Job ID = 10487576 sra ファイルのダウンロード中... Completed: 5419551K bytes transferred in 209 seconds (211555K 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 80967124 spots for /home/okishinya/chipatlas/results/rn6/SRX2611106/SRR5311150.sra Written 80967124 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 04:29:59 80967124 reads; of these: 80967124 (100.00%) were unpaired; of these: 19990874 (24.69%) aligned 0 times 51970639 (64.19%) aligned exactly 1 time 9005611 (11.12%) aligned >1 times 75.31% overall alignment rate Time searching: 04:30:03 Overall time: 04:30:03 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 48 files... [bam_rmdupse_core] 17148665 / 60976250 = 0.2812 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 @ Sun, 18 Mar 2018 14:42:28: # Command line: callpeak -t SRX2611106.bam -f BAM -g 2.15e9 -n SRX2611106.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611106.10 # format = BAM # ChIP-seq file = ['SRX2611106.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 @ Sun, 18 Mar 2018 14:42:28: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:42:28: # Command line: callpeak -t SRX2611106.bam -f BAM -g 2.15e9 -n SRX2611106.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611106.05 # format = BAM # ChIP-seq file = ['SRX2611106.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 @ Sun, 18 Mar 2018 14:42:28: # Command line: callpeak -t SRX2611106.bam -f BAM -g 2.15e9 -n SRX2611106.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611106.20 # format = BAM # ChIP-seq file = ['SRX2611106.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 @ Sun, 18 Mar 2018 14:42:28: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:42:28: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:42:28: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:42:28: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:42:28: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:42:39: 1000000 INFO @ Sun, 18 Mar 2018 14:42:40: 1000000 INFO @ Sun, 18 Mar 2018 14:42:41: 1000000 INFO @ Sun, 18 Mar 2018 14:42:49: 2000000 INFO @ Sun, 18 Mar 2018 14:42:51: 2000000 INFO @ Sun, 18 Mar 2018 14:42:53: 2000000 INFO @ Sun, 18 Mar 2018 14:42:59: 3000000 INFO @ Sun, 18 Mar 2018 14:43:01: 3000000 INFO @ Sun, 18 Mar 2018 14:43:04: 3000000 INFO @ Sun, 18 Mar 2018 14:43:09: 4000000 INFO @ Sun, 18 Mar 2018 14:43:11: 4000000 INFO @ Sun, 18 Mar 2018 14:43:14: 4000000 INFO @ Sun, 18 Mar 2018 14:43:20: 5000000 INFO @ Sun, 18 Mar 2018 14:43:21: 5000000 INFO @ Sun, 18 Mar 2018 14:43:24: 5000000 INFO @ Sun, 18 Mar 2018 14:43:30: 6000000 INFO @ Sun, 18 Mar 2018 14:43:31: 6000000 INFO @ Sun, 18 Mar 2018 14:43:35: 6000000 INFO @ Sun, 18 Mar 2018 14:43:40: 7000000 INFO @ Sun, 18 Mar 2018 14:43:41: 7000000 INFO @ Sun, 18 Mar 2018 14:43:45: 7000000 INFO @ Sun, 18 Mar 2018 14:43:50: 8000000 INFO @ Sun, 18 Mar 2018 14:43:52: 8000000 INFO @ Sun, 18 Mar 2018 14:43:57: 8000000 INFO @ Sun, 18 Mar 2018 14:44:00: 9000000 INFO @ Sun, 18 Mar 2018 14:44:02: 9000000 INFO @ Sun, 18 Mar 2018 14:44:07: 9000000 INFO @ Sun, 18 Mar 2018 14:44:11: 10000000 INFO @ Sun, 18 Mar 2018 14:44:12: 10000000 INFO @ Sun, 18 Mar 2018 14:44:19: 10000000 INFO @ Sun, 18 Mar 2018 14:44:21: 11000000 INFO @ Sun, 18 Mar 2018 