Job ID = 10194801 sra ファイルのダウンロード中... Completed: 1993324K bytes transferred in 27 seconds (587886K 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 70880928 spots for /home/okishinya/chipatlas/results/rn6/SRX1819027/SRR3624103.sra Written 70880928 spots total 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: 01:00:52 70880928 reads; of these: 70880928 (100.00%) were unpaired; of these: 5125281 (7.23%) aligned 0 times 49951401 (70.47%) aligned exactly 1 time 15804246 (22.30%) aligned >1 times 92.77% overall alignment rate Time searching: 01:00:57 Overall time: 01:00:57 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 20 files... [bam_rmdupse_core] 10756312 / 65755647 = 0.1636 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, 10 Nov 2017 22:23:15: # Command line: callpeak -t SRX1819027.bam -f BAM -g 2.15e9 -n SRX1819027.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1819027.05 # format = BAM # ChIP-seq file = ['SRX1819027.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, 10 Nov 2017 22:23:15: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:23:15: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:23:15: # Command line: callpeak -t SRX1819027.bam -f BAM -g 2.15e9 -n SRX1819027.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1819027.10 # format = BAM # ChIP-seq file = ['SRX1819027.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, 10 Nov 2017 22:23:15: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:23:15: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:23:15: # Command line: callpeak -t SRX1819027.bam -f BAM -g 2.15e9 -n SRX1819027.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1819027.20 # format = BAM # ChIP-seq file = ['SRX1819027.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, 10 Nov 2017 22:23:15: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:23:15: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:23:23: 1000000 INFO @ Fri, 10 Nov 2017 22:23:24: 1000000 INFO @ Fri, 10 Nov 2017 22:23:24: 1000000 INFO @ Fri, 10 Nov 2017 22:23:32: 2000000 INFO @ Fri, 10 Nov 2017 22:23:32: 2000000 INFO @ Fri, 10 Nov 2017 22:23:32: 2000000 INFO @ Fri, 10 Nov 2017 22:23:40: 3000000 INFO @ Fri, 10 Nov 2017 22:23:41: 3000000 INFO @ Fri, 10 Nov 2017 22:23:41: 3000000 INFO @ Fri, 10 Nov 2017 22:23:48: 4000000 INFO @ Fri, 10 Nov 2017 22:23:49: 4000000 INFO @ Fri, 10 Nov 2017 22:23:49: 4000000 INFO @ Fri, 10 Nov 2017 22:23:56: 5000000 INFO @ Fri, 10 Nov 2017 22:23:58: 5000000 INFO @ Fri, 10 Nov 2017 22:23:58: 5000000 INFO @ Fri, 10 Nov 2017 22:24:04: 6000000 INFO @ Fri, 10 Nov 2017 22:24:06: 6000000 INFO @ Fri, 10 Nov 2017 22:24:06: 6000000 INFO @ Fri, 10 Nov 2017 22:24:12: 7000000 INFO @ Fri, 10 Nov 2017 22:24:15: 7000000 INFO @ Fri, 10 Nov 2017 22:24:15: 7000000 INFO @ Fri, 10 Nov 2017 22:24:20: 8000000 INFO @ Fri, 10 Nov 2017 22:24:24: 8000000 INFO @ Fri, 10 Nov 2017 22:24:24: 8000000 INFO @ Fri, 10 Nov 2017 22:24:28: 9000000 INFO @ Fri, 10 Nov 2017 22:24:32: 9000000 INFO @ Fri, 10 Nov 2017 22:24:32: 9000000 INFO @ Fri, 10 Nov 2017 22:24:36: 10000000 INFO @ Fri, 10 Nov 2017 22:24:40: 10000000 INFO @ Fri, 10 Nov 2017 22:24:40: 10000000 INFO @ Fri, 10 Nov 2017 22:24:44: 11000000 INFO @ Fri, 10 Nov 2017 22:24:49: 11000000 INFO @ Fri, 10 Nov 2017 22:24:49: 11000000 INFO @ Fri, 10 Nov 2017 22:24:52: 12000000 INFO @ Fri, 10 Nov 2017 22:24:57: 12000000 INFO @ Fri, 10 Nov 2017 22:24:57: 12000000 INFO @ Fri, 10 Nov 2017 22:25:01: 13000000 INFO @ Fri, 