Job ID = 10194936 sra ファイルのダウンロード中... Completed: 638636K bytes transferred in 8 seconds (647137K bits/sec), in 1 file. Completed: 755750K bytes transferred in 10 seconds (594422K 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 29543932 spots for /home/okishinya/chipatlas/results/rn6/SRX2512946/SRR5197460.sra Written 29543932 spots total Written 37381797 spots for /home/okishinya/chipatlas/results/rn6/SRX2512946/SRR5197461.sra Written 37381797 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:53:04 66925729 reads; of these: 66925729 (100.00%) were unpaired; of these: 12448702 (18.60%) aligned 0 times 37221588 (55.62%) aligned exactly 1 time 17255439 (25.78%) aligned >1 times 81.40% overall alignment rate Time searching: 00:53:08 Overall time: 00:53:08 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 16 files... [bam_rmdupse_core] 3679869 / 54477027 = 0.0675 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 01:03:21: # Command line: callpeak -t SRX2512946.bam -f BAM -g 2.15e9 -n SRX2512946.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512946.20 # format = BAM # ChIP-seq file = ['SRX2512946.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 01:03:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:03:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:03:21: # Command line: callpeak -t SRX2512946.bam -f BAM -g 2.15e9 -n SRX2512946.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512946.05 # format = BAM # ChIP-seq file = ['SRX2512946.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 01:03:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:03:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:03:21: # Command line: callpeak -t SRX2512946.bam -f BAM -g 2.15e9 -n SRX2512946.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512946.10 # format = BAM # ChIP-seq file = ['SRX2512946.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 01:03:21: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:03:21: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:03:29: 1000000 INFO @ Sat, 11 Nov 2017 01:03:30: 1000000 INFO @ Sat, 11 Nov 2017 01:03:30: 1000000 INFO @ Sat, 11 Nov 2017 01:03:36: 2000000 INFO @ Sat, 11 Nov 2017 01:03:39: 2000000 INFO @ Sat, 11 Nov 2017 01:03:39: 2000000 INFO @ Sat, 11 Nov 2017 01:03:44: 3000000 INFO @ Sat, 11 Nov 2017 01:03:48: 3000000 INFO @ Sat, 11 Nov 2017 01:03:48: 3000000 INFO @ Sat, 11 Nov 2017 01:03:51: 4000000 INFO @ Sat, 11 Nov 2017 01:03:56: 4000000 INFO @ Sat, 11 Nov 2017 01:03:57: 4000000 INFO @ Sat, 11 Nov 2017 01:03:59: 5000000 INFO @ Sat, 11 Nov 2017 01:04:04: 5000000 INFO @ Sat, 11 Nov 2017 01:04:04: 5000000 INFO @ Sat, 11 Nov 2017 01:04:06: 6000000 INFO @ Sat, 11 Nov 2017 01:04:11: 6000000 INFO @ Sat, 11 Nov 2017 01:04:12: 6000000 INFO @ Sat, 11 Nov 2017 01:04:14: 7000000 INFO @ Sat, 11 Nov 2017 01:04:18: 7000000 INFO @ Sat, 11 Nov 2017 01:04:20: 7000000 INFO @ Sat, 11 Nov 2017 01:04:21: 8000000 INFO @ Sat, 11 Nov 2017 01:04:25: 8000000 INFO @ Sat, 11 Nov 2017 01:04:28: 8000000 INFO @ Sat, 11 Nov 2017 01:04:29: 9000000 INFO @ Sat, 11 Nov 2017 01:04:32: 9000000 INFO @ Sat, 11 Nov 2017 01:04:36: 9000000 INFO @ Sat, 11 Nov 2017 01:04:37: 10000000 INFO @ Sat, 11 Nov 2017 01:04:39: 10000000 INFO @ Sat, 11 Nov 2017 01:04:44: 10000000 INFO @ Sat, 11 Nov 2017 01:04:46: 11000000 INFO @ Sat, 11 Nov 2017 01:04:46: 11000000 INFO @ Sat, 11 Nov 2017 01:04:52: 11000000 INFO @ Sat, 11 Nov 2017 01:04:53: 12000000 INFO @ Sat, 11 Nov 2017 01:04:54: 12000000 INFO @ Sat, 11 Nov 2017 01:05:00: 12000000 INFO @ Sat, 11 Nov 2017 01:05:00: 13000000 INFO @ Sat, 11 Nov 2017 01:05:03: 13000000 INFO @ Sat, 11 Nov 2017 