Job ID = 10194729 sra ファイルのダウンロード中... Completed: 1266029K bytes transferred in 17 seconds (592321K bits/sec), in 1 file. Completed: 1496953K bytes transferred in 20 seconds (592041K 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 21905258 spots for /home/okishinya/chipatlas/results/rn6/SRX1056325/SRR2060191.sra Written 21905258 spots total Written 24587538 spots for /home/okishinya/chipatlas/results/rn6/SRX1056325/SRR2060192.sra Written 24587538 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: 03:19:30 46492796 reads; of these: 46492796 (100.00%) were unpaired; of these: 7732082 (16.63%) aligned 0 times 28714023 (61.76%) aligned exactly 1 time 10046691 (21.61%) aligned >1 times 83.37% overall alignment rate Time searching: 03:19:34 Overall time: 03:19:34 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 16 files... [bam_rmdupse_core] 2303301 / 38760714 = 0.0594 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 23:19:26: # Command line: callpeak -t SRX1056325.bam -f BAM -g 2.15e9 -n SRX1056325.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056325.10 # format = BAM # ChIP-seq file = ['SRX1056325.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 23:19:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:19:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:19:26: # Command line: callpeak -t SRX1056325.bam -f BAM -g 2.15e9 -n SRX1056325.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056325.20 # format = BAM # ChIP-seq file = ['SRX1056325.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 23:19:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:19:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:19:26: # Command line: callpeak -t SRX1056325.bam -f BAM -g 2.15e9 -n SRX1056325.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056325.05 # format = BAM # ChIP-seq file = ['SRX1056325.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 23:19:26: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:19:26: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:19:40: 1000000 INFO @ Fri, 10 Nov 2017 23:19:41: 1000000 INFO @ Fri, 10 Nov 2017 23:19:41: 1000000 INFO @ Fri, 10 Nov 2017 23:19:54: 2000000 INFO @ Fri, 10 Nov 2017 23:19:56: 2000000 INFO @ Fri, 10 Nov 2017 23:19:57: 2000000 INFO @ Fri, 10 Nov 2017 23:20:09: 3000000 INFO @ Fri, 10 Nov 2017 23:20:12: 3000000 INFO @ Fri, 10 Nov 2017 23:20:13: 3000000 INFO @ Fri, 10 Nov 2017 23:20:21: 4000000 INFO @ Fri, 10 Nov 2017 23:20:26: 4000000 INFO @ Fri, 10 Nov 2017 23:20:27: 4000000 INFO @ Fri, 10 Nov 2017 23:20:34: 5000000 INFO @ Fri, 10 Nov 2017 23:20:40: 5000000 INFO @ Fri, 10 Nov 2017 23:20:41: 5000000 INFO @ Fri, 10 Nov 2017 23:20:47: 6000000 INFO @ Fri, 10 Nov 2017 23:20:54: 6000000 INFO @ Fri, 10 Nov 2017 23:20:54: 6000000 INFO @ Fri, 10 Nov 2017 23:20:59: 7000000 INFO @ Fri, 10 Nov 2017 23:21:06: 7000000 INFO @ Fri, 10 Nov 2017 23:21:08: 7000000 INFO @ Fri, 10 Nov 2017 23:21:11: 8000000 INFO @ Fri, 10 Nov 2017 23:21:19: 8000000 INFO @ Fri, 10 Nov 2017 23:21:20: 8000000 INFO @ Fri, 10 Nov 2017 23:21:23: 9000000 INFO @ Fri, 10 Nov 2017 23:21:31: 9000000 INFO @ Fri, 10 Nov 2017 23:21:32: 9000000 INFO @ Fri, 10 Nov 2017 23:21:34: 10000000 INFO @ Fri, 10 Nov 2017 23:21:43: 10000000 INFO @ Fri, 10 Nov 2017 23:21:44: 10000000 INFO @ Fri, 10 Nov 2017 23:21:46: 11000000 INFO @ Fri, 10 Nov 2017 23:21:56: 11000000 INFO @ Fri, 10 Nov 2017 23:21:56: 11000000 INFO @ Fri, 10 Nov 2017 23:21:57: 12000000 INFO @ Fri, 10 Nov 2017 23:22:08: 12000000 INFO @ Fri, 10 Nov 2017 23:22:10: 12000000 INFO @ Fri, 10 Nov 2017 23:22:11: 13000000 INFO @ Fri, 10 Nov 2017 23:22:22: 13000000 INFO @ Fri, 10 Nov 2017 23:22:25: 14000000 INFO @ Fri, 10 Nov 2017 23:22:25: 13000000 INFO @ Fri, 10 Nov 2017 23:22:36: 14000000 INFO @ Fri, 10 Nov 2017 23:22:38: 15000000 INFO @ Fri, 10 Nov 2017 23:22:39: 14000000 INFO @ Fri, 10 Nov 2017 23:22:49: 15000000 INFO @ Fri, 10 Nov 2017 23:22:49: 16000000 INFO @ Fri, 10 Nov 2017 23:22:51: 15000000 INFO @ Fri, 10 Nov 2017 23:23:01: 17000000 INFO @ Fri, 10 Nov 2017 23:23:01: 16000000 INFO @ Fri, 10 Nov 2017 23:23:07: 16000000 