Job ID = 10194731 sra ファイルのダウンロード中... Completed: 1476605K bytes transferred in 13 seconds (868423K bits/sec), in 1 file. Completed: 1151326K bytes transferred in 14 seconds (639309K 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 19422835 spots for /home/okishinya/chipatlas/results/rn6/SRX1056327/SRR2060196.sra Written 19422835 spots total Written 25048479 spots for /home/okishinya/chipatlas/results/rn6/SRX1056327/SRR2060195.sra Written 25048479 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: 01:59:40 44471314 reads; of these: 44471314 (100.00%) were unpaired; of these: 5753274 (12.94%) aligned 0 times 29187312 (65.63%) aligned exactly 1 time 9530728 (21.43%) aligned >1 times 87.06% overall alignment rate Time searching: 01:59:44 Overall time: 01:59:44 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] 4043063 / 38718040 = 0.1044 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 22:06:54: # Command line: callpeak -t SRX1056327.bam -f BAM -g 2.15e9 -n SRX1056327.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056327.20 # format = BAM # ChIP-seq file = ['SRX1056327.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 22:06:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:06:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:06:54: # Command line: callpeak -t SRX1056327.bam -f BAM -g 2.15e9 -n SRX1056327.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056327.10 # format = BAM # ChIP-seq file = ['SRX1056327.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 22:06:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:06:54: # Command line: callpeak -t SRX1056327.bam -f BAM -g 2.15e9 -n SRX1056327.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056327.05 # format = BAM # ChIP-seq file = ['SRX1056327.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 22:06:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:06:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:06:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:07:04: 1000000 INFO @ Fri, 10 Nov 2017 22:07:10: 1000000 INFO @ Fri, 10 Nov 2017 22:07:10: 1000000 INFO @ Fri, 10 Nov 2017 22:07:14: 2000000 INFO @ Fri, 10 Nov 2017 22:07:25: 3000000 INFO @ Fri, 10 Nov 2017 22:07:25: 2000000 INFO @ Fri, 10 Nov 2017 22:07:27: 2000000 INFO @ Fri, 10 Nov 2017 22:07:35: 4000000 INFO @ Fri, 10 Nov 2017 22:07:41: 3000000 INFO @ Fri, 10 Nov 2017 22:07:43: 3000000 INFO @ Fri, 10 Nov 2017 22:07:46: 5000000 INFO @ Fri, 10 Nov 2017 22:07:56: 6000000 INFO @ Fri, 10 Nov 2017 22:07:58: 4000000 INFO @ Fri, 10 Nov 2017 22:08:00: 4000000 INFO @ Fri, 10 Nov 2017 22:08:06: 7000000 INFO @ Fri, 10 Nov 2017 22:08:14: 5000000 INFO @ Fri, 10 Nov 2017 22:08:17: 8000000 INFO @ Fri, 10 Nov 2017 22:08:17: 5000000 INFO @ Fri, 10 Nov 2017 22:08:27: 9000000 INFO @ Fri, 10 Nov 2017 22:08:31: 6000000 INFO @ Fri, 10 Nov 2017 22:08:35: 6000000 INFO @ Fri, 10 Nov 2017 22:08:38: 10000000 INFO @ Fri, 10 Nov 2017 22:08:48: 7000000 INFO @ Fri, 10 Nov 2017 22:08:48: 11000000 INFO @ Fri, 10 Nov 2017 22:08:53: 7000000 INFO @ Fri, 10 Nov 2017 22:08:58: 12000000 INFO @ Fri, 10 Nov 2017 22:09:04: 8000000 INFO @ Fri, 10 Nov 2017 22:09:09: 13000000 INFO @ Fri, 10 Nov 2017 22:09:10: 8000000 INFO @ Fri, 10 Nov 2017 22:09:19: 14000000 INFO @ Fri, 10 Nov 2017 22:09:20: 9000000 INFO @ Fri, 10 Nov 2017 22:09:26: 9000000 INFO @ Fri, 10 Nov 2017 22:09:30: 15000000 INFO @ Fri, 10 Nov 2017 22:09:35: 10000000 INFO @ Fri, 10 Nov 2017 22:09:40: 16000000 INFO @ Fri, 10 Nov 2017 22:09:42: 10000000 INFO @ Fri, 10 Nov 2017 22:09:51: 17000000 INFO @ Fri, 10 Nov 2017 22:09:51: 11000000 INFO @ Fri, 10 Nov 2017 22:09:58: 11000000 INFO @ Fri, 10 Nov 2017 22:10:01: 18000000 INFO @ Fri, 10 Nov 2017 22:10:07: 12000000 INFO @ Fri, 10 Nov 2017 22:10:11: 19000000 INFO @ Fri, 10 Nov 2017 22:10:15: 12000000 INFO @ Fri, 10 Nov 2017 22:10:22: 20000000 INFO @ Fri, 10 Nov 2017 22:10:23: 13000000 INFO @ Fri, 10 Nov 2017 22:10:31: 13000000 INFO @ Fri, 10 Nov 2017 22:10:32: 21000000 INFO @ Fri, 10 Nov 2017 22:10:40: 14000000 INFO @ Fri, 10 Nov 