Job ID = 11632710 sra ファイルのダウンロード中... Completed: 1125891K bytes transferred in 13 seconds (678233K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 72865082 spots for /home/okishinya/chipatlas/results/rn6/SRX3782469/SRR6826287.sra Written 72865082 spots for /home/okishinya/chipatlas/results/rn6/SRX3782469/SRR6826287.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:30:16 72865082 reads; of these: 72865082 (100.00%) were unpaired; of these: 4521759 (6.21%) aligned 0 times 52900703 (72.60%) aligned exactly 1 time 15442620 (21.19%) aligned >1 times 93.79% overall alignment rate Time searching: 00:30:21 Overall time: 00:30:21 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 20 files... [bam_rmdupse_core] 7817606 / 68343323 = 0.1144 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, 15 Feb 2019 07:20:49: # Command line: callpeak -t SRX3782469.bam -f BAM -g 2.15e9 -n SRX3782469.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782469.05 # format = BAM # ChIP-seq file = ['SRX3782469.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, 15 Feb 2019 07:20:49: # Command line: callpeak -t SRX3782469.bam -f BAM -g 2.15e9 -n SRX3782469.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782469.20 # format = BAM # ChIP-seq file = ['SRX3782469.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, 15 Feb 2019 07:20:49: # Command line: callpeak -t SRX3782469.bam -f BAM -g 2.15e9 -n SRX3782469.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782469.10 # format = BAM # ChIP-seq file = ['SRX3782469.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, 15 Feb 2019 07:20:49: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:20:49: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:20:49: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:20:49: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:20:49: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:20:49: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:20:55: 1000000 INFO @ Fri, 15 Feb 2019 07:20:55: 1000000 INFO @ Fri, 15 Feb 2019 07:20:55: 1000000 INFO @ Fri, 15 Feb 2019 07:21:01: 2000000 INFO @ Fri, 15 Feb 2019 07:21:01: 2000000 INFO @ Fri, 15 Feb 2019 07:21:02: 2000000 INFO @ Fri, 15 Feb 2019 07:21:07: 3000000 INFO @ Fri, 15 Feb 2019 07:21:08: 3000000 INFO @ Fri, 15 Feb 2019 07:21:08: 3000000 INFO @ Fri, 15 Feb 2019 07:21:13: 4000000 INFO @ Fri, 15 Feb 2019 07:21:14: 4000000 INFO @ Fri, 15 Feb 2019 07:21:15: 4000000 INFO @ Fri, 15 Feb 2019 07:21:18: 5000000 INFO @ Fri, 15 Feb 2019 07:21:21: 5000000 INFO @ Fri, 15 Feb 2019 07:21:21: 5000000 INFO @ Fri, 15 Feb 2019 07:21:24: 6000000 INFO @ Fri, 15 Feb 2019 07:21:27: 6000000 INFO @ Fri, 15 Feb 2019 07:21:28: 6000000 INFO @ Fri, 15 Feb 2019 07:21:30: 7000000 INFO @ Fri, 15 Feb 2019 07:21:33: 7000000 INFO @ Fri, 15 Feb 2019 07:21:34: 7000000 INFO @ Fri, 15 Feb 2019 07:21:36: 8000000 INFO @ Fri, 15 Feb 2019 07:21:39: 8000000 INFO @ Fri, 15 Feb 2019 07:21:40: 8000000 