01:05:07: 13000000 INFO @ Sat, 11 Nov 2017 01:05:07: 14000000 INFO @ Sat, 11 Nov 2017 01:05:11: 14000000 INFO @ Sat, 11 Nov 2017 01:05:14: 15000000 INFO @ Sat, 11 Nov 2017 01:05:15: 14000000 INFO @ Sat, 11 Nov 2017 01:05:19: 15000000 INFO @ Sat, 11 Nov 2017 01:05:21: 16000000 INFO @ Sat, 11 Nov 2017 01:05:22: 15000000 INFO @ Sat, 11 Nov 2017 01:05:26: 16000000 INFO @ Sat, 11 Nov 2017 01:05:28: 17000000 INFO @ Sat, 11 Nov 2017 01:05:30: 16000000 INFO @ Sat, 11 Nov 2017 01:05:34: 17000000 INFO @ Sat, 11 Nov 2017 01:05:35: 18000000 INFO @ Sat, 11 Nov 2017 01:05:38: 17000000 INFO @ Sat, 11 Nov 2017 01:05:42: 18000000 INFO @ Sat, 11 Nov 2017 01:05:42: 19000000 INFO @ Sat, 11 Nov 2017 01:05:45: 18000000 INFO @ Sat, 11 Nov 2017 01:05:49: 20000000 INFO @ Sat, 11 Nov 2017 01:05:50: 19000000 INFO @ Sat, 11 Nov 2017 01:05:53: 19000000 INFO @ Sat, 11 Nov 2017 01:05:56: 21000000 INFO @ Sat, 11 Nov 2017 01:05:58: 20000000 INFO @ Sat, 11 Nov 2017 01:06:01: 20000000 INFO @ Sat, 11 Nov 2017 01:06:03: 22000000 INFO @ Sat, 11 Nov 2017 01:06:06: 21000000 INFO @ Sat, 11 Nov 2017 01:06:08: 21000000 INFO @ Sat, 11 Nov 2017 01:06:10: 23000000 INFO @ Sat, 11 Nov 2017 01:06:14: 22000000 INFO @ Sat, 11 Nov 2017 01:06:16: 22000000 INFO @ Sat, 11 Nov 2017 01:06:18: 24000000 INFO @ Sat, 11 Nov 2017 01:06:22: 23000000 INFO @ Sat, 11 Nov 2017 01:06:24: 23000000 INFO @ Sat, 11 Nov 2017 01:06:25: 25000000 INFO @ Sat, 11 Nov 2017 01:06:31: 24000000 INFO @ Sat, 11 Nov 2017 01:06:32: 24000000 INFO @ Sat, 11 Nov 2017 01:06:32: 26000000 INFO @ Sat, 11 Nov 2017 01:06:40: 27000000 INFO @ Sat, 11 Nov 2017 01:06:40: 25000000 INFO @ Sat, 11 Nov 2017 01:06:40: 25000000 INFO @ Sat, 11 Nov 2017 01:06:47: 28000000 INFO @ Sat, 11 Nov 2017 01:06:48: 26000000 INFO @ Sat, 11 Nov 2017 01:06:49: 26000000 INFO @ Sat, 11 Nov 2017 01:06:55: 29000000 INFO @ Sat, 11 Nov 2017 01:06:56: 27000000 INFO @ Sat, 11 Nov 2017 01:06:57: 27000000 INFO @ Sat, 11 Nov 2017 01:07:02: 30000000 INFO @ Sat, 11 Nov 2017 01:07:04: 28000000 INFO @ Sat, 11 Nov 2017 01:07:06: 28000000 INFO @ Sat, 11 Nov 2017 01:07:10: 31000000 INFO @ Sat, 11 Nov 2017 01:07:12: 29000000 INFO @ Sat, 11 Nov 2017 01:07:15: 29000000 INFO @ Sat, 11 Nov 2017 01:07:17: 32000000 INFO @ Sat, 11 Nov 2017 01:07:19: 30000000 INFO @ Sat, 11 Nov 2017 01:07:23: 30000000 INFO @ Sat, 11 Nov 2017 01:07:24: 33000000 INFO @ Sat, 11 Nov 2017 01:07:27: 31000000 INFO @ Sat, 11 Nov 2017 01:07:30: 31000000 INFO @ Sat, 11 Nov 2017 01:07:31: 34000000 INFO @ Sat, 11 Nov 2017 01:07:35: 32000000 INFO @ Sat, 11 Nov 2017 01:07:38: 32000000 INFO @ Sat, 11 Nov 2017 01:07:38: 35000000 INFO @ Sat, 11 Nov 2017 01:07:42: 33000000 INFO @ Sat, 11 Nov 2017 01:07:45: 36000000 INFO @ Sat, 11 Nov 2017 01:07:45: 33000000 INFO @ Sat, 11 Nov 2017 01:07:50: 34000000 INFO @ Sat, 11 Nov 2017 01:07:52: 37000000 INFO @ Sat, 11 Nov 2017 01:07:52: 34000000 INFO @ Sat, 11 Nov 2017 01:07:57: 35000000 INFO @ Sat, 11 Nov 2017 01:07:59: 38000000 INFO @ Sat, 11 Nov 2017 01:07:59: 35000000 INFO @ Sat, 11 Nov 2017 01:08:05: 36000000 INFO @ Sat, 11 Nov 2017 01:08:06: 39000000 INFO @ Sat, 11 Nov 2017 01:08:07: 36000000 INFO @ Sat, 11 Nov 2017 01:08:13: 37000000 INFO @ Sat, 11 Nov 2017 01:08:13: 40000000 INFO @ Sat, 11 Nov 2017 01:08:14: 37000000 INFO @ Sat, 11 Nov 2017 01:08:20: 41000000 INFO @ Sat, 11 Nov 2017 01:08:20: 38000000 INFO @ Sat, 11 Nov 2017 01:08:21: 38000000 INFO @ Sat, 11 Nov 2017 01:08:27: 42000000 INFO @ Sat, 11 Nov 2017 01:08:27: 39000000 INFO @ Sat, 11 Nov 2017 01:08:28: 39000000 INFO @ Sat, 11 Nov 2017 01:08:35: 43000000 INFO @ Sat, 11 Nov 2017 01:08:35: 40000000 INFO @ Sat, 11 Nov 2017 01:08:36: 40000000 