2017 22:10:42: 22000000 INFO @ Fri, 10 Nov 2017 22:10:49: 14000000 INFO @ Fri, 10 Nov 2017 22:10:52: 23000000 INFO @ Fri, 10 Nov 2017 22:10:57: 15000000 INFO @ Fri, 10 Nov 2017 22:11:03: 24000000 INFO @ Fri, 10 Nov 2017 22:11:07: 15000000 INFO @ Fri, 10 Nov 2017 22:11:13: 25000000 INFO @ Fri, 10 Nov 2017 22:11:15: 16000000 INFO @ Fri, 10 Nov 2017 22:11:23: 26000000 INFO @ Fri, 10 Nov 2017 22:11:25: 16000000 INFO @ Fri, 10 Nov 2017 22:11:32: 17000000 INFO @ Fri, 10 Nov 2017 22:11:33: 27000000 INFO @ Fri, 10 Nov 2017 22:11:43: 17000000 INFO @ Fri, 10 Nov 2017 22:11:43: 28000000 INFO @ Fri, 10 Nov 2017 22:11:49: 18000000 INFO @ Fri, 10 Nov 2017 22:11:54: 29000000 INFO @ Fri, 10 Nov 2017 22:12:01: 18000000 INFO @ Fri, 10 Nov 2017 22:12:04: 30000000 INFO @ Fri, 10 Nov 2017 22:12:06: 19000000 INFO @ Fri, 10 Nov 2017 22:12:14: 31000000 INFO @ Fri, 10 Nov 2017 22:12:18: 19000000 INFO @ Fri, 10 Nov 2017 22:12:23: 20000000 INFO @ Fri, 10 Nov 2017 22:12:24: 32000000 INFO @ Fri, 10 Nov 2017 22:12:35: 33000000 INFO @ Fri, 10 Nov 2017 22:12:36: 20000000 INFO @ Fri, 10 Nov 2017 22:12:39: 21000000 INFO @ Fri, 10 Nov 2017 22:12:45: 34000000 INFO @ Fri, 10 Nov 2017 22:12:53: 21000000 INFO @ Fri, 10 Nov 2017 22:12:53: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:12:53: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:12:53: #1 total tags in treatment: 34674977 INFO @ Fri, 10 Nov 2017 22:12:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:12:53: #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 22:12:54: #1 tags after filtering in treatment: 34674894 INFO @ Fri, 10 Nov 2017 22:12:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:12:54: #1 finished! INFO @ Fri, 10 Nov 2017 22:12:54: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:12:56: 22000000 INFO @ Fri, 10 Nov 2017 22:12:58: #2 number of paired peaks: 6441 INFO @ Fri, 10 Nov 2017 22:12:58: start model_add_line... INFO @ Fri, 10 Nov 2017 22:12:59: start X-correlation... INFO @ Fri, 10 Nov 2017 22:12:59: end of X-cor INFO @ Fri, 10 Nov 2017 22:12:59: #2 finished! INFO @ Fri, 10 Nov 2017 22:12:59: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Nov 2017 22:12:59: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 10 Nov 2017 22:12:59: #2.2 Generate R script for model : SRX1056327.05_model.r WARNING @ Fri, 10 Nov 2017 22:12:59: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:12:59: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 10 Nov 2017 22:12:59: #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 22:12:59: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:12:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:13:10: 22000000 INFO @ Fri, 10 Nov 2017 22:13:13: 23000000 INFO @ Fri, 10 Nov 2017 22:13:29: 23000000 INFO @ Fri, 10 Nov 2017 22:13:30: 24000000 INFO @ Fri, 10 Nov 2017 22:13:46: 25000000 INFO @ Fri, 10 Nov 2017 22:13:48: 24000000 INFO @ Fri, 10 Nov 2017 22:14:01: 26000000 INFO @ Fri, 10 Nov 2017 22:14:09: 25000000 INFO @ Fri, 10 Nov 2017 22:14:17: 27000000 INFO @ Fri, 10 Nov 2017 22:14:29: 26000000 INFO @ Fri, 10 Nov 2017 22:14:32: 28000000 INFO @ Fri, 10 Nov 2017 22:14:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:14:48: 29000000 INFO @ Fri, 10 Nov 2017 22:14:49: 27000000 INFO @ Fri, 10 Nov 2017 22:15:03: 30000000 INFO @ Fri, 10 Nov 2017 22:15:09: 28000000 INFO @ Fri, 10 Nov 2017 22:15:15: 31000000 INFO @ Fri, 10 Nov 2017 22:15:28: 29000000 INFO @ Fri, 10 Nov 2017 22:15:30: 32000000 INFO @ Fri, 10 Nov 2017 22:15:34: #4 Write output xls file... SRX1056327.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:15:34: #4 Write peak in narrowPeak format file... SRX1056327.