFO @ Fri, 05 Jul 2019 05:12:21: 7000000 INFO @ Fri, 05 Jul 2019 05:12:22: 7000000 INFO @ Fri, 05 Jul 2019 05:12:27: 6000000 INFO @ Fri, 05 Jul 2019 05:12:28: 8000000 INFO @ Fri, 05 Jul 2019 05:12:29: 8000000 INFO @ Fri, 05 Jul 2019 05:12:34: 9000000 INFO @ Fri, 05 Jul 2019 05:12:35: 7000000 INFO @ Fri, 05 Jul 2019 05:12:35: 9000000 INFO @ Fri, 05 Jul 2019 05:12:41: 10000000 INFO @ Fri, 05 Jul 2019 05:12:42: 10000000 INFO @ Fri, 05 Jul 2019 05:12:43: 8000000 INFO @ Fri, 05 Jul 2019 05:12:48: 11000000 INFO @ Fri, 05 Jul 2019 05:12:49: 11000000 INFO @ Fri, 05 Jul 2019 05:12:52: 9000000 INFO @ Fri, 05 Jul 2019 05:12:55: 12000000 INFO @ Fri, 05 Jul 2019 05:12:56: 12000000 INFO @ Fri, 05 Jul 2019 05:13:00: 10000000 INFO @ Fri, 05 Jul 2019 05:13:01: 13000000 INFO @ Fri, 05 Jul 2019 05:13:02: 13000000 INFO @ Fri, 05 Jul 2019 05:13:08: 14000000 INFO @ Fri, 05 Jul 2019 05:13:09: 11000000 INFO @ Fri, 05 Jul 2019 05:13:09: 14000000 INFO @ Fri, 05 Jul 2019 05:13:15: 15000000 INFO @ Fri, 05 Jul 2019 05:13:16: 15000000 INFO @ Fri, 05 Jul 2019 05:13:17: 12000000 INFO @ Fri, 05 Jul 2019 05:13:22: 16000000 INFO @ Fri, 05 Jul 2019 05:13:23: 16000000 INFO @ Fri, 05 Jul 2019 05:13:26: 13000000 INFO @ Fri, 05 Jul 2019 05:13:28: 17000000 INFO @ Fri, 05 Jul 2019 05:13:30: 17000000 INFO @ Fri, 05 Jul 2019 05:13:34: 14000000 INFO @ Fri, 05 Jul 2019 05:13:35: 18000000 INFO @ Fri, 05 Jul 2019 05:13:36: 18000000 INFO @ Fri, 05 Jul 2019 05:13:42: 19000000 INFO @ Fri, 05 Jul 2019 05:13:43: 15000000 INFO @ Fri, 05 Jul 2019 05:13:43: 19000000 INFO @ Fri, 05 Jul 2019 05:13:49: 20000000 INFO @ Fri, 05 Jul 2019 05:13:50: 20000000 INFO @ Fri, 05 Jul 2019 05:13:51: 16000000 INFO @ Fri, 05 Jul 2019 05:13:55: 21000000 INFO @ Fri, 05 Jul 2019 05:13:57: 21000000 INFO @ Fri, 05 Jul 2019 05:13:59: 17000000 INFO @ Fri, 05 Jul 2019 05:14:02: 22000000 INFO @ Fri, 05 Jul 2019 05:14:04: 22000000 INFO @ Fri, 05 Jul 2019 05:14:08: 18000000 INFO @ Fri, 05 Jul 2019 05:14:09: 23000000 INFO @ Fri, 05 Jul 2019 05:14:11: 23000000 INFO @ Fri, 05 Jul 2019 05:14:16: 24000000 INFO @ Fri, 05 Jul 2019 05:14:16: 19000000 INFO @ Fri, 05 Jul 2019 05:14:17: 24000000 INFO @ Fri, 05 Jul 2019 05:14:23: 25000000 INFO @ Fri, 05 Jul 2019 05:14:24: 25000000 INFO @ Fri, 05 Jul 2019 05:14:25: 20000000 INFO @ Fri, 05 Jul 2019 05:14:30: 26000000 INFO @ Fri, 05 Jul 2019 05:14:31: 26000000 INFO @ Fri, 05 Jul 2019 05:14:31: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:14:31: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:14:31: #1 total tags in treatment: 26212331 INFO @ Fri, 05 Jul 2019 05:14:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:14:31: #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 05:14:32: #1 tags after filtering in treatment: 26212167 INFO @ Fri, 05 Jul 2019 05:14:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:14:32: #1 finished! INFO @ Fri, 05 Jul 2019 05:14:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:14:33: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:14:33: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:14:33: #1 total tags in treatment: 26212331 INFO @ Fri, 05 Jul 2019 05:14:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:14:33: #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 05:14:33: 21000000 INFO @ Fri, 05 Jul 2019 05:14:34: #1 tags after filtering in treatment: 26212167 INFO @ Fri, 05 Jul 2019 05:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:14:34: #1 finished! INFO @ Fri, 05 Jul 2019 05:14:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:14:37: #2 number of paired peaks: 57076 INFO @ Fri, 05 Jul 2019 05:14:37: start model_add_line... INFO @ Fri, 05 Jul 2019 05:14:37: start X-correlation... INFO @ Fri, 05 Jul 2019 05:14:37: end of X-cor INFO @ Fri, 05 Jul 2019 05:14:37: #2 finished! INFO @ Fri, 05 Jul 2019 05:14:37: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:14:37: #2 alternative fragment length(s) may be 2,130,291,501 bps INFO @ Fri, 05 Jul 2019 05:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.05_model.r INFO @ Fri, 05 Jul 2019 05:14:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:14:39: #2 number of paired peaks: 57076 INFO @ Fri, 05 Jul 2019 05:14:39: start model_add_line... INFO @ Fri, 05 Jul 2019 05:14:39: start X-correlation... INFO @ Fri, 05 Jul 2019 05:14:39: end of X-cor INFO @ Fri, 05 Jul 2019 05:14:39: #2 finished! INFO @ Fri, 05 Jul 2019 05:14:39: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:14:39: #2 alternative fragment length(s) may be 2,130,291,501 bps INFO @ Fri, 05 Jul 2019 05:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.10_model.r INFO @ Fri, 05 Jul 2019 05:14:39: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:14:41: 22000000 INFO @ Fri, 05 Jul 2019 05:14:50: 23000000 INFO @ Fri, 05 Jul 2019 05:14:58: 24000000 INFO @ Fri, 05 Jul 2019 05:15:06: 25000000 INFO @ Fri, 05 Jul 2019 05:15:15: 26000000 INFO @ Fri, 05 Jul 2019 05:15:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:15:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:15:17: #1 total tags in treatment: 26212331 INFO @ Fri, 05 Jul 2019 05:15:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:15:17: #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 05:15:17: #1 tags after filtering in treatment: 26212167 INFO @ Fri, 05 Jul 2019 05:15:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:15:17: #1 finished! INFO @ Fri, 05 Jul 2019 05:15:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:15:23: #2 number of paired peaks: 57076 INFO @ Fri, 05 Jul 2019 05:15:23: start model_add_line... INFO @ Fri, 05 Jul 2019 05:15:23: start X-correlation... INFO @ Fri, 05 Jul 2019 05:15:23: end of X-cor INFO @ Fri, 05 Jul 2019 05:15:23: #2 finished! INFO @ Fri, 05 Jul 2019 05:15:23: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 05:15:23: #2 alternative fragment length(s) may be 2,130,291,501 bps INFO @ Fri, 05 Jul 2019 05:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.20_model.r INFO @ Fri, 05 Jul 2019 05:15:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:15:59: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:16:01: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.05_summits.bed INFO @ Fri, 05 Jul 2019 05:16:42: Done! pass1 - making usageList (57 chroms): 3 millis pass2 - checking and writing primary data (3834 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:16:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:16:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:16:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.10_summits.bed INFO @ Fri, 05 Jul 2019 05:16:42: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (729 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:16:45: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101898/ERX101898.20_summits.bed INFO @ Fri, 05 Jul 2019 05:17:32: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。