INFO @ Fri, 10 Nov 2017 23:23:13: 18000000 INFO @ Fri, 10 Nov 2017 23:23:14: 17000000 INFO @ Fri, 10 Nov 2017 23:23:21: 17000000 INFO @ Fri, 10 Nov 2017 23:23:26: 19000000 INFO @ Fri, 10 Nov 2017 23:23:27: 18000000 INFO @ Fri, 10 Nov 2017 23:23:34: 18000000 INFO @ Fri, 10 Nov 2017 23:23:38: 20000000 INFO @ Fri, 10 Nov 2017 23:23:40: 19000000 INFO @ Fri, 10 Nov 2017 23:23:46: 19000000 INFO @ Fri, 10 Nov 2017 23:23:50: 21000000 INFO @ Fri, 10 Nov 2017 23:23:51: 20000000 INFO @ Fri, 10 Nov 2017 23:23:58: 20000000 INFO @ Fri, 10 Nov 2017 23:24:02: 22000000 INFO @ Fri, 10 Nov 2017 23:24:04: 21000000 INFO @ Fri, 10 Nov 2017 23:24:10: 21000000 INFO @ Fri, 10 Nov 2017 23:24:14: 23000000 INFO @ Fri, 10 Nov 2017 23:24:16: 22000000 INFO @ Fri, 10 Nov 2017 23:24:21: 22000000 INFO @ Fri, 10 Nov 2017 23:24:26: 24000000 INFO @ Fri, 10 Nov 2017 23:24:29: 23000000 INFO @ Fri, 10 Nov 2017 23:24:33: 23000000 INFO @ Fri, 10 Nov 2017 23:24:38: 25000000 INFO @ Fri, 10 Nov 2017 23:24:41: 24000000 INFO @ Fri, 10 Nov 2017 23:24:45: 24000000 INFO @ Fri, 10 Nov 2017 23:24:50: 26000000 INFO @ Fri, 10 Nov 2017 23:24:54: 25000000 INFO @ Fri, 10 Nov 2017 23:24:57: 25000000 INFO @ Fri, 10 Nov 2017 23:25:01: 27000000 INFO @ Fri, 10 Nov 2017 23:25:06: 26000000 INFO @ Fri, 10 Nov 2017 23:25:09: 26000000 INFO @ Fri, 10 Nov 2017 23:25:13: 28000000 INFO @ Fri, 10 Nov 2017 23:25:19: 27000000 INFO @ Fri, 10 Nov 2017 23:25:21: 27000000 INFO @ Fri, 10 Nov 2017 23:25:25: 29000000 INFO @ Fri, 10 Nov 2017 23:25:32: 28000000 INFO @ Fri, 10 Nov 2017 23:25:33: 28000000 INFO @ Fri, 10 Nov 2017 23:25:38: 30000000 INFO @ Fri, 10 Nov 2017 23:25:44: 29000000 INFO @ Fri, 10 Nov 2017 23:25:45: 29000000 INFO @ Fri, 10 Nov 2017 23:25:50: 31000000 INFO @ Fri, 10 Nov 2017 23:25:56: 30000000 INFO @ Fri, 10 Nov 2017 23:25:57: 30000000 INFO @ Fri, 10 Nov 2017 23:26:02: 32000000 INFO @ Fri, 10 Nov 2017 23:26:08: 31000000 INFO @ Fri, 10 Nov 2017 23:26:09: 31000000 INFO @ Fri, 10 Nov 2017 23:26:14: 33000000 INFO @ Fri, 10 Nov 2017 23:26:20: 32000000 INFO @ Fri, 10 Nov 2017 23:26:21: 32000000 INFO @ Fri, 10 Nov 2017 23:26:26: 34000000 INFO @ Fri, 10 Nov 2017 23:26:34: 33000000 INFO @ Fri, 10 Nov 2017 23:26:34: 33000000 INFO @ Fri, 10 Nov 2017 23:26:40: 35000000 INFO @ Fri, 10 Nov 2017 23:26:46: 34000000 INFO @ Fri, 10 Nov 2017 23:26:48: 34000000 INFO @ Fri, 10 Nov 2017 23:26:53: 36000000 INFO @ Fri, 10 Nov 2017 23:26:59: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:26:59: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:26:59: #1 total tags in treatment: 36457413 INFO @ Fri, 10 Nov 2017 23:26:59: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:26:59: #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 23:26:59: 35000000 INFO @ Fri, 10 Nov 2017 23:27:00: #1 tags after filtering in treatment: 36457330 INFO @ Fri, 10 Nov 2017 23:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:27:00: #1 finished! INFO @ Fri, 10 Nov 2017 23:27:00: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:27:01: 35000000 INFO @ Fri, 10 Nov 2017 23:27:04: #2 number of paired peaks: 6436 INFO @ Fri, 10 Nov 2017 23:27:04: start model_add_line... INFO @ Fri, 10 Nov 2017 23:27:05: start X-correlation... INFO @ Fri, 10 Nov 2017 23:27:05: end of X-cor INFO @ Fri, 10 Nov 2017 23:27:05: #2 finished! INFO @ Fri, 10 Nov 2017 23:27:05: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Nov 2017 23:27:05: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Nov 2017 23:27:05: #2.2 Generate R script for model : SRX1056325.05_model.r WARNING @ Fri, 10 Nov 2017 23:27:05: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:27:05: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Nov 2017 23:27:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:27:05: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:27:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:27:10: 36000000 INFO @ Fri, 10 Nov 2017 23:27:15: 36000000 INFO @ Fri, 10 Nov 2017 23:27:16: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:27:16: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:27:16: #1 total tags in