INFO @ Fri, 15 Feb 2019 07:21:41: 9000000 INFO @ Fri, 15 Feb 2019 07:21:45: 9000000 INFO @ Fri, 15 Feb 2019 07:21:46: 9000000 INFO @ Fri, 15 Feb 2019 07:21:47: 10000000 INFO @ Fri, 15 Feb 2019 07:21:51: 10000000 INFO @ Fri, 15 Feb 2019 07:21:52: 10000000 INFO @ Fri, 15 Feb 2019 07:21:53: 11000000 INFO @ Fri, 15 Feb 2019 07:21:57: 11000000 INFO @ Fri, 15 Feb 2019 07:21:58: 11000000 INFO @ Fri, 15 Feb 2019 07:21:59: 12000000 INFO @ Fri, 15 Feb 2019 07:22:03: 12000000 INFO @ Fri, 15 Feb 2019 07:22:04: 12000000 INFO @ Fri, 15 Feb 2019 07:22:05: 13000000 INFO @ Fri, 15 Feb 2019 07:22:09: 13000000 INFO @ Fri, 15 Feb 2019 07:22:10: 13000000 INFO @ Fri, 15 Feb 2019 07:22:10: 14000000 INFO @ Fri, 15 Feb 2019 07:22:15: 14000000 INFO @ Fri, 15 Feb 2019 07:22:16: 15000000 INFO @ Fri, 15 Feb 2019 07:22:17: 14000000 INFO @ Fri, 15 Feb 2019 07:22:21: 15000000 INFO @ Fri, 15 Feb 2019 07:22:22: 16000000 INFO @ Fri, 15 Feb 2019 07:22:23: 15000000 INFO @ Fri, 15 Feb 2019 07:22:27: 16000000 INFO @ Fri, 15 Feb 2019 07:22:28: 17000000 INFO @ Fri, 15 Feb 2019 07:22:29: 16000000 INFO @ Fri, 15 Feb 2019 07:22:34: 18000000 INFO @ Fri, 15 Feb 2019 07:22:34: 17000000 INFO @ Fri, 15 Feb 2019 07:22:35: 17000000 INFO @ Fri, 15 Feb 2019 07:22:39: 19000000 INFO @ Fri, 15 Feb 2019 07:22:39: 18000000 INFO @ Fri, 15 Feb 2019 07:22:41: 18000000 INFO @ Fri, 15 Feb 2019 07:22:45: 20000000 INFO @ Fri, 15 Feb 2019 07:22:45: 19000000 INFO @ Fri, 15 Feb 2019 07:22:47: 19000000 INFO @ Fri, 15 Feb 2019 07:22:51: 21000000 INFO @ Fri, 15 Feb 2019 07:22:51: 20000000 INFO @ Fri, 15 Feb 2019 07:22:53: 20000000 INFO @ Fri, 15 Feb 2019 07:22:57: 22000000 INFO @ Fri, 15 Feb 2019 07:22:57: 21000000 INFO @ Fri, 15 Feb 2019 07:23:00: 21000000 INFO @ Fri, 15 Feb 2019 07:23:03: 23000000 INFO @ Fri, 15 Feb 2019 07:23:04: 22000000 INFO @ Fri, 15 Feb 2019 07:23:07: 22000000 INFO @ Fri, 15 Feb 2019 07:23:10: 24000000 INFO @ Fri, 15 Feb 2019 07:23:11: 23000000 INFO @ Fri, 15 Feb 2019 07:23:13: 23000000 INFO @ Fri, 15 Feb 2019 07:23:17: 25000000 INFO @ Fri, 15 Feb 2019 07:23:17: 24000000 INFO @ Fri, 15 Feb 2019 07:23:20: 24000000 INFO @ Fri, 15 Feb 2019 07:23:23: 25000000 INFO @ Fri, 15 Feb 2019 07:23:24: 26000000 INFO @ Fri, 15 Feb 2019 07:23:26: 25000000 INFO @ Fri, 15 Feb 2019 07:23:30: 26000000 INFO @ Fri, 15 Feb 2019 07:23:31: 27000000 INFO @ Fri, 15 Feb 2019 07:23:33: 26000000 INFO @ Fri, 15 Feb 2019 07:23:36: 27000000 INFO @ Fri, 15 Feb 2019 07:23:38: 28000000 INFO @ Fri, 15 Feb 2019 07:23:40: 27000000 INFO @ Fri, 15 Feb 2019 07:23:43: 28000000 INFO @ Fri, 15 Feb 2019 07:23:45: 29000000 INFO @ Fri, 15 Feb 2019 07:23:46: 28000000 INFO @ Fri, 15 Feb 2019 07:23:49: 29000000 INFO @ Fri, 15 Feb 2019 07:23:52: 30000000 INFO @ Fri, 15 Feb 2019 07:23:53: 29000000 INFO @ Fri, 15 Feb 2019 07:23:56: 30000000 INFO @ Fri, 15 Feb 2019 07:23:59: 31000000 INFO @ Fri, 15 Feb 2019 07:24:00: 30000000 INFO @ Fri, 15 Feb 2019 07:24:02: 31000000 INFO @ Fri, 15 Feb 2019 