10 Nov 2017 22:25:06: 13000000 INFO @ Fri, 10 Nov 2017 22:25:06: 13000000 INFO @ Fri, 10 Nov 2017 22:25:09: 14000000 INFO @ Fri, 10 Nov 2017 22:25:14: 14000000 INFO @ Fri, 10 Nov 2017 22:25:14: 14000000 INFO @ Fri, 10 Nov 2017 22:25:17: 15000000 INFO @ Fri, 10 Nov 2017 22:25:22: 15000000 INFO @ Fri, 10 Nov 2017 22:25:22: 15000000 INFO @ Fri, 10 Nov 2017 22:25:25: 16000000 INFO @ Fri, 10 Nov 2017 22:25:31: 16000000 INFO @ Fri, 10 Nov 2017 22:25:31: 16000000 INFO @ Fri, 10 Nov 2017 22:25:33: 17000000 INFO @ Fri, 10 Nov 2017 22:25:39: 17000000 INFO @ Fri, 10 Nov 2017 22:25:39: 17000000 INFO @ Fri, 10 Nov 2017 22:25:41: 18000000 INFO @ Fri, 10 Nov 2017 22:25:47: 18000000 INFO @ Fri, 10 Nov 2017 22:25:47: 18000000 INFO @ Fri, 10 Nov 2017 22:25:49: 19000000 INFO @ Fri, 10 Nov 2017 22:25:56: 19000000 INFO @ Fri, 10 Nov 2017 22:25:56: 19000000 INFO @ Fri, 10 Nov 2017 22:25:57: 20000000 INFO @ Fri, 10 Nov 2017 22:26:04: 20000000 INFO @ Fri, 10 Nov 2017 22:26:04: 20000000 INFO @ Fri, 10 Nov 2017 22:26:05: 21000000 INFO @ Fri, 10 Nov 2017 22:26:13: 21000000 INFO @ Fri, 10 Nov 2017 22:26:13: 21000000 INFO @ Fri, 10 Nov 2017 22:26:13: 22000000 INFO @ Fri, 10 Nov 2017 22:26:21: 23000000 INFO @ Fri, 10 Nov 2017 22:26:22: 22000000 INFO @ Fri, 10 Nov 2017 22:26:22: 22000000 INFO @ Fri, 10 Nov 2017 22:26:29: 24000000 INFO @ Fri, 10 Nov 2017 22:26:30: 23000000 INFO @ Fri, 10 Nov 2017 22:26:30: 23000000 INFO @ Fri, 10 Nov 2017 22:26:37: 25000000 INFO @ Fri, 10 Nov 2017 22:26:39: 24000000 INFO @ Fri, 10 Nov 2017 22:26:39: 24000000 INFO @ Fri, 10 Nov 2017 22:26:46: 26000000 INFO @ Fri, 10 Nov 2017 22:26:47: 25000000 INFO @ Fri, 10 Nov 2017 22:26:47: 25000000 INFO @ Fri, 10 Nov 2017 22:26:54: 27000000 INFO @ Fri, 10 Nov 2017 22:26:56: 26000000 INFO @ Fri, 10 Nov 2017 22:26:56: 26000000 INFO @ Fri, 10 Nov 2017 22:27:02: 28000000 INFO @ Fri, 10 Nov 2017 22:27:04: 27000000 INFO @ Fri, 10 Nov 2017 22:27:04: 27000000 INFO @ Fri, 10 Nov 2017 22:27:10: 29000000 INFO @ Fri, 10 Nov 2017 22:27:12: 28000000 INFO @ Fri, 10 Nov 2017 22:27:12: 28000000 INFO @ Fri, 10 Nov 2017 22:27:18: 30000000 INFO @ Fri, 10 Nov 2017 22:27:20: 29000000 INFO @ Fri, 10 Nov 2017 22:27:20: 29000000 INFO @ Fri, 10 Nov 2017 22:27:26: 31000000 INFO @ Fri, 10 Nov 2017 22:27:28: 30000000 INFO @ Fri, 10 Nov 2017 22:27:28: 30000000 INFO @ Fri, 10 Nov 2017 22:27:33: 32000000 INFO @ Fri, 10 Nov 2017 22:27:36: 31000000 INFO @ Fri, 10 Nov 2017 22:27:36: 31000000 INFO @ Fri, 10 Nov 2017 22:27:41: 33000000 INFO @ Fri, 10 Nov 2017 22:27:44: 32000000 INFO @ Fri, 10 Nov 2017 22:27:44: 32000000 INFO @ Fri, 10 Nov 2017 22:27:49: 34000000 INFO @ Fri, 10 Nov 2017 22:27:51: 33000000 INFO @ Fri, 10 Nov 2017 22:27:51: 33000000 INFO @ Fri, 10 Nov 2017 22:27:57: 35000000 INFO @ Fri, 10 Nov 2017 22:27:59: 34000000 INFO @ Fri, 10 Nov 2017 22:27:59: 34000000 INFO @ Fri, 10 Nov 2017 22:28:05: 36000000 INFO @ Fri, 10 Nov 2017 22:28:07: 35000000 INFO @ Fri, 10 Nov 2017 22:28:07: 35000000 INFO @ Fri, 10 Nov 2017 22:28:13: 37000000 INFO @ Fri, 10 Nov 2017 22:28:15: 36000000 INFO @ Fri, 10 Nov 2017 22:28:15: 36000000 INFO @ Fri, 10 Nov 2017 22:28:21: 38000000 INFO @ Fri, 10 Nov 2017 22:28:23: 37000000 INFO @ Fri, 10 Nov 2017 22:28:23: 37000000 INFO @ Fri, 10 Nov 2017 22:28:29: 39000000 INFO @ Fri, 10 Nov 2017 22:28:32: 38000000 INFO @ Fri, 10 Nov 2017 22:28:32: 38000000 INFO @ Fri, 10 Nov 2017 22:28:37: 40000000 INFO @ Fri, 10 Nov 2017 22:28:39: 39000000 INFO @ Fri, 10 Nov 2017 22:28:39: 