Job ID = 10194937 sra ファイルのダウンロード中... Completed: 847552K bytes transferred in 13 seconds (526802K 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 36589407 spots for /home/okishinya/chipatlas/results/rn6/SRX2512947/SRR5197462.sra Written 36589407 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: 00:37:04 36589407 reads; of these: 36589407 (100.00%) were unpaired; of these: 1584997 (4.33%) aligned 0 times 24007738 (65.61%) aligned exactly 1 time 10996672 (30.05%) aligned >1 times 95.67% overall alignment rate Time searching: 00:37:08 Overall time: 00:37:08 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 12 files... [bam_rmdupse_core] 1303721 / 35004410 = 0.0372 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 00:43:31: # Command line: callpeak -t SRX2512947.bam -f BAM -g 2.15e9 -n SRX2512947.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512947.20 # format = BAM # ChIP-seq file = ['SRX2512947.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 00:43:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:43:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:43:31: # Command line: callpeak -t SRX2512947.bam -f BAM -g 2.15e9 -n SRX2512947.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512947.10 # format = BAM # ChIP-seq file = ['SRX2512947.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 00:43:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:43:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:43:31: # Command line: callpeak -t SRX2512947.bam -f BAM -g 2.15e9 -n SRX2512947.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512947.05 # format = BAM # ChIP-seq file = ['SRX2512947.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 00:43:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:43:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:43:41: 1000000 INFO @ Sat, 11 Nov 2017 00:43:43: 1000000 INFO @ Sat, 11 Nov 2017 00:43:45: 1000000 INFO @ Sat, 11 Nov 2017 00:43:50: 2000000 INFO @ Sat, 11 Nov 2017 00:43:57: 2000000 INFO @ Sat, 11 Nov 2017 00:43:59: 2000000 INFO @ Sat, 11 Nov 2017 00:44:00: 3000000 INFO @ Sat, 11 Nov 2017 00:44:09: 4000000 INFO @ Sat, 11 Nov 2017 00:44:11: 3000000 INFO @ Sat, 11 Nov 2017 00:44:14: 3000000 INFO @ Sat, 11 Nov 2017 00:44:19: 5000000 INFO @ Sat, 11 Nov 2017 00:44:23: 4000000 INFO @ Sat, 11 Nov 2017 00:44:29: 4000000 INFO @ Sat, 11 Nov 2017 00:44:29: 6000000 INFO @ Sat, 11 Nov 2017 00:44:36: 5000000 INFO @ Sat, 11 Nov 2017 00:44:39: 7000000 INFO @ Sat, 11 Nov 2017 00:44:42: 5000000 INFO @ Sat, 11 Nov 2017 00:44:49: 6000000 INFO @ Sat, 11 Nov 2017 00:44:49: 8000000 INFO @ Sat, 11 Nov 2017 00:44:58: 6000000 INFO @ Sat, 11 Nov 2017 00:44:59: 9000000 INFO @ Sat, 11 Nov 2017 00:45:01: 7000000 INFO @ Sat, 11 Nov 2017 00:45:09: 10000000 INFO @ Sat, 11 Nov 2017 00:45:11: 7000000 INFO @ Sat, 11 Nov 2017 00:45:14: 8000000 INFO @ Sat, 11 Nov 2017 00:45:20: 11000000 INFO @ Sat, 11 Nov 2017 00:45:26: 9000000 INFO @ Sat, 11 Nov 2017 00:45:26: 8000000 INFO @ Sat, 11 Nov 2017 00:45:31: 12000000 INFO @ Sat, 11 Nov 2017 00:45:37: 10000000 INFO @ Sat, 11 Nov 2017 00:45:39: 9000000 INFO @ Sat, 11 Nov 2017 00:45:41: 13000000 INFO @ Sat, 11 Nov 2017 00:45:49: 11000000 INFO @ Sat, 11 Nov 2017 00:45:51: 14000000 INFO @ Sat, 11 Nov 2017 00:45:54: 10000000 INFO @ Sat, 11 Nov 2017 00:46:00: 15000000 INFO @ Sat, 11 Nov 2017 00:46:01: 12000000 INFO @ Sat, 11 Nov 2017 00:46:08: 11000000 INFO @ Sat, 11 Nov 2017 00:46:10: 16000000 INFO @ Sat, 11 Nov 2017 00:46:13: 13000000 INFO @ Sat, 11 Nov 2017 00:46:19: 17000000 INFO @ Sat, 11 Nov 2017 00:46:23: 12000000 INFO @ Sat, 11 Nov 2017 00:46:25: 14000000 INFO @ Sat, 11 Nov 2017 00:46:28: 18000000 INFO @ Sat, 11 Nov 2017 00:46:35: 13000000 INFO @ Sat, 11 Nov 2017 00:46:37: 15000000 INFO @ Sat, 11 Nov 2017 00:46:38: 19000000 INFO @ Sat, 11 Nov 2017 00:46:46: 14000000 INFO @ Sat, 11 Nov 2017 00:46:48: 20000000 