Job ID = 10194930 sra ファイルのダウンロード中... Completed: 611948K bytes transferred in 10 seconds (497424K bits/sec), in 1 file. Completed: 1605459K bytes transferred in 23 seconds (564642K 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 17302977 spots for /home/okishinya/chipatlas/results/rn6/SRX2224392/SRR4370053.sra Written 17302977 spots total Written 45094539 spots for /home/okishinya/chipatlas/results/rn6/SRX2224392/SRR4370054.sra Written 45094539 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 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: 01:25:21 62397516 reads; of these: 62397516 (100.00%) were unpaired; of these: 10585172 (16.96%) aligned 0 times 36164480 (57.96%) aligned exactly 1 time 15647864 (25.08%) aligned >1 times 83.04% overall alignment rate Time searching: 01:25:25 Overall time: 01:25:25 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 24 files... [bam_rmdupse_core] 7092635 / 51812344 = 0.1369 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 @ Sat, 11 Nov 2017 01:23:39: # Command line: callpeak -t SRX2224392.bam -f BAM -g 2.15e9 -n SRX2224392.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2224392.20 # format = BAM # ChIP-seq file = ['SRX2224392.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 @ Sat, 11 Nov 2017 01:23:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:23:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:23:39: # Command line: callpeak -t SRX2224392.bam -f BAM -g 2.15e9 -n SRX2224392.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2224392.10 # format = BAM # ChIP-seq file = ['SRX2224392.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 @ Sat, 11 Nov 2017 01:23:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:23:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:23:39: # Command line: callpeak -t SRX2224392.bam -f BAM -g 2.15e9 -n SRX2224392.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2224392.05 # format = BAM # ChIP-seq file = ['SRX2224392.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 @ Sat, 11 Nov 2017 01:23:39: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:23:39: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:23:47: 1000000 INFO @ Sat, 11 Nov 2017 01:23:51: 1000000 INFO @ Sat, 11 Nov 2017 01:23:55: 2000000 INFO @ Sat, 11 Nov 2017 01:23:55: 1000000 INFO @ Sat, 11 Nov 2017 01:24:04: 3000000 INFO @ Sat, 11 Nov 2017 01:24:05: 2000000 INFO @ Sat, 11 Nov 2017 01:24:09: 2000000 INFO @ Sat, 11 Nov 2017 01:24:14: 4000000 INFO @ Sat, 11 Nov 2017 01:24:20: 3000000 INFO @ Sat, 11 Nov 2017 01:24:22: 3000000 INFO @ Sat, 11 Nov 2017 01:24:25: 5000000 INFO @ Sat, 11 Nov 2017 01:24:35: 4000000 INFO @ Sat, 11 Nov 2017 01:24:37: 4000000 INFO @ Sat, 11 Nov 2017 01:24:45: 6000000 INFO @ Sat, 11 Nov 2017 01:24:47: 5000000 INFO @ Sat, 11 Nov 2017 01:24:54: 5000000 INFO @ Sat, 11 Nov 2017 01:25:03: 6000000 INFO @ Sat, 11 Nov 2017 01:25:05: 7000000 INFO @ Sat, 11 Nov 2017 01:25:09: 6000000 INFO @ Sat, 11 Nov 2017 01:25:18: 7000000 INFO @ Sat, 11 Nov 2017 01:25:22: 7000000 INFO @ Sat, 11 Nov 2017 01:25:25: 8000000 INFO @ Sat, 11 Nov 2017 01:25:32: 8000000 INFO @ Sat, 11 Nov 2017 01:25:35: 8000000 INFO @ Sat, 11 Nov 2017 01:25:43: 9000000 INFO @ Sat, 11 Nov 2017 01:25:44: 9000000 INFO @ Sat, 11 Nov 2017 01:25:50: 9000000 INFO @ Sat, 11 Nov 2017 01:25:55: 10000000 INFO @ Sat, 11 Nov 2017 01:26:03: 10000000 