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:15:34: #4 Write summits bed file... SRX1056327.05_summits.bed INFO @ Fri, 10 Nov 2017 22:15:34: Done! pass1 - making usageList (60 chroms): 2 millis pass2 - checking and writing primary data (2101 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:15:45: 33000000 INFO @ Fri, 10 Nov 2017 22:15:50: 30000000 INFO @ Fri, 10 Nov 2017 22:16:00: 34000000 INFO @ Fri, 10 Nov 2017 22:16:06: 31000000 INFO @ Fri, 10 Nov 2017 22:16:12: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:16:12: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:16:12: #1 total tags in treatment: 34674977 INFO @ Fri, 10 Nov 2017 22:16:12: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:16:12: #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 22:16:13: #1 tags after filtering in treatment: 34674894 INFO @ Fri, 10 Nov 2017 22:16:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:16:13: #1 finished! INFO @ Fri, 10 Nov 2017 22:16:13: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:16:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:16:17: #2 number of paired peaks: 6441 INFO @ Fri, 10 Nov 2017 22:16:17: start model_add_line... INFO @ Fri, 10 Nov 2017 22:16:17: start X-correlation... INFO @ Fri, 10 Nov 2017 22:16:17: end of X-cor INFO @ Fri, 10 Nov 2017 22:16:17: #2 finished! INFO @ Fri, 10 Nov 2017 22:16:17: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Nov 2017 22:16:17: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 10 Nov 2017 22:16:17: #2.2 Generate R script for model : SRX1056327.20_model.r WARNING @ Fri, 10 Nov 2017 22:16:17: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:16:17: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 10 Nov 2017 22:16:17: #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 22:16:17: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:16:25: 32000000 INFO @ Fri, 10 Nov 2017 22:16:35: 33000000 INFO @ Fri, 10 Nov 2017 22:16:45: 34000000 INFO @ Fri, 10 Nov 2017 22:16:53: #1 tag size is determined as 100 bps INFO @ Fri, 10 Nov 2017 22:16:53: #1 tag size = 100 INFO @ Fri, 10 Nov 2017 22:16:53: #1 total tags in treatment: 34674977 INFO @ Fri, 10 Nov 2017 22:16:53: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:16:53: #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 22:16:54: #1 tags after filtering in treatment: 34674894 INFO @ Fri, 10 Nov 2017 22:16:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:16:54: #1 finished! INFO @ Fri, 10 Nov 2017 22:16:54: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:16:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:16:58: #2 number of paired peaks: 6441 INFO @ Fri, 10 Nov 2017 22:16:58: start model_add_line... INFO @ Fri, 10 Nov 2017 22:16:58: start X-correlation... INFO @ Fri, 10 Nov 2017 22:16:58: end of X-cor INFO @ Fri, 10 Nov 2017 22:16:58: #2 finished! INFO @ Fri, 10 Nov 2017 22:16:58: #2 predicted fragment length is 100 bps INFO @ Fri, 10 Nov 2017 22:16:58: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 10 Nov 2017 22:16:58: #2.2 Generate R script for model : SRX1056327.10_model.r WARNING @ Fri, 10 Nov 2017 22:16:58: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 22:16:58: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 10 Nov 2017 22:16:58: #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 22:16:58: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:16:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:17:54: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:18:34: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:18:49: #4 Write output xls file... SRX1056327.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:18:49: #4 Write peak in narrowPeak format file... SRX1056327.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:18:49: #4 Write summits bed file... SRX1056327.20_summits.bed INFO @ Fri, 10 Nov 2017 22:18:49: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (554 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:19:29: #4 Write output xls file... SRX1056327.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:19:29: #4 Write peak in narrowPeak format file... SRX1056327.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:19:29: #4 Write summits bed file... SRX1056327.10_summits.bed INFO @ Fri, 10 Nov 2017 22:19:29: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1055 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。