07:24:06: 31000000 INFO @ Fri, 15 Feb 2019 07:24:06: 32000000 INFO @ Fri, 15 Feb 2019 07:24:09: 32000000 INFO @ Fri, 15 Feb 2019 07:24:13: 32000000 INFO @ Fri, 15 Feb 2019 07:24:14: 33000000 INFO @ Fri, 15 Feb 2019 07:24:15: 33000000 INFO @ Fri, 15 Feb 2019 07:24:20: 33000000 INFO @ Fri, 15 Feb 2019 07:24:21: 34000000 INFO @ Fri, 15 Feb 2019 07:24:22: 34000000 INFO @ Fri, 15 Feb 2019 07:24:26: 34000000 INFO @ Fri, 15 Feb 2019 07:24:27: 35000000 INFO @ Fri, 15 Feb 2019 07:24:28: 35000000 INFO @ Fri, 15 Feb 2019 07:24:33: 35000000 INFO @ Fri, 15 Feb 2019 07:24:33: 36000000 INFO @ Fri, 15 Feb 2019 07:24:34: 36000000 INFO @ Fri, 15 Feb 2019 07:24:39: 36000000 INFO @ Fri, 15 Feb 2019 07:24:39: 37000000 INFO @ Fri, 15 Feb 2019 07:24:40: 37000000 INFO @ Fri, 15 Feb 2019 07:24:45: 38000000 INFO @ Fri, 15 Feb 2019 07:24:45: 37000000 INFO @ Fri, 15 Feb 2019 07:24:46: 38000000 INFO @ Fri, 15 Feb 2019 07:24:51: 39000000 INFO @ Fri, 15 Feb 2019 07:24:51: 38000000 INFO @ Fri, 15 Feb 2019 07:24:52: 39000000 INFO @ Fri, 15 Feb 2019 07:24:57: 40000000 INFO @ Fri, 15 Feb 2019 07:24:58: 39000000 INFO @ Fri, 15 Feb 2019 07:24:59: 40000000 INFO @ Fri, 15 Feb 2019 07:25:02: 41000000 INFO @ Fri, 15 Feb 2019 07:25:04: 40000000 INFO @ Fri, 15 Feb 2019 07:25:05: 41000000 INFO @ Fri, 15 Feb 2019 07:25:08: 42000000 INFO @ Fri, 15 Feb 2019 07:25:10: 41000000 INFO @ Fri, 15 Feb 2019 07:25:11: 42000000 INFO @ Fri, 15 Feb 2019 07:25:14: 43000000 INFO @ Fri, 15 Feb 2019 07:25:16: 42000000 INFO @ Fri, 15 Feb 2019 07:25:17: 43000000 INFO @ Fri, 15 Feb 2019 07:25:20: 44000000 INFO @ Fri, 15 Feb 2019 07:25:22: 43000000 INFO @ Fri, 15 Feb 2019 07:25:23: 44000000 INFO @ Fri, 15 Feb 2019 07:25:26: 45000000 INFO @ Fri, 15 Feb 2019 07:25:29: 44000000 INFO @ Fri, 15 Feb 2019 07:25:29: 45000000 INFO @ Fri, 15 Feb 2019 07:25:31: 46000000 INFO @ Fri, 15 Feb 2019 07:25:36: 45000000 INFO @ Fri, 15 Feb 2019 07:25:36: 46000000 INFO @ Fri, 15 Feb 2019 07:25:37: 47000000 INFO @ Fri, 15 Feb 2019 07:25:43: 46000000 INFO @ Fri, 15 Feb 2019 07:25:43: 47000000 INFO @ Fri, 15 Feb 2019 07:25:43: 48000000 INFO @ Fri, 15 Feb 2019 07:25:49: 49000000 INFO @ Fri, 15 Feb 2019 07:25:50: 47000000 INFO @ Fri, 15 Feb 2019 07:25:50: 48000000 INFO @ Fri, 15 Feb 2019 07:25:55: 50000000 INFO @ Fri, 15 Feb 2019 07:25:57: 49000000 INFO @ Fri, 15 Feb 2019 07:25:57: 48000000 INFO @ Fri, 15 Feb 2019 07:26:00: 51000000 INFO @ Fri, 15 Feb 2019 07:26:03: 50000000 INFO @ Fri, 15 Feb 2019 07:26:03: 49000000 INFO @ Fri, 15 Feb 2019 07:26:06: 52000000 INFO @ Fri, 15 Feb 2019 07:26:09: 51000000 INFO @ Fri, 15 Feb 2019 07:26:09: 50000000 INFO @ Fri, 15 Feb 2019 07:26:12: 53000000 INFO @ Fri, 15 Feb 2019 07:26:15: 52000000 INFO @ Fri, 15 Feb 2019 07:26:15: 51000000 INFO @ Fri, 15 Feb 2019 07:26:18: 54000000 INFO @ Fri, 15 Feb 2019 07:26:21: 53000000 INFO @ Fri, 15 Feb 2019 07:26:21: 52000000 INFO @ Fri, 15 Feb 2019 07:26:24: 55000000 INFO @ Fri, 15 Feb 2019 07:26:27: 54000000 