INFO @ Sat, 11 Nov 2017 00:46:50: 16000000 INFO @ Sat, 11 Nov 2017 00:46:57: 15000000 INFO @ Sat, 11 Nov 2017 00:47:00: 21000000 INFO @ Sat, 11 Nov 2017 00:47:02: 17000000 INFO @ Sat, 11 Nov 2017 00:47:09: 16000000 INFO @ Sat, 11 Nov 2017 00:47:11: 22000000 INFO @ Sat, 11 Nov 2017 00:47:15: 18000000 INFO @ Sat, 11 Nov 2017 00:47:20: 17000000 INFO @ Sat, 11 Nov 2017 00:47:23: 23000000 INFO @ Sat, 11 Nov 2017 00:47:27: 19000000 INFO @ Sat, 11 Nov 2017 00:47:32: 18000000 INFO @ Sat, 11 Nov 2017 00:47:34: 24000000 INFO @ Sat, 11 Nov 2017 00:47:38: 20000000 INFO @ Sat, 11 Nov 2017 00:47:43: 19000000 INFO @ Sat, 11 Nov 2017 00:47:46: 25000000 INFO @ Sat, 11 Nov 2017 00:47:51: 21000000 INFO @ Sat, 11 Nov 2017 00:47:55: 20000000 INFO @ Sat, 11 Nov 2017 00:47:58: 26000000 INFO @ Sat, 11 Nov 2017 00:48:05: 22000000 INFO @ Sat, 11 Nov 2017 00:48:09: 21000000 INFO @ Sat, 11 Nov 2017 00:48:10: 27000000 INFO @ Sat, 11 Nov 2017 00:48:18: 23000000 INFO @ Sat, 11 Nov 2017 00:48:21: 28000000 INFO @ Sat, 11 Nov 2017 00:48:23: 22000000 INFO @ Sat, 11 Nov 2017 00:48:32: 24000000 INFO @ Sat, 11 Nov 2017 00:48:33: 29000000 INFO @ Sat, 11 Nov 2017 00:48:36: 23000000 INFO @ Sat, 11 Nov 2017 00:48:45: 25000000 INFO @ Sat, 11 Nov 2017 00:48:45: 30000000 INFO @ Sat, 11 Nov 2017 00:48:50: 24000000 INFO @ Sat, 11 Nov 2017 00:48:57: 31000000 INFO @ Sat, 11 Nov 2017 00:48:58: 26000000 INFO @ Sat, 11 Nov 2017 00:49:02: 25000000 INFO @ Sat, 11 Nov 2017 00:49:09: 32000000 INFO @ Sat, 11 Nov 2017 00:49:11: 27000000 INFO @ Sat, 11 Nov 2017 00:49:15: 26000000 INFO @ Sat, 11 Nov 2017 00:49:21: 33000000 INFO @ Sat, 11 Nov 2017 00:49:24: 28000000 INFO @ Sat, 11 Nov 2017 00:49:29: 27000000 INFO @ Sat, 11 Nov 2017 00:49:30: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:49:30: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:49:30: #1 total tags in treatment: 33700689 INFO @ Sat, 11 Nov 2017 00:49:30: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:49:30: #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 00:49:31: #1 tags after filtering in treatment: 33700607 INFO @ Sat, 11 Nov 2017 00:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:49:31: #1 finished! INFO @ Sat, 11 Nov 2017 00:49:31: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:49:35: #2 number of paired peaks: 7461 INFO @ Sat, 11 Nov 2017 00:49:35: start model_add_line... INFO @ Sat, 11 Nov 2017 00:49:35: start X-correlation... INFO @ Sat, 11 Nov 2017 00:49:35: end of X-cor INFO @ Sat, 11 Nov 2017 00:49:35: #2 finished! INFO @ Sat, 11 Nov 2017 00:49:35: #2 predicted fragment length is 39 bps INFO @ Sat, 11 Nov 2017 00:49:35: #2 alternative fragment length(s) may be 39,93 bps INFO @ Sat, 11 Nov 2017 00:49:35: #2.2 Generate R script for model : SRX2512947.10_model.r WARNING @ Sat, 11 Nov 2017 00:49:35: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:49:35: #2 You may need to consider one of the other alternative d(s): 39,93 WARNING @ Sat, 11 Nov 2017 00:49:35: #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 00:49:35: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:49:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:49:38: 29000000 INFO @ Sat, 11 Nov 2017 00:49:41: 28000000 INFO @ Sat, 11 Nov 2017 00:49:51: 30000000 INFO @ Sat, 11 Nov 2017 00:49:54: 29000000 INFO @ Sat, 11 Nov 2017 00:50:04: 31000000 INFO @ Sat, 11 Nov 2017 00:50:06: 30000000 INFO @ Sat, 11 Nov 2017 00:50:16: 32000000 INFO @ Sat, 11 Nov 2017 00:50:18: 31000000 INFO @ Sat, 11 Nov 2017 00:50:29: 33000000 INFO @ Sat, 11 Nov 2017 00:50:29: 32000000 INFO @ Sat, 11 Nov 2017 00:50:38: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:50:38: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:50:38: #1 total tags in treatment: 33700689 INFO @ Sat, 11 Nov 2017 00:50:38: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:50:38: #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 