Job ID = 10453670 sra ファイルのダウンロード中... Completed: 689559K bytes transferred in 20 seconds (277705K 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... Written 38920312 spots for /home/okishinya/chipatlas/results/rn6/SRX3478275/SRR6384654.sra Written 38920312 spots total rm: cannot remove `[DSE]RX*': No such file or directory rm: cannot remove `[DSE]RR*.fastq': 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:10:53 38920312 reads; of these: 38920312 (100.00%) were unpaired; of these: 1783214 (4.58%) aligned 0 times 26700353 (68.60%) aligned exactly 1 time 10436745 (26.82%) aligned >1 times 95.42% overall alignment rate Time searching: 01:10:57 Overall time: 01:10:57 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] 6175331 / 37137098 = 0.1663 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 @ Thu, 08 Feb 2018 18:24:37: # Command line: callpeak -t SRX3478275.bam -f BAM -g 2.15e9 -n SRX3478275.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478275.10 # format = BAM # ChIP-seq file = ['SRX3478275.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 @ Thu, 08 Feb 2018 18:24:37: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:24:37: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:24:37: # Command line: callpeak -t SRX3478275.bam -f BAM -g 2.15e9 -n SRX3478275.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478275.20 # format = BAM # ChIP-seq file = ['SRX3478275.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 @ Thu, 08 Feb 2018 18:24:37: # Command line: callpeak -t SRX3478275.bam -f BAM -g 2.15e9 -n SRX3478275.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478275.05 # format = BAM # ChIP-seq file = ['SRX3478275.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 @ Thu, 08 Feb 2018 18:24:37: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:24:37: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:24:37: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:24:37: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:24:47: 1000000 INFO @ Thu, 08 Feb 2018 18:24:47: 1000000 INFO @ Thu, 08 Feb 2018 18:24:54: 1000000 INFO @ Thu, 08 Feb 2018 18:24:56: 2000000 INFO @ Thu, 08 Feb 2018 18:24:56: 2000000 INFO @ Thu, 08 Feb 2018 18:25:05: 3000000 INFO @ Thu, 08 Feb 2018 18:25:05: 3000000 INFO @ Thu, 08 Feb 2018 18:25:11: 2000000 INFO @ Thu, 08 Feb 2018 18:25:14: 4000000 INFO @ Thu, 08 Feb 2018 18:25:14: 4000000 INFO @ Thu, 08 Feb 2018 18:25:23: 5000000 INFO @ Thu, 08 Feb 2018 18:25:23: 5000000 INFO @ Thu, 08 Feb 2018 18:25:30: 3000000 INFO @ Thu, 08 Feb 2018 18:25:32: 6000000 INFO @ Thu, 08 Feb 2018 18:25:32: 6000000 INFO @ Thu, 08 Feb 2018 18:25:41: 7000000 INFO @ Thu, 08 Feb 2018 18:25:41: 7000000 INFO @ Thu, 08 Feb 2018 18:25:49: 4000000 INFO @ Thu, 08 Feb 2018 18:25:50: 8000000 INFO @ Thu, 08 Feb 2018 18:25:50: 8000000 INFO @ Thu, 08 Feb 2018 18:25:59: 9000000 INFO @ Thu, 08 Feb 2018 18:25:59: 9000000 INFO @ Thu, 08 Feb 2018 18:26:08: 5000000 INFO @ Thu, 08 Feb 2018 18:26:08: 10000000 INFO @ Thu, 08 Feb 2018 18:26:08: 10000000 INFO @ Thu, 08 Feb 2018 18:26:18: 11000000 INFO @ Thu, 08 Feb 2018 18:26:18: 11000000 INFO @ Thu, 08 Feb 2018 18:26:27: 6000000 INFO @ Thu, 08 Feb 2018 18:26:27: 12000000 INFO @ Thu, 08 Feb 2018 18:26:27: 12000000 INFO @ Thu, 08 Feb 2018 18:26:37: 13000000 INFO @ Thu, 08 Feb 2018 18:26:37: 13000000 INFO @ Thu, 08 Feb 2018 18:26:47: 14000000 INFO @ Thu, 08 Feb 2018 18:26:47: 14000000 INFO @ Thu, 08 Feb 2018 18:26:47: 7000000 INFO @ Thu, 08 Feb 2018 18:26:56: 15000000 INFO @ Thu, 08 Feb 2018 18:26:56: 15000000 INFO @ Thu, 08 Feb 2018 18:27:05: 16000000 INFO @ Thu, 08 Feb 2018 18:27:05: 16000000 INFO @ Thu, 08 Feb 2018 18:27:07: 8000000 INFO @ Thu, 08 Feb 2018 18:27:15: 17000000 INFO @ Thu, 08 Feb 2018 18:27:15: 17000000 INFO @ Thu, 08 Feb 2018 18:27:25: 18000000 INFO @ Thu, 08 Feb 2018 18:27:25: 18000000 INFO @ Thu, 08 Feb 2018 18:27:26: 9000000 INFO @ Thu, 08 Feb 2018 18:27:35: 19000000 INFO @ Thu, 08 Feb 2018 18:27:35: 19000000 INFO @ Thu, 08 Feb 2018 18:27:45: 20000000 INFO @ Thu, 08 Feb 2018 18:27:45: 20000000 INFO @ Thu, 08 Feb 2018 18:27:47: 10000000 INFO @ Thu, 08 Feb 2018 18:27:54: 21000000 INFO @ Thu, 08 Feb 2018 18:27:55: 21000000 INFO @ Thu, 08 Feb 2018 18:28:04: 22000000 INFO @ Thu, 08 Feb 2018 18:28:04: 22000000 INFO @ Thu, 08 Feb 2018 18:28:08: 11000000 INFO @ Thu, 08 Feb 2018 18:28:13: 23000000 INFO @ Thu, 08 Feb 2018 18:28:13: 23000000 INFO @ Thu, 08 Feb 2018 18:28:23: 24000000 INFO @ Thu, 08 Feb 2018 18:28:23: 24000000 INFO @ Thu, 08 Feb 2018 18:28:27: 12000000 INFO @ Thu, 08 Feb 2018 18:28:32: 25000000 INFO @ Thu, 08 Feb 2018 18:28:32: 25000000 INFO @ Thu, 08 Feb 2018 18:28:42: 26000000 INFO @ Thu, 08 Feb 2018 18:28:42: 26000000 INFO @ Thu, 08 Feb 2018 18:28:45: 13000000 INFO @ Thu, 08 Feb 2018 18:28:56: 27000000 INFO @ Thu, 08 Feb 2018 18:28:56: 27000000 INFO @ Thu, 08 Feb 2018 18:29:04: 14000000 INFO @ Thu, 08 Feb 2018 18:29:10: 28000000 INFO @ Thu, 08 Feb 2018 18:29:10: 28000000 INFO @ Thu, 08 Feb 2018 18:29:24: 29000000 INFO @ Thu, 08 Feb 2018 18:29:24: 29000000 INFO @ Thu, 08 Feb 2018 18:29:24: 15000000 INFO @ Thu, 08 Feb 2018 18:29:36: 30000000 INFO @ Thu, 08 Feb 2018 18:29:36: 30000000 INFO @ Thu, 08 Feb 2018 18:29:44: 16000000 INFO @ Thu, 08 Feb 2018 18:29:46: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:29:46: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:29:46: #1 total tags in treatment: 30961767 INFO @ Thu, 08 Feb 2018 18:29:46: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:29:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:29:46: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:29:46: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:29:46: #1 total tags in treatment: 30961767 INFO @ Thu, 08 Feb 2018 18:29:46: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:29:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:29:47: #1 tags after filtering in treatment: 30961656 INFO @ Thu, 08 Feb 2018 18:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:29:47: #1 finished! INFO @ Thu, 08 Feb 2018 18:29:47: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:29:47: #1 tags after filtering in treatment: 30961656 INFO @ Thu, 08 Feb 2018 18:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:29:47: #1 finished! INFO @ Thu, 08 Feb 2018 18:29:47: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:29:53: #2 number of paired peaks: 57306 INFO @ Thu, 08 Feb 2018 18:29:53: start model_add_line... INFO @ Thu, 08 Feb 2018 18:29:54: #2 number of paired peaks: 57306 INFO @ Thu, 08 Feb 2018 18:29:54: start model_add_line... INFO @ Thu, 08 Feb 2018 18:29:54: start X-correlation... INFO @ Thu, 08 Feb 2018 18:29:54: end of X-cor INFO @ Thu, 08 Feb 2018 18:29:54: #2 finished! INFO @ Thu, 08 Feb 2018 18:29:54: #2 predicted fragment length is 151 bps INFO @ Thu, 08 Feb 2018 18:29:54: #2 alternative fragment length(s) may be 2,151,256,272 bps INFO @ Thu, 08 Feb 2018 18:29:54: #2.2 Generate R script for model : SRX3478275.05_model.r INFO @ Thu, 08 Feb 2018 18:29:54: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:29:54: start X-correlation... INFO @ Thu, 08 Feb 2018 18:29:54: end of X-cor INFO @ Thu, 08 Feb 2018 18:29:54: #2 