14:44:23: 11000000 INFO @ Sun, 18 Mar 2018 14:44:30: 11000000 INFO @ Sun, 18 Mar 2018 14:44:31: 12000000 INFO @ Sun, 18 Mar 2018 14:44:34: 12000000 INFO @ Sun, 18 Mar 2018 14:44:41: 13000000 INFO @ Sun, 18 Mar 2018 14:44:42: 12000000 INFO @ Sun, 18 Mar 2018 14:44:45: 13000000 INFO @ Sun, 18 Mar 2018 14:44:51: 14000000 INFO @ Sun, 18 Mar 2018 14:44:53: 13000000 INFO @ Sun, 18 Mar 2018 14:44:55: 14000000 INFO @ Sun, 18 Mar 2018 14:45:01: 15000000 INFO @ Sun, 18 Mar 2018 14:45:05: 14000000 INFO @ Sun, 18 Mar 2018 14:45:06: 15000000 INFO @ Sun, 18 Mar 2018 14:45:11: 16000000 INFO @ Sun, 18 Mar 2018 14:45:17: 15000000 INFO @ Sun, 18 Mar 2018 14:45:17: 16000000 INFO @ Sun, 18 Mar 2018 14:45:21: 17000000 INFO @ Sun, 18 Mar 2018 14:45:27: 17000000 INFO @ Sun, 18 Mar 2018 14:45:28: 16000000 INFO @ Sun, 18 Mar 2018 14:45:32: 18000000 INFO @ Sun, 18 Mar 2018 14:45:37: 18000000 INFO @ Sun, 18 Mar 2018 14:45:38: 17000000 INFO @ Sun, 18 Mar 2018 14:45:42: 19000000 INFO @ Sun, 18 Mar 2018 14:45:47: 19000000 INFO @ Sun, 18 Mar 2018 14:45:49: 18000000 INFO @ Sun, 18 Mar 2018 14:45:52: 20000000 INFO @ Sun, 18 Mar 2018 14:45:58: 20000000 INFO @ Sun, 18 Mar 2018 14:46:00: 19000000 INFO @ Sun, 18 Mar 2018 14:46:02: 21000000 INFO @ Sun, 18 Mar 2018 14:46:08: 21000000 INFO @ Sun, 18 Mar 2018 14:46:10: 20000000 INFO @ Sun, 18 Mar 2018 14:46:13: 22000000 INFO @ Sun, 18 Mar 2018 14:46:18: 22000000 INFO @ Sun, 18 Mar 2018 14:46:21: 21000000 INFO @ Sun, 18 Mar 2018 14:46:23: 23000000 INFO @ Sun, 18 Mar 2018 14:46:29: 23000000 INFO @ Sun, 18 Mar 2018 14:46:33: 22000000 INFO @ Sun, 18 Mar 2018 14:46:34: 24000000 INFO @ Sun, 18 Mar 2018 14:46:40: 24000000 INFO @ Sun, 18 Mar 2018 14:46:44: 23000000 INFO @ Sun, 18 Mar 2018 14:46:45: 25000000 INFO @ Sun, 18 Mar 2018 14:46:50: 25000000 INFO @ Sun, 18 Mar 2018 14:46:55: 26000000 INFO @ Sun, 18 Mar 2018 14:46:55: 24000000 INFO @ Sun, 18 Mar 2018 14:47:01: 26000000 INFO @ Sun, 18 Mar 2018 14:47:05: 27000000 INFO @ Sun, 18 Mar 2018 14:47:06: 25000000 INFO @ Sun, 18 Mar 2018 14:47:11: 27000000 INFO @ Sun, 18 Mar 2018 14:47:15: 28000000 INFO @ Sun, 18 Mar 2018 14:47:17: 26000000 INFO @ Sun, 18 Mar 2018 14:47:21: 28000000 INFO @ Sun, 18 Mar 2018 14:47:25: 29000000 INFO @ Sun, 18 Mar 2018 14:47:27: 27000000 INFO @ Sun, 18 Mar 2018 14:47:31: 29000000 INFO @ Sun, 18 Mar 2018 14:47:35: 30000000 INFO @ Sun, 18 Mar 2018 14:47:38: 28000000 INFO @ Sun, 18 Mar 2018 14:47:42: 30000000 INFO @ Sun, 18 Mar 2018 14:47:45: 31000000 INFO @ Sun, 18 Mar 2018 14:47:49: 29000000 INFO @ Sun, 18 Mar 2018 14:47:52: 31000000 INFO @ Sun, 18 Mar 2018 14:47:55: 32000000 INFO @ Sun, 18 Mar 2018 14:48:01: 30000000 INFO @ Sun, 18 Mar 2018 14:48:03: 32000000 INFO @ Sun, 18 Mar 2018 14:48:05: 33000000 INFO @ Sun, 18 Mar 2018 14:48:12: 31000000 INFO @ Sun, 18 Mar 2018 14:48:14: 33000000 INFO @ Sun, 18 Mar 2018 14:48:15: 34000000 INFO @ Sun, 18 Mar 2018 14:48:24: 32000000 INFO @ Sun, 18 Mar 2018 14:48:25: 34000000 INFO @ Sun, 18 Mar 2018 14:48:25: 35000000 INFO @ Sun, 18 Mar 2018 14:48:35: 35000000 INFO @ Sun, 18 Mar 2018 14:48:35: 33000000 INFO @ Sun, 18 Mar 2018 14:48:35: 36000000 INFO @ Sun, 18 Mar 2018 14:48:45: 36000000 INFO @ Sun, 18 Mar 2018 14:48:45: 37000000 INFO @ Sun, 18 Mar 2018 14:48:46: 