39000000 INFO @ Fri, 10 Nov 2017 22:28:45: 41000000 INFO @ Fri, 10 Nov 2017 22:28:47: 40000000 INFO @ Fri, 10 Nov 2017 22:28:47: 40000000 INFO @ Fri, 10 Nov 2017 22:28:53: 42000000 INFO @ Fri, 10 Nov 2017 22:28:55: 41000000 INFO @ Fri, 10 Nov 2017 22:28:55: 41000000 INFO @ Fri, 10 Nov 2017 22:29:01: 43000000 INFO @ Fri, 10 Nov 2017 22:29:03: 42000000 INFO @ Fri, 10 Nov 2017 22:29:03: 42000000 INFO @ Fri, 10 Nov 2017 22:29:09: 44000000 INFO @ Fri, 10 Nov 2017 22:29:12: 43000000 INFO @ Fri, 10 Nov 2017 22:29:12: 43000000 INFO @ Fri, 10 Nov 2017 22:29:18: 45000000 INFO @ Fri, 10 Nov 2017 22:29:20: 44000000 INFO @ Fri, 10 Nov 2017 22:29:20: 44000000 INFO @ Fri, 10 Nov 2017 22:29:26: 46000000 INFO @ Fri, 10 Nov 2017 22:29:28: 45000000 INFO @ Fri, 10 Nov 2017 22:29:28: 45000000 INFO @ Fri, 10 Nov 2017 22:29:34: 47000000 INFO @ Fri, 10 Nov 2017 22:29:37: 46000000 INFO @ Fri, 10 Nov 2017 22:29:37: 46000000 INFO @ Fri, 10 Nov 2017 22:29:44: 48000000 INFO @ Fri, 10 Nov 2017 22:29:45: 47000000 INFO @ Fri, 10 Nov 2017 22:29:45: 47000000 INFO @ Fri, 10 Nov 2017 22:29:53: 48000000 INFO @ Fri, 10 Nov 2017 22:29:53: 48000000 INFO @ Fri, 10 Nov 2017 22:29:54: 49000000 INFO @ Fri, 10 Nov 2017 22:30:01: 49000000 INFO @ Fri, 10 Nov 2017 22:30:01: 49000000 INFO @ Fri, 10 Nov 2017 22:30:03: 50000000 INFO @ Fri, 10 Nov 2017 22:30:10: 50000000 INFO @ Fri, 10 Nov 2017 22:30:10: 50000000 INFO @ Fri, 10 Nov 2017 22:30:12: 51000000 INFO @ Fri, 10 Nov 2017 22:30:18: 51000000 INFO @ Fri, 10 Nov 2017 22:30:18: 51000000 INFO @ Fri, 10 Nov 2017 22:30:21: 52000000 INFO @ Fri, 10 Nov 2017 22:30:26: 52000000 INFO @ Fri, 10 Nov 2017 22:30:26: 52000000 INFO @ Fri, 10 Nov 2017 22:30:30: 53000000 INFO @ Fri, 10 Nov 2017 22:30:36: 53000000 INFO @ Fri, 10 Nov 2017 22:30:36: 53000000 INFO @ Fri, 10 Nov 2017 22:30:39: 54000000 INFO @ Fri, 10 Nov 2017 22:30:44: 54000000 INFO @ Fri, 10 Nov 2017 22:30:44: 54000000 INFO @ Fri, 10 Nov 2017 22:30:49: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 22:30:49: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 22:30:49: #1 total tags in treatment: 54999335 INFO @ Fri, 10 Nov 2017 22:30:49: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:30:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:30:51: #1 tags after filtering in treatment: 54999271 INFO @ Fri, 10 Nov 2017 22:30:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:30:51: #1 finished! INFO @ Fri, 10 Nov 2017 22:30:51: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:30:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:30:53: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 22:30:53: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 22:30:53: #1 total tags in treatment: 54999335 INFO @ Fri, 10 Nov 2017 22:30:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:30:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:30:53: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 22:30:53: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 22:30:53: #1 total tags in treatment: 54999335 INFO @ Fri, 10 Nov 2017 22:30:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:30:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 22:30:55: #1 tags after filtering in treatment: 54999271 INFO @ Fri, 10 Nov 2017 22:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:30:55: #1 finished! INFO @ Fri, 10 Nov 2017 22:30:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:30:55: #1 tags after filtering in treatment: 54999271 