00:50:40: #1 tags after filtering in treatment: 33700607 INFO @ Sat, 11 Nov 2017 00:50:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:50:40: #1 finished! INFO @ Sat, 11 Nov 2017 00:50:40: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:50:42: 33000000 INFO @ Sat, 11 Nov 2017 00:50:44: #2 number of paired peaks: 7461 INFO @ Sat, 11 Nov 2017 00:50:44: start model_add_line... INFO @ Sat, 11 Nov 2017 00:50:44: start X-correlation... INFO @ Sat, 11 Nov 2017 00:50:44: end of X-cor INFO @ Sat, 11 Nov 2017 00:50:44: #2 finished! INFO @ Sat, 11 Nov 2017 00:50:44: #2 predicted fragment length is 39 bps INFO @ Sat, 11 Nov 2017 00:50:44: #2 alternative fragment length(s) may be 39,93 bps INFO @ Sat, 11 Nov 2017 00:50:44: #2.2 Generate R script for model : SRX2512947.20_model.r WARNING @ Sat, 11 Nov 2017 00:50:44: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:50:44: #2 You may need to consider one of the other alternative d(s): 39,93 WARNING @ Sat, 11 Nov 2017 00:50:44: #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 00:50:44: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:50:51: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 00:50:51: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 00:50:51: #1 total tags in treatment: 33700689 INFO @ Sat, 11 Nov 2017 00:50:51: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:50:51: #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 00:50:52: #1 tags after filtering in treatment: 33700607 INFO @ Sat, 11 Nov 2017 00:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:50:52: #1 finished! INFO @ Sat, 11 Nov 2017 00:50:52: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:50:56: #2 number of paired peaks: 7461 INFO @ Sat, 11 Nov 2017 00:50:56: start model_add_line... INFO @ Sat, 11 Nov 2017 00:50:57: start X-correlation... INFO @ Sat, 11 Nov 2017 00:50:57: end of X-cor INFO @ Sat, 11 Nov 2017 00:50:57: #2 finished! INFO @ Sat, 11 Nov 2017 00:50:57: #2 predicted fragment length is 39 bps INFO @ Sat, 11 Nov 2017 00:50:57: #2 alternative fragment length(s) may be 39,93 bps INFO @ Sat, 11 Nov 2017 00:50:57: #2.2 Generate R script for model : SRX2512947.05_model.r WARNING @ Sat, 11 Nov 2017 00:50:57: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:50:57: #2 You may need to consider one of the other alternative d(s): 39,93 WARNING @ Sat, 11 Nov 2017 00:50:57: #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 00:50:57: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:51:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:52:08: #4 Write output xls file... SRX2512947.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:52:08: #4 Write peak in narrowPeak format file... SRX2512947.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:52:08: #4 Write summits bed file... SRX2512947.10_summits.bed INFO @ Sat, 11 Nov 2017 00:52:08: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1782 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:52:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:52:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:53:18: #4 Write output xls file... SRX2512947.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:53:18: #4 Write peak in narrowPeak format file... SRX2512947.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:53:18: #4 Write summits bed file... SRX2512947.20_summits.bed INFO @ Sat, 11 Nov 2017 00:53:18: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:53:30: #4 Write output xls file... SRX2512947.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:53:30: #4 Write peak in narrowPeak format file... SRX2512947.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:53:30: #4 Write summits bed file... SRX2512947.05_summits.bed INFO @ Sat, 11 Nov 2017 00:53:30: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (4547 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。