34000000 INFO @ Sun, 18 Mar 2018 14:48:56: 38000000 INFO @ Sun, 18 Mar 2018 14:48:56: 37000000 INFO @ Sun, 18 Mar 2018 14:48:58: 35000000 INFO @ Sun, 18 Mar 2018 14:49:06: 39000000 INFO @ Sun, 18 Mar 2018 14:49:06: 38000000 INFO @ Sun, 18 Mar 2018 14:49:08: 36000000 INFO @ Sun, 18 Mar 2018 14:49:16: 40000000 INFO @ Sun, 18 Mar 2018 14:49:16: 39000000 INFO @ Sun, 18 Mar 2018 14:49:20: 37000000 INFO @ Sun, 18 Mar 2018 14:49:27: 41000000 INFO @ Sun, 18 Mar 2018 14:49:27: 40000000 INFO @ Sun, 18 Mar 2018 14:49:31: 38000000 INFO @ Sun, 18 Mar 2018 14:49:37: 41000000 INFO @ Sun, 18 Mar 2018 14:49:37: 42000000 INFO @ Sun, 18 Mar 2018 14:49:42: 39000000 INFO @ Sun, 18 Mar 2018 14:49:47: 42000000 INFO @ Sun, 18 Mar 2018 14:49:48: 43000000 INFO @ Sun, 18 Mar 2018 14:49:53: 40000000 INFO @ Sun, 18 Mar 2018 14:49:57: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:49:57: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:49:57: #1 total tags in treatment: 43827585 INFO @ Sun, 18 Mar 2018 14:49:57: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:49:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:49:58: 43000000 INFO @ Sun, 18 Mar 2018 14:49:58: #1 tags after filtering in treatment: 43827495 INFO @ Sun, 18 Mar 2018 14:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:49:58: #1 finished! INFO @ Sun, 18 Mar 2018 14:49:58: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:50:02: #2 number of paired peaks: 7768 INFO @ Sun, 18 Mar 2018 14:50:02: start model_add_line... INFO @ Sun, 18 Mar 2018 14:50:02: start X-correlation... INFO @ Sun, 18 Mar 2018 14:50:02: end of X-cor INFO @ Sun, 18 Mar 2018 14:50:02: #2 finished! INFO @ Sun, 18 Mar 2018 14:50:02: #2 predicted fragment length is 154 bps INFO @ Sun, 18 Mar 2018 14:50:02: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 18 Mar 2018 14:50:02: #2.2 Generate R script for model : SRX2611106.20_model.r WARNING @ Sun, 18 Mar 2018 14:50:02: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:50:02: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 18 Mar 2018 14:50:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:50:02: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:50:04: 41000000 INFO @ Sun, 18 Mar 2018 14:50:07: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:50:07: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:50:07: #1 total tags in treatment: 43827585 INFO @ Sun, 18 Mar 2018 14:50:07: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:50:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:50:08: #1 tags after filtering in treatment: 43827495 INFO @ Sun, 18 Mar 2018 14:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:50:08: #1 finished! INFO @ Sun, 18 Mar 2018 14:50:08: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:50:12: #2 number of paired peaks: 7768 INFO @ Sun, 18 Mar 2018 14:50:12: start model_add_line... INFO @ Sun, 18 Mar 2018 14:50:13: start X-correlation... INFO @ Sun, 18 Mar 2018 14:50:13: end of X-cor INFO @ Sun, 18 Mar 2018 14:50:13: #2 finished! INFO @ Sun, 18 Mar 2018 14:50:13: #2 predicted fragment length is 154 bps INFO @ Sun, 18 Mar 2018 14:50:13: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 18 Mar 2018 14:50:13: #2.2 Generate R script for model : SRX2611106.10_model.r WARNING @ Sun, 18 Mar 2018 14:50:13: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:50:13: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 18 Mar 2018 14:50:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:50:13: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:50:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:50:14: 42000000 INFO @ Sun, 18 Mar 2018 14:50:24: 43000000 INFO @ Sun, 18 Mar 2018 14:50:32: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:50:32: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:50:32: #1 total tags in treatment: 43827585 INFO @ Sun, 18 Mar 2018 14:50:32: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:50:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:50:33: #1 tags after filtering in treatment: 43827495 INFO @ Sun, 18 Mar 2018 14:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:50:33: #1 finished! INFO @ Sun, 18 Mar 2018 14:50:33: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:50:38: #2 number of paired peaks: 7768 INFO @ Sun, 18 Mar 2018 14:50:38: start model_add_line... INFO @ Sun, 18 Mar 2018 14:50:38: start X-correlation... INFO @ Sun, 18 Mar 2018 14:50:38: end of X-cor INFO @ Sun, 18 Mar 2018 14:50:38: #2 finished! INFO @ Sun, 18 Mar 2018 14:50:38: #2 predicted fragment length is 154 bps INFO @ Sun, 18 Mar 2018 14:50:38: #2 alternative fragment length(s) may be 154 bps INFO @ Sun, 18 Mar 2018 14:50:38: #2.2 Generate R script for model : SRX2611106.05_model.r WARNING @ Sun, 18 Mar 2018 14:50:38: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:50:38: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Sun, 18 Mar 2018 14:50:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:50:38: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:51:50: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:52:07: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:52:21: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:52:51: #4 Write output xls file... SRX2611106.20_peaks.xls INFO @ Sun, 18 Mar 2018 14:52:51: #4 Write peak in narrowPeak format file... SRX2611106.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:52:51: #4 Write summits bed file... SRX2611106.20_summits.bed INFO @ Sun, 18 Mar 2018 14:52:51: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (537 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:53:05: #4 Write output xls file... SRX2611106.10_peaks.xls INFO @ Sun, 18 Mar 2018 14:53:05: #4 Write peak in narrowPeak format file... SRX2611106.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:53:05: #4 Write summits bed file... SRX2611106.10_summits.bed INFO @ Sun, 18 Mar 2018 14:53:05: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (1766 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:53:18: #4 Write output xls file... SRX2611106.05_peaks.xls INFO @ Sun, 18 Mar 2018 14:53:18: #4 Write peak in narrowPeak format file... SRX2611106.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:53:18: #4 Write summits bed file... SRX2611106.05_summits.bed INFO @ Sun, 18 Mar 2018 14:53:18: Done! pass1 - making usageList (70 chroms): 3 millis pass2 - checking and writing primary data (7216 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。