INFO @ Fri, 10 Nov 2017 22:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:30:55: #1 finished! INFO @ Fri, 10 Nov 2017 22:30:55: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:30:57: #2 number of paired peaks: 18570 INFO @ Fri, 10 Nov 2017 22:30:57: start model_add_line... INFO @ Fri, 10 Nov 2017 22:30:58: start X-correlation... INFO @ Fri, 10 Nov 2017 22:30:58: end of X-cor INFO @ Fri, 10 Nov 2017 22:30:58: #2 finished! INFO @ Fri, 10 Nov 2017 22:30:58: #2 predicted fragment length is 247 bps INFO @ Fri, 10 Nov 2017 22:30:58: #2 alternative fragment length(s) may be 247 bps INFO @ Fri, 10 Nov 2017 22:30:58: #2.2 Generate R script for model : SRX1819027.20_model.r INFO @ Fri, 10 Nov 2017 22:30:58: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:31:02: #2 number of paired peaks: 18570 INFO @ Fri, 10 Nov 2017 22:31:02: start model_add_line... INFO @ Fri, 10 Nov 2017 22:31:02: #2 number of paired peaks: 18570 INFO @ Fri, 10 Nov 2017 22:31:02: start model_add_line... INFO @ Fri, 10 Nov 2017 22:31:03: start X-correlation... INFO @ Fri, 10 Nov 2017 22:31:03: end of X-cor INFO @ Fri, 10 Nov 2017 22:31:03: #2 finished! INFO @ Fri, 10 Nov 2017 22:31:03: #2 predicted fragment length is 247 bps INFO @ Fri, 10 Nov 2017 22:31:03: #2 alternative fragment length(s) may be 247 bps INFO @ Fri, 10 Nov 2017 22:31:03: #2.2 Generate R script for model : SRX1819027.05_model.r INFO @ Fri, 10 Nov 2017 22:31:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:31:03: start X-correlation... INFO @ Fri, 10 Nov 2017 22:31:03: end of X-cor INFO @ Fri, 10 Nov 2017 22:31:03: #2 finished! INFO @ Fri, 10 Nov 2017 22:31:03: #2 predicted fragment length is 247 bps INFO @ Fri, 10 Nov 2017 22:31:03: #2 alternative fragment length(s) may be 247 bps INFO @ Fri, 10 Nov 2017 22:31:03: #2.2 Generate R script for model : SRX1819027.10_model.r INFO @ Fri, 10 Nov 2017 22:31:03: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:33:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:33:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:33:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:35:27: #4 Write output xls file... SRX1819027.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:35:27: #4 Write peak in narrowPeak format file... SRX1819027.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:35:27: #4 Write summits bed file... SRX1819027.20_summits.bed INFO @ Fri, 10 Nov 2017 22:35:27: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (2282 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:35:31: #4 Write output xls file... SRX1819027.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:35:31: #4 Write peak in narrowPeak format file... SRX1819027.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:35:31: #4 Write summits bed file... SRX1819027.10_summits.bed INFO @ Fri, 10 Nov 2017 22:35:31: Done! pass1 - making usageList (54 chroms): 3 millis pass2 - checking and writing primary data (8091 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:36:03: #4 Write output xls file... SRX1819027.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:36:03: #4 Write peak in narrowPeak format file... SRX1819027.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:36:03: #4 Write summits bed file... SRX1819027.05_summits.bed INFO @ Fri, 10 Nov 2017 22:36:03: Done! pass1 - making usageList (82 chroms): 6 millis pass2 - checking and writing primary data (17473 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。