treatment: 36457413 INFO @ Fri, 10 Nov 2017 23:27:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:27:16: #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 23:27:18: #1 tags after filtering in treatment: 36457330 INFO @ Fri, 10 Nov 2017 23:27:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:27:18: #1 finished! INFO @ Fri, 10 Nov 2017 23:27:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:27:21: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 23:27:21: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 23:27:21: #1 total tags in treatment: 36457413 INFO @ Fri, 10 Nov 2017 23:27:21: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:27:21: #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 23:27:22: #2 number of paired peaks: 6436 INFO @ Fri, 10 Nov 2017 23:27:22: start model_add_line... INFO @ Fri, 10 Nov 2017 23:27:22: #1 tags after filtering in treatment: 36457330 INFO @ Fri, 10 Nov 2017 23:27:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:27:22: #1 finished! INFO @ Fri, 10 Nov 2017 23:27:22: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:27:22: start X-correlation... INFO @ Fri, 10 Nov 2017 23:27:22: end of X-cor INFO @ Fri, 10 Nov 2017 23:27:22: #2 finished! INFO @ Fri, 10 Nov 2017 23:27:22: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Nov 2017 23:27:22: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Nov 2017 23:27:22: #2.2 Generate R script for model : SRX1056325.10_model.r WARNING @ Fri, 10 Nov 2017 23:27:22: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:27:22: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Nov 2017 23:27:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:27:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:27:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:27:26: #2 number of paired peaks: 6436 INFO @ Fri, 10 Nov 2017 23:27:26: start model_add_line... INFO @ Fri, 10 Nov 2017 23:27:27: start X-correlation... INFO @ Fri, 10 Nov 2017 23:27:27: end of X-cor INFO @ Fri, 10 Nov 2017 23:27:27: #2 finished! INFO @ Fri, 10 Nov 2017 23:27:27: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Nov 2017 23:27:27: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Nov 2017 23:27:27: #2.2 Generate R script for model : SRX1056325.20_model.r WARNING @ Fri, 10 Nov 2017 23:27:27: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:27:27: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Nov 2017 23:27:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:27:27: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:27:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:28:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:29:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:29:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:29:42: #4 Write output xls file... SRX1056325.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:29:42: #4 Write peak in narrowPeak format file... SRX1056325.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:29:42: #4 Write summits bed file... SRX1056325.05_summits.bed INFO @ Fri, 10 Nov 2017 23:29:42: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (2245 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:30:00: #4 Write output xls file... SRX1056325.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:30:00: #4 Write peak in narrowPeak format file... SRX1056325.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:30:00: #4 Write summits bed file... SRX1056325.10_summits.bed INFO @ Fri, 10 Nov 2017 23:30:00: Done! pass1 - making usageList (52 chroms): 2 millis pass2 - checking and writing primary data (1177 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:30:12: #4 Write output xls file... SRX1056325.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:30:12: #4 Write peak in narrowPeak format file... SRX1056325.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:30:12: #4 Write summits bed file... SRX1056325.20_summits.bed INFO @ Fri, 10 Nov 2017 23:30:12: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (603 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。