Job ID = 10194931 sra ファイルのダウンロード中... Completed: 593831K bytes transferred in 10 seconds (466894K bits/sec), in 1 file. Completed: 1384517K bytes transferred in 19 seconds (574048K 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 16827370 spots for /home/okishinya/chipatlas/results/rn6/SRX2224393/SRR4370055.sra Written 16827370 spots total Written 38912542 spots for /home/okishinya/chipatlas/results/rn6/SRX2224393/SRR4370056.sra Written 38912542 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: 01:19:04 55739912 reads; of these: 55739912 (100.00%) were unpaired; of these: 8697866 (15.60%) aligned 0 times 33016591 (59.23%) aligned exactly 1 time 14025455 (25.16%) aligned >1 times 84.40% overall alignment rate Time searching: 01:19:08 Overall time: 01:19:08 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] 2969959 / 47042046 = 0.0631 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 01:18:12: # Command line: callpeak -t SRX2224393.bam -f BAM -g 2.15e9 -n SRX2224393.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2224393.10 # format = BAM # ChIP-seq file = ['SRX2224393.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 01:18:12: # Command line: callpeak -t SRX2224393.bam -f BAM -g 2.15e9 -n SRX2224393.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2224393.05 # format = BAM # ChIP-seq file = ['SRX2224393.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 01:18:12: # Command line: callpeak -t SRX2224393.bam -f BAM -g 2.15e9 -n SRX2224393.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2224393.20 # format = BAM # ChIP-seq file = ['SRX2224393.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 01:18:12: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:18:12: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:18:12: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:18:12: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:18:12: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:18:12: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:18:23: 1000000 INFO @ Sat, 11 Nov 2017 01:18:25: 1000000 INFO @ Sat, 11 Nov 2017 01:18:25: 1000000 INFO @ Sat, 11 Nov 2017 01:18:32: 2000000 INFO @ Sat, 11 Nov 2017 01:18:39: 2000000 INFO @ Sat, 11 Nov 2017 01:18:39: 2000000 INFO @ Sat, 11 Nov 2017 01:18:41: 3000000 INFO @ Sat, 11 Nov 2017 01:18:51: 3000000 INFO @ Sat, 11 Nov 2017 01:18:52: 3000000 INFO @ Sat, 11 Nov 2017 01:18:56: 4000000 INFO @ Sat, 11 Nov 2017 01:19:03: 4000000 INFO @ Sat, 11 Nov 2017 01:19:05: 4000000 INFO @ Sat, 11 Nov 2017 01:19:13: 5000000 INFO @ Sat, 11 Nov 2017 01:19:15: 5000000 INFO @ Sat, 11 Nov 2017 01:19:19: 5000000 INFO @ Sat, 11 Nov 2017 01:19:27: 6000000 INFO @ Sat, 11 Nov 2017 01:19:29: 6000000 INFO @ Sat, 11 Nov 2017 01:19:31: 6000000 INFO @ Sat, 11 Nov 2017 01:19:40: 7000000 INFO @ Sat, 11 Nov 2017 01:19:43: 7000000 INFO @ Sat, 11 Nov 2017 01:19:45: 7000000 INFO @ Sat, 11 Nov 2017 01:19:52: 8000000 INFO @ Sat, 11 Nov 2017 01:19:55: 8000000 INFO @ Sat, 11 Nov 2017 01:20:00: 8000000 INFO @ Sat, 11 Nov 2017 01:20:04: 9000000 INFO @ Sat, 11 Nov 2017 01:20:07: 9000000 INFO @ Sat, 11 Nov 2017 01:20:16: 9000000 INFO @ Sat, 11 Nov 2017 01:20:16: 10000000 INFO @ Sat, 11 Nov 2017 01:20:18: 10000000 INFO @ Sat, 11 Nov 2017 01:20:29: 11000000 INFO @ Sat, 11 Nov 2017 01:20:31: 11000000 INFO @ Sat, 11 Nov 2017 01:20:33: 10000000 INFO @ Sat, 