INFO @ Sat, 11 Nov 2017 01:26:05: 10000000 INFO @ Sat, 11 Nov 2017 01:26:07: 11000000 INFO @ Sat, 11 Nov 2017 01:26:15: 11000000 INFO @ Sat, 11 Nov 2017 01:26:18: 11000000 INFO @ Sat, 11 Nov 2017 01:26:18: 12000000 INFO @ Sat, 11 Nov 2017 01:26:24: 12000000 INFO @ Sat, 11 Nov 2017 01:26:32: 13000000 INFO @ Sat, 11 Nov 2017 01:26:33: 12000000 INFO @ Sat, 11 Nov 2017 01:26:34: 13000000 INFO @ Sat, 11 Nov 2017 01:26:44: 14000000 INFO @ Sat, 11 Nov 2017 01:26:45: 13000000 INFO @ Sat, 11 Nov 2017 01:26:47: 14000000 INFO @ Sat, 11 Nov 2017 01:26:56: 15000000 INFO @ Sat, 11 Nov 2017 01:26:56: 14000000 INFO @ Sat, 11 Nov 2017 01:27:01: 15000000 INFO @ Sat, 11 Nov 2017 01:27:06: 15000000 INFO @ Sat, 11 Nov 2017 01:27:07: 16000000 INFO @ Sat, 11 Nov 2017 01:27:15: 16000000 INFO @ Sat, 11 Nov 2017 01:27:16: 16000000 INFO @ Sat, 11 Nov 2017 01:27:18: 17000000 INFO @ Sat, 11 Nov 2017 01:27:26: 17000000 INFO @ Sat, 11 Nov 2017 01:27:30: 18000000 INFO @ Sat, 11 Nov 2017 01:27:30: 17000000 INFO @ Sat, 11 Nov 2017 01:27:39: 18000000 INFO @ Sat, 11 Nov 2017 01:27:43: 19000000 INFO @ Sat, 11 Nov 2017 01:27:47: 18000000 INFO @ Sat, 11 Nov 2017 01:27:53: 20000000 INFO @ Sat, 11 Nov 2017 01:27:54: 19000000 INFO @ Sat, 11 Nov 2017 01:28:02: 19000000 INFO @ Sat, 11 Nov 2017 01:28:07: 20000000 INFO @ Sat, 11 Nov 2017 01:28:07: 21000000 INFO @ Sat, 11 Nov 2017 01:28:16: 20000000 INFO @ Sat, 11 Nov 2017 01:28:19: 21000000 INFO @ Sat, 11 Nov 2017 01:28:19: 22000000 INFO @ Sat, 11 Nov 2017 01:28:27: 21000000 INFO @ Sat, 11 Nov 2017 01:28:28: 23000000 INFO @ Sat, 11 Nov 2017 01:28:32: 22000000 INFO @ Sat, 11 Nov 2017 01:28:37: 22000000 INFO @ Sat, 11 Nov 2017 01:28:38: 24000000 INFO @ Sat, 11 Nov 2017 01:28:43: 23000000 INFO @ Sat, 11 Nov 2017 01:28:47: 25000000 INFO @ Sat, 11 Nov 2017 01:28:49: 23000000 INFO @ Sat, 11 Nov 2017 01:28:53: 24000000 INFO @ Sat, 11 Nov 2017 01:28:57: 26000000 INFO @ Sat, 11 Nov 2017 01:29:00: 24000000 INFO @ Sat, 11 Nov 2017 01:29:03: 25000000 INFO @ Sat, 11 Nov 2017 01:29:06: 27000000 INFO @ Sat, 11 Nov 2017 01:29:13: 25000000 INFO @ Sat, 11 Nov 2017 01:29:15: 26000000 INFO @ Sat, 11 Nov 2017 01:29:16: 28000000 INFO @ Sat, 11 Nov 2017 01:29:25: 26000000 INFO @ Sat, 11 Nov 2017 01:29:26: 27000000 INFO @ Sat, 11 Nov 2017 01:29:29: 29000000 INFO @ Sat, 11 Nov 2017 01:29:35: 27000000 INFO @ Sat, 11 Nov 2017 01:29:36: 28000000 INFO @ Sat, 11 Nov 2017 01:29:42: 30000000 INFO @ Sat, 11 Nov 2017 01:29:46: 28000000 INFO @ Sat, 11 Nov 2017 01:29:47: 29000000 INFO @ Sat, 11 Nov 2017 01:29:54: 31000000 INFO @ Sat, 11 Nov 2017 01:29:56: 29000000 INFO @ Sat, 11 Nov 2017 01:29:57: 30000000 INFO @ Sat, 11 Nov 2017 01:30:06: 30000000 INFO @ Sat, 11 Nov 2017 01:30:07: 31000000 INFO @ Sat, 11 Nov 2017 01:30:11: 32000000 INFO @ Sat, 11 Nov 2017 01:30:16: 31000000 INFO @ Sat, 11 Nov 2017 01:30:21: 32000000 INFO @ Sat, 11 Nov 2017 01:30:25: 32000000 INFO @ Sat, 11 Nov 2017 01:30:29: 33000000 INFO @ Sat, 11 Nov 2017 01:30:34: 33000000 INFO @ Sat, 11 Nov 2017 01:30:35: 33000000 INFO @ Sat, 11 Nov 2017 01:30:45: 34000000 INFO @ Sat, 11 Nov 2017 01:30:47: 34000000 INFO @ Sat, 11 Nov 2017 01:30:47: 34000000 INFO @ Sat, 11 Nov 2017 01:30:54: 35000000 INFO @ Sat, 11 Nov 2017 01:31:00: 35000000 INFO @ Sat, 11 Nov 2017 01:31:04: 36000000 INFO @ Sat, 11 Nov 2017 01:31:05: 35000000 INFO @ Sat, 11 Nov 2017 01:31:13: 37000000 INFO @ Sat, 11 Nov 2017 01:31:14: 36000000 INFO @ Sat, 11 Nov 2017 01:31:23: 38000000 INFO @ Sat, 11 Nov 2017 01:31:23: 36000000 INFO @ Sat, 11 Nov 2017 01:31:28: 37000000 INFO @ Sat, 11 Nov 2017 01:31:32: 39000000 INFO @ Sat, 11 Nov 2017 01:31:41: 38000000 INFO @ Sat, 11 Nov 2017 01:31:42: 37000000 INFO @ Sat, 11 Nov 2017 01:31:42: 40000000 INFO @ Sat, 11 Nov 2017 01:31:52: 41000000 INFO @ Sat, 11 Nov 2017 01:31:54: 39000000 INFO @ Sat, 11 Nov 2017 01:32:00: 38000000 INFO @ Sat, 11 Nov 2017 01:32:01: 42000000 INFO @ Sat, 11 Nov 2017 01:32:07: 40000000 INFO @ Sat, 11 Nov 2017 01:32:14: 43000000 INFO @ Sat, 11 Nov 2017 01:32:19: 39000000 INFO @ Sat, 11 Nov 2017 01:32:20: 41000000 INFO @ Sat, 11 Nov 2017 01:32:25: 44000000 INFO @ Sat, 11 Nov 2017 01:32:33: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:32:33: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:32:33: #1 total tags in treatment: 44719709 INFO @ Sat, 11 Nov 2017 01:32:33: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:32:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:32:33: 42000000 INFO @ Sat, 11 Nov 2017 01:32:34: #1 tags after filtering in treatment: 44719648 INFO @ Sat, 11 Nov 2017 01:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:32:34: #1 finished! INFO @ Sat, 11 Nov 2017 01:32:34: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:32:37: 40000000 INFO @ Sat, 11 Nov 2017 01:32:39: #2 number of paired peaks: 5994 INFO @ Sat, 11 Nov 2017 01:32:39: start model_add_line... INFO @ Sat, 11 Nov 2017 01:32:40: start X-correlation... INFO @ Sat, 11 Nov 2017 01:32:40: end of X-cor INFO @ Sat, 11 Nov 2017 01:32:40: #2 finished! INFO @ Sat, 11 Nov 2017 01:32:40: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 01:32:40: #2 alternative fragment length(s) may be 51,224,400 bps INFO @ Sat, 11 Nov 2017 01:32:40: #2.2 Generate R script for model : SRX2224392.05_model.r WARNING @ Sat, 11 Nov 2017 01:32:40: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:32:40: #2 You may need to consider one of the other alternative d(s): 51,224,400 WARNING @ Sat, 11 Nov 2017 01:32:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:32:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:32:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:32:42: 43000000 INFO @ Sat, 11 Nov 2017 01:32:50: 44000000 INFO @ Sat, 11 Nov 2017 01:32:52: 41000000 INFO @ Sat, 11 Nov 2017 01:32:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:32:57: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:32:57: #1 total tags in treatment: 44719709 INFO @ Sat, 11 Nov 2017 01:32:57: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:32:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:32:59: #1 tags after filtering in treatment: 44719648 INFO @ Sat, 11 Nov 2017 01:32:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:32:59: #1 finished! INFO @ Sat, 11 Nov 2017 01:32:59: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:33:04: #2 number of paired peaks: 5994 INFO @ Sat, 11 Nov 2017 01:33:04: start model_add_line... INFO @ Sat, 11 Nov 2017 01:33:05: start X-correlation... INFO @ Sat, 11 Nov 2017 01:33:05: end of X-cor INFO @ Sat, 11 Nov 2017 01:33:05: #2 finished! INFO @ Sat, 11 Nov 2017 01:33:05: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 01:33:05: #2 alternative fragment length(s) may be 51,224,400 bps INFO @ Sat, 11 Nov 2017 