finished! INFO @ Thu, 08 Feb 2018 18:29:54: #2 predicted fragment length is 151 bps INFO @ Thu, 08 Feb 2018 18:29:54: #2 alternative fragment length(s) may be 2,151,256,272 bps INFO @ Thu, 08 Feb 2018 18:29:54: #2.2 Generate R script for model : SRX3478275.10_model.r INFO @ Thu, 08 Feb 2018 18:29:54: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:30:04: 17000000 INFO @ Thu, 08 Feb 2018 18:30:24: 18000000 INFO @ Thu, 08 Feb 2018 18:30:45: 19000000 INFO @ Thu, 08 Feb 2018 18:31:06: 20000000 INFO @ Thu, 08 Feb 2018 18:31:24: 21000000 INFO @ Thu, 08 Feb 2018 18:31:43: 22000000 INFO @ Thu, 08 Feb 2018 18:32:04: 23000000 INFO @ Thu, 08 Feb 2018 18:32:23: 24000000 INFO @ Thu, 08 Feb 2018 18:32:31: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:32:38: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:32:42: 25000000 INFO @ Thu, 08 Feb 2018 18:33:00: 26000000 INFO @ Thu, 08 Feb 2018 18:33:19: 27000000 INFO @ Thu, 08 Feb 2018 18:33:38: 28000000 INFO @ Thu, 08 Feb 2018 18:33:40: #4 Write output xls file... SRX3478275.05_peaks.xls INFO @ Thu, 08 Feb 2018 18:33:40: #4 Write peak in narrowPeak format file... SRX3478275.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:33:40: #4 Write summits bed file... SRX3478275.05_summits.bed INFO @ Thu, 08 Feb 2018 18:33:40: Done! pass1 - making usageList (98 chroms): 4 millis pass2 - checking and writing primary data (11173 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:33:54: #4 Write output xls file... SRX3478275.10_peaks.xls INFO @ Thu, 08 Feb 2018 18:33:54: #4 Write peak in narrowPeak format file... SRX3478275.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:33:54: #4 Write summits bed file... SRX3478275.10_summits.bed INFO @ Thu, 08 Feb 2018 18:33:54: Done! pass1 - making usageList (54 chroms): 3 millis pass2 - checking and writing primary data (2027 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:33:57: 29000000 INFO @ Thu, 08 Feb 2018 18:34:15: 30000000 INFO @ Thu, 08 Feb 2018 18:34:32: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:34:32: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:34:32: #1 total tags in treatment: 30961767 INFO @ Thu, 08 Feb 2018 18:34:32: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:34:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:34:34: #1 tags after filtering in treatment: 30961656 INFO @ Thu, 08 Feb 2018 18:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:34:34: #1 finished! INFO @ Thu, 08 Feb 2018 18:34:34: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:34:40: #2 number of paired peaks: 57306 INFO @ Thu, 08 Feb 2018 18:34:40: start model_add_line... INFO @ Thu, 08 Feb 2018 18:34:41: start X-correlation... INFO @ Thu, 08 Feb 2018 18:34:41: end of X-cor INFO @ Thu, 08 Feb 2018 18:34:41: #2 finished! INFO @ Thu, 08 Feb 2018 18:34:41: #2 predicted fragment length is 151 bps INFO @ Thu, 08 Feb 2018 18:34:41: #2 alternative fragment length(s) may be 2,151,256,272 bps INFO @ Thu, 08 Feb 2018 18:34:41: #2.2 Generate R script for model : SRX3478275.20_model.r INFO @ Thu, 08 Feb 2018 18:34:41: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:36:23: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:37:21: #4 Write output xls file... SRX3478275.20_peaks.xls INFO @ Thu, 08 Feb 2018 18:37:21: #4 Write peak in narrowPeak format file... SRX3478275.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:37:21: #4 Write summits bed file... SRX3478275.20_summits.bed INFO @ Thu, 08 Feb 2018 18:37:21: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (384 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。