11 Nov 2017 01:20:41: 12000000 INFO @ Sat, 11 Nov 2017 01:20:43: 12000000 INFO @ Sat, 11 Nov 2017 01:20:52: 11000000 INFO @ Sat, 11 Nov 2017 01:20:53: 13000000 INFO @ Sat, 11 Nov 2017 01:20:57: 13000000 INFO @ Sat, 11 Nov 2017 01:21:05: 14000000 INFO @ Sat, 11 Nov 2017 01:21:10: 12000000 INFO @ Sat, 11 Nov 2017 01:21:12: 14000000 INFO @ Sat, 11 Nov 2017 01:21:17: 15000000 INFO @ Sat, 11 Nov 2017 01:21:24: 13000000 INFO @ Sat, 11 Nov 2017 01:21:27: 15000000 INFO @ Sat, 11 Nov 2017 01:21:30: 16000000 INFO @ Sat, 11 Nov 2017 01:21:34: 14000000 INFO @ Sat, 11 Nov 2017 01:21:42: 17000000 INFO @ Sat, 11 Nov 2017 01:21:43: 16000000 INFO @ Sat, 11 Nov 2017 01:21:48: 15000000 INFO @ Sat, 11 Nov 2017 01:21:54: 18000000 INFO @ Sat, 11 Nov 2017 01:21:59: 17000000 INFO @ Sat, 11 Nov 2017 01:22:02: 16000000 INFO @ Sat, 11 Nov 2017 01:22:06: 19000000 INFO @ Sat, 11 Nov 2017 01:22:15: 18000000 INFO @ Sat, 11 Nov 2017 01:22:17: 20000000 INFO @ Sat, 11 Nov 2017 01:22:19: 17000000 INFO @ Sat, 11 Nov 2017 01:22:28: 19000000 INFO @ Sat, 11 Nov 2017 01:22:28: 21000000 INFO @ Sat, 11 Nov 2017 01:22:36: 18000000 INFO @ Sat, 11 Nov 2017 01:22:40: 20000000 INFO @ Sat, 11 Nov 2017 01:22:40: 22000000 INFO @ Sat, 11 Nov 2017 01:22:52: 21000000 INFO @ Sat, 11 Nov 2017 01:22:54: 23000000 INFO @ Sat, 11 Nov 2017 01:22:55: 19000000 INFO @ Sat, 11 Nov 2017 01:23:03: 22000000 INFO @ Sat, 11 Nov 2017 01:23:08: 24000000 INFO @ Sat, 11 Nov 2017 01:23:13: 20000000 INFO @ Sat, 11 Nov 2017 01:23:13: 23000000 INFO @ Sat, 11 Nov 2017 01:23:20: 25000000 INFO @ Sat, 11 Nov 2017 01:23:25: 24000000 INFO @ Sat, 11 Nov 2017 01:23:31: 21000000 INFO @ Sat, 11 Nov 2017 01:23:32: 26000000 INFO @ Sat, 11 Nov 2017 01:23:36: 25000000 INFO @ Sat, 11 Nov 2017 01:23:44: 27000000 INFO @ Sat, 11 Nov 2017 01:23:47: 26000000 INFO @ Sat, 11 Nov 2017 01:23:52: 22000000 INFO @ Sat, 11 Nov 2017 01:23:57: 28000000 INFO @ Sat, 11 Nov 2017 01:24:00: 27000000 INFO @ Sat, 11 Nov 2017 01:24:09: 23000000 INFO @ Sat, 11 Nov 2017 01:24:12: 28000000 INFO @ Sat, 11 Nov 2017 01:24:12: 29000000 INFO @ Sat, 11 Nov 2017 01:24:24: 29000000 INFO @ Sat, 11 Nov 2017 01:24:27: 24000000 INFO @ Sat, 11 Nov 2017 01:24:28: 30000000 INFO @ Sat, 11 Nov 2017 01:24:35: 30000000 INFO @ Sat, 11 Nov 2017 01:24:46: 31000000 INFO @ Sat, 11 Nov 2017 01:24:46: 31000000 INFO @ Sat, 11 Nov 2017 01:24:47: 25000000 INFO @ Sat, 11 Nov 2017 01:24:58: 32000000 INFO @ Sat, 11 Nov 2017 01:25:03: 32000000 INFO @ Sat, 11 Nov 2017 01:25:06: 26000000 INFO @ Sat, 11 Nov 2017 01:25:09: 33000000 INFO @ Sat, 11 Nov 2017 01:25:21: 33000000 INFO @ Sat, 11 Nov 2017 01:25:21: 34000000 INFO @ Sat, 11 Nov 2017 01:25:25: 27000000 INFO @ Sat, 11 Nov 2017 01:25:35: 35000000 INFO @ Sat, 11 Nov 2017 01:25:38: 34000000 INFO @ Sat, 11 Nov 2017 01:25:43: 28000000 INFO @ Sat, 11 Nov 2017 01:25:50: 36000000 INFO @ Sat, 11 Nov 2017 01:25:55: 35000000 INFO @ Sat, 11 Nov 2017 01:26:00: 29000000 INFO @ Sat, 11 Nov 2017 01:26:07: 37000000 INFO @ Sat, 11 Nov 2017 01:26:13: 36000000 INFO @ Sat, 11 Nov 2017 01:26:18: 30000000 INFO @ Sat, 11 Nov 2017 01:26:21: 38000000 INFO @ Sat, 11 Nov 2017 01:26:31: 37000000 INFO @ Sat, 11 Nov 2017 01:26:35: 31000000 INFO @ Sat, 11 Nov 2017 01:26:35: 39000000 INFO @ Sat, 11 Nov 2017 01:26:44: 32000000 INFO @ Sat, 11 Nov 2017 01:26:47: 38000000 INFO @ Sat, 11 Nov 2017 01:26:51: 40000000 INFO @ Sat, 11 Nov 2017 01:26:55: 33000000 INFO @ Sat, 11 Nov 2017 01:27:02: 39000000 INFO @ Sat, 11 Nov 2017 01:27:05: 34000000 INFO @ Sat, 11 Nov 2017 01:27:09: 41000000 INFO @ Sat, 11 Nov 2017 01:27:17: 40000000 INFO @ Sat, 11 Nov 2017 01:27:18: 35000000 INFO @ Sat, 11 Nov 2017 01:27:26: 42000000 INFO @ Sat, 11 Nov 2017 01:27:30: 36000000 INFO @ Sat, 11 Nov 2017 01:27:31: 41000000 INFO @ Sat, 11 Nov 2017 01:27:43: 37000000 INFO @ Sat, 11 Nov 2017 01:27:43: 42000000 INFO @ Sat, 11 Nov 2017 01:27:45: 43000000 INFO @ Sat, 11 Nov 2017 01:27:56: 43000000 INFO @ Sat, 11 Nov 2017 01:27:59: 38000000 INFO @ Sat, 11 Nov 2017 01:28:03: 44000000 INFO @ Sat, 11 Nov 2017 01:28:06: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:28:06: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:28:06: #1 total tags in treatment: 44072087 INFO @ Sat, 11 Nov 2017 01:28:06: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:28:06: #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 01:28:07: #1 tags after filtering in treatment: 44072036 INFO @ Sat, 11 Nov 2017 01:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:28:07: #1 finished! INFO @ Sat, 11 Nov 2017 01:28:07: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:28:08: 44000000 INFO @ Sat, 11 Nov 2017 01:28:10: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:28:10: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:28:10: #1 total tags in treatment: 44072087 INFO @ Sat, 11 Nov 2017 01:28:10: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:28:10: #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 01:28:11: #1 tags after filtering in treatment: 44072036 INFO @ Sat, 11 Nov 2017 01:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:28:11: #1 finished! INFO @ Sat, 11 Nov 2017 01:28:11: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:28:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:28:12: #2 number of paired peaks: 5478 INFO @ Sat, 11 Nov 2017 01:28:12: start model_add_line... INFO @ Sat, 11 Nov 2017 01:28:13: start X-correlation... INFO @ Sat, 11 Nov 2017 01:28:13: end of X-cor INFO @ Sat, 11 Nov 2017 01:28:13: #2 finished! INFO @ Sat, 11 Nov 2017 01:28:13: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 01:28:13: #2 alternative fragment length(s) may be 50,217 bps INFO @ Sat, 11 Nov 2017 01:28:13: #2.2 Generate R script for model : SRX2224393.10_model.r WARNING @ Sat, 11 Nov 2017 01:28:13: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:28:13: #2 You may need to consider one of the other alternative d(s): 50,217 WARNING @ Sat, 11 Nov 2017 01:28:13: #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 01:28:13: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:28:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:28:14: 39000000 INFO @ Sat, 11 Nov 2017 01:28:17: #2 number of paired peaks: 5478 INFO @ Sat, 11 Nov 2017 01:28:17: start model_add_line... INFO @ Sat, 11 Nov 2017 01:28:17: start X-correlation... INFO @ Sat, 11 Nov 2017 01:28:17: end of X-cor INFO @ Sat, 11 Nov 2017 01:28:17: #2 finished! INFO @ Sat, 11 Nov 2017 01:28:17: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 01:28:17: #2 alternative fragment length(s) may be 50,217 bps INFO @ Sat, 11 Nov 2017 01:28:17: #2.2 Generate R script for model : SRX2224393.20_model.r WARNING @ Sat, 11 Nov 2017 01:28:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:28:17: #2 You may need to consider one of the other alternative d(s): 50,217 WARNING @ Sat, 11 Nov 2017 01:28:17: #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 01:28:17: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:28:29: 40000000 INFO @ Sat, 11 Nov 2017 01:28:42: 41000000 INFO @ Sat, 11 Nov 2017 01:28:58: 42000000 INFO @ Sat, 11 Nov 2017 01:29:13: 43000000 INFO @ Sat, 11 Nov 2017 01:29:28: 44000000 INFO @ Sat, 11 Nov 2017 01:29:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Nov 2017 01:29:30: #1 tag size = 50 INFO @ Sat, 11 Nov 2017 01:29:30: #1 total tags in treatment: 44072087 INFO @ Sat, 11 Nov 2017 01:29:30: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:29:30: #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 01:29:31: #1 tags after filtering in treatment: 44072036 INFO @ Sat, 11 Nov 2017 01:29:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:29:31: #1 finished! INFO @ Sat, 11 Nov 2017 01:29:31: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:29:36: #2 number of paired peaks: 5478 INFO @ Sat, 11 Nov 2017 01:29:36: start model_add_line... INFO @ Sat, 11 Nov 2017 01:29:37: start X-correlation... INFO @ Sat, 11 Nov 2017 01:29:37: end of X-cor INFO @ Sat, 11 Nov 2017 01:29:37: #2 finished! INFO @ Sat, 11 Nov 2017 01:29:37: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 01:29:37: #2 alternative fragment length(s) may be 50,217 bps INFO @ Sat, 11 Nov 2017 01:29:37: #2.2 Generate R script for model : SRX2224393.05_model.r WARNING @ Sat, 11 Nov 2017 01:29:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:29:37: #2 You may need to consider one of the other alternative d(s): 50,217 WARNING @ Sat, 11 Nov 2017 01:29:37: #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 01:29:37: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:30:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:30:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:31:38: #4 Write output xls file... SRX2224393.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:31:38: #4 Write peak in narrowPeak format file... SRX2224393.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:31:38: #4 Write summits bed file... SRX2224393.10_summits.bed INFO @ Sat, 11 Nov 2017 01:31:38: Done! pass1 - making usageList (46 chroms): 2 millis pass2 - checking and writing primary data (1404 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:31:41: #4 Write output xls file... SRX2224393.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:31:41: #4 Write peak in narrowPeak format file... SRX2224393.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:31:41: #4 Write summits bed file... SRX2224393.20_summits.bed INFO @ Sat, 11 Nov 2017 01:31:41: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (642 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:31:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:32:58: #4 Write output xls file... SRX2224393.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:32:58: #4 Write peak in narrowPeak format file... SRX2224393.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:32:58: #4 Write summits bed file... SRX2224393.05_summits.bed INFO @ Sat, 11 Nov 2017 01:32:58: Done! pass1 - making usageList (69 chroms): 2 millis pass2 - checking and writing primary data (2779 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。