01:33:05: #2.2 Generate R script for model : SRX2224392.20_model.r WARNING @ Sat, 11 Nov 2017 01:33:05: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:33:05: #2 You may need to consider one of the other alternative d(s): 51,224,400 WARNING @ Sat, 11 Nov 2017 01:33:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:33:05: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:33:06: 42000000 INFO @ Sat, 11 Nov 2017 01:33:19: 43000000 INFO @ Sat, 11 Nov 2017 01:33:31: 44000000 INFO @ Sat, 11 Nov 2017 01:33:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:33:41: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:33:41: #1 total tags in treatment: 44719709 INFO @ Sat, 11 Nov 2017 01:33:41: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:33:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:33:43: #1 tags after filtering in treatment: 44719648 INFO @ Sat, 11 Nov 2017 01:33:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:33:43: #1 finished! INFO @ Sat, 11 Nov 2017 01:33:43: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:33:48: #2 number of paired peaks: 5994 INFO @ Sat, 11 Nov 2017 01:33:48: start model_add_line... INFO @ Sat, 11 Nov 2017 01:33:49: start X-correlation... INFO @ Sat, 11 Nov 2017 01:33:49: end of X-cor INFO @ Sat, 11 Nov 2017 01:33:49: #2 finished! INFO @ Sat, 11 Nov 2017 01:33:49: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Nov 2017 01:33:49: #2 alternative fragment length(s) may be 51,224,400 bps INFO @ Sat, 11 Nov 2017 01:33:49: #2.2 Generate R script for model : SRX2224392.10_model.r WARNING @ Sat, 11 Nov 2017 01:33:49: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:33:49: #2 You may need to consider one of the other alternative d(s): 51,224,400 WARNING @ Sat, 11 Nov 2017 01:33:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:33:49: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:35:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:35:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:36:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:36:23: #4 Write output xls file... SRX2224392.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:36:23: #4 Write peak in narrowPeak format file... SRX2224392.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:36:23: #4 Write summits bed file... SRX2224392.05_summits.bed INFO @ Sat, 11 Nov 2017 01:36:23: Done! pass1 - making usageList (79 chroms): 2 millis pass2 - checking and writing primary data (3275 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:36:49: #4 Write output xls file... SRX2224392.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:36:49: #4 Write peak in narrowPeak format file... SRX2224392.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:36:49: #4 Write summits bed file... SRX2224392.20_summits.bed INFO @ Sat, 11 Nov 2017 01:36:49: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (736 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:37:26: #4 Write output xls file... SRX2224392.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:37:26: #4 Write peak in narrowPeak format file... SRX2224392.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:37:26: #4 Write summits bed file... SRX2224392.10_summits.bed INFO @ Sat, 11 Nov 2017 01:37:26: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1548 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。