INFO @ Fri, 15 Feb 2019 07:26:28: 53000000 INFO @ Fri, 15 Feb 2019 07:26:30: 56000000 INFO @ Fri, 15 Feb 2019 07:26:33: 55000000 INFO @ Fri, 15 Feb 2019 07:26:34: 54000000 INFO @ Fri, 15 Feb 2019 07:26:35: 57000000 INFO @ Fri, 15 Feb 2019 07:26:39: 56000000 INFO @ Fri, 15 Feb 2019 07:26:40: 55000000 INFO @ Fri, 15 Feb 2019 07:26:41: 58000000 INFO @ Fri, 15 Feb 2019 07:26:45: 57000000 INFO @ Fri, 15 Feb 2019 07:26:46: 56000000 INFO @ Fri, 15 Feb 2019 07:26:47: 59000000 INFO @ Fri, 15 Feb 2019 07:26:51: 58000000 INFO @ Fri, 15 Feb 2019 07:26:53: 57000000 INFO @ Fri, 15 Feb 2019 07:26:53: 60000000 INFO @ Fri, 15 Feb 2019 07:26:57: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:26:57: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:26:57: #1 total tags in treatment: 60525717 INFO @ Fri, 15 Feb 2019 07:26:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:26:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:26:57: 59000000 INFO @ Fri, 15 Feb 2019 07:26:58: #1 tags after filtering in treatment: 60525656 INFO @ Fri, 15 Feb 2019 07:26:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:26:58: #1 finished! INFO @ Fri, 15 Feb 2019 07:26:58: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:26:59: 58000000 INFO @ Fri, 15 Feb 2019 07:27:04: 60000000 INFO @ Fri, 15 Feb 2019 07:27:05: #2 number of paired peaks: 31079 INFO @ Fri, 15 Feb 2019 07:27:05: start model_add_line... INFO @ Fri, 15 Feb 2019 07:27:05: start X-correlation... INFO @ Fri, 15 Feb 2019 07:27:05: end of X-cor INFO @ Fri, 15 Feb 2019 07:27:05: #2 finished! INFO @ Fri, 15 Feb 2019 07:27:05: #2 predicted fragment length is 369 bps INFO @ Fri, 15 Feb 2019 07:27:05: #2 alternative fragment length(s) may be 369 bps INFO @ Fri, 15 Feb 2019 07:27:05: #2.2 Generate R script for model : SRX3782469.10_model.r INFO @ Fri, 15 Feb 2019 07:27:05: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:27:06: 59000000 INFO @ Fri, 15 Feb 2019 07:27:08: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:27:08: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:27:08: #1 total tags in treatment: 60525717 INFO @ Fri, 15 Feb 2019 07:27:08: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:27:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:27:10: #1 tags after filtering in treatment: 60525656 INFO @ Fri, 15 Feb 2019 07:27:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:27:10: #1 finished! INFO @ Fri, 15 Feb 2019 07:27:10: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:27:12: 60000000 INFO @ Fri, 15 Feb 2019 07:27:16: #2 number of paired peaks: 31079 INFO @ Fri, 15 Feb 2019 07:27:16: start model_add_line... INFO @ Fri, 15 Feb 2019 07:27:16: #1 tag size is determined as 40 bps INFO @ Fri, 15 Feb 2019 07:27:16: #1 tag size = 40 INFO @ Fri, 15 Feb 2019 07:27:16: #1 total tags in treatment: 60525717 INFO @ Fri, 15 Feb 2019 07:27:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:27:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:27:17: start X-correlation... INFO @ Fri, 15 Feb 2019 07:27:17: end of X-cor INFO @ Fri, 15 Feb 2019 07:27:17: #2 finished! INFO @ Fri, 15 Feb 2019 07:27:17: #2 predicted fragment length is 369 bps INFO @ Fri, 15 Feb 2019 07:27:17: #2 alternative fragment length(s) may be 369 bps INFO @ Fri, 15 Feb 2019 07:27:17: #2.2 Generate R script for model : SRX3782469.05_model.r INFO @ Fri, 15 Feb 2019 07:27:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:27:18: #1 tags after filtering in treatment: 60525656 INFO @ Fri, 15 Feb 2019 07:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:27:18: #1 finished! INFO @ Fri, 15 Feb 2019 07:27:18: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:27:24: #2 number of paired peaks: 31079 INFO @ Fri, 15 Feb 2019 07:27:24: start model_add_line... INFO @ Fri, 15 Feb 2019 07:27:25: start X-correlation... INFO @ Fri, 15 Feb 2019 07:27:25: end of X-cor INFO @ Fri, 15 Feb 2019 07:27:25: #2 finished! INFO @ Fri, 15 Feb 2019 07:27:25: #2 predicted fragment length is 369 bps INFO @ Fri, 15 Feb 2019 07:27:25: #2 alternative fragment length(s) may be 369 bps INFO @ Fri, 15 Feb 2019 07:27:25: #2.2 Generate R script for model : SRX3782469.20_model.r INFO @ Fri, 15 Feb 2019 07:27:25: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:27:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:29:48: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:29:54: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:30:26: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:31:20: #4 Write output xls file... SRX3782469.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:31:20: #4 Write peak in narrowPeak format file... SRX3782469.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:31:21: #4 Write summits bed file... SRX3782469.10_summits.bed INFO @ Fri, 15 Feb 2019 07:31:21: Done! pass1 - making usageList (81 chroms): 3 millis pass2 - checking and writing primary data (13142 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:31:23: #4 Write output xls file... SRX3782469.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:31:23: #4 Write peak in narrowPeak format file... SRX3782469.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:31:23: #4 Write summits bed file... SRX3782469.05_summits.bed INFO @ Fri, 15 Feb 2019 07:31:23: Done! pass1 - making usageList (101 chroms): 4 millis pass2 - checking and writing primary data (16985 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:31:56: #4 Write output xls file... SRX3782469.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:31:56: #4 Write peak in narrowPeak format file... SRX3782469.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:31:56: #4 Write summits bed file... SRX3782469.20_summits.bed INFO @ Fri, 15 Feb 2019 07:31:56: Done! pass1 - making usageList (60 chroms): 5 millis pass2 - checking and writing primary data (9700 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。