INFO @ Sat, 11 Nov 2017 01:08:42: 41000000 INFO @ Sat, 11 Nov 2017 01:08:42: 44000000 INFO @ Sat, 11 Nov 2017 01:08:43: 41000000 INFO @ Sat, 11 Nov 2017 01:08:49: 45000000 INFO @ Sat, 11 Nov 2017 01:08:50: 42000000 INFO @ Sat, 11 Nov 2017 01:08:50: 42000000 INFO @ Sat, 11 Nov 2017 01:08:56: 46000000 INFO @ Sat, 11 Nov 2017 01:08:57: 43000000 INFO @ Sat, 11 Nov 2017 01:08:57: 43000000 INFO @ Sat, 11 Nov 2017 01:09:04: 47000000 INFO @ Sat, 11 Nov 2017 01:09:05: 44000000 INFO @ Sat, 11 Nov 2017 01:09:05: 44000000 INFO @ Sat, 11 Nov 2017 01:09:11: 48000000 INFO @ Sat, 11 Nov 2017 01:09:12: 45000000 INFO @ Sat, 11 Nov 2017 01:09:13: 45000000 INFO @ Sat, 11 Nov 2017 01:09:18: 49000000 INFO @ Sat, 11 Nov 2017 01:09:19: 46000000 INFO @ Sat, 11 Nov 2017 01:09:21: 46000000 INFO @ Sat, 11 Nov 2017 01:09:26: 50000000 INFO @ Sat, 11 Nov 2017 01:09:26: 47000000 INFO @ Sat, 11 Nov 2017 01:09:29: 47000000 INFO @ Sat, 11 Nov 2017 01:09:32: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:09:32: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:09:32: #1 total tags in treatment: 50797158 INFO @ Sat, 11 Nov 2017 01:09:32: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:09:32: #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 01:09:34: 48000000 INFO @ Sat, 11 Nov 2017 01:09:34: #1 tags after filtering in treatment: 50797112 INFO @ Sat, 11 Nov 2017 01:09:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:09:34: #1 finished! INFO @ Sat, 11 Nov 2017 01:09:34: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:09:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:09:36: 48000000 INFO @ Sat, 11 Nov 2017 01:09:39: #2 number of paired peaks: 7659 INFO @ Sat, 11 Nov 2017 01:09:39: start model_add_line... INFO @ Sat, 11 Nov 2017 01:09:40: start X-correlation... INFO @ Sat, 11 Nov 2017 01:09:40: end of X-cor INFO @ Sat, 11 Nov 2017 01:09:40: #2 finished! INFO @ Sat, 11 Nov 2017 01:09:40: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Nov 2017 01:09:40: #2 alternative fragment length(s) may be 42,106 bps INFO @ Sat, 11 Nov 2017 01:09:40: #2.2 Generate R script for model : SRX2512946.20_model.r WARNING @ Sat, 11 Nov 2017 01:09:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:09:40: #2 You may need to consider one of the other alternative d(s): 42,106 WARNING @ Sat, 11 Nov 2017 01:09:40: #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 01:09:40: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:09:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:09:41: 49000000 INFO @ Sat, 11 Nov 2017 01:09:44: 49000000 INFO @ Sat, 11 Nov 2017 01:09:48: 50000000 INFO @ Sat, 11 Nov 2017 01:09:51: 50000000 INFO @ Sat, 11 Nov 2017 01:09:55: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:09:55: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:09:55: #1 total tags in treatment: 50797158 INFO @ Sat, 11 Nov 2017 01:09:55: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:09:55: #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 01:09:57: #1 tags after filtering in treatment: 50797112 INFO @ Sat, 11 Nov 2017 01:09:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:09:57: #1 finished! INFO @ Sat, 11 Nov 2017 01:09:57: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:09:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:09:58: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:09:58: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:09:58: #1 total tags in treatment: 50797158 INFO @ Sat, 11 Nov 2017 01:09:58: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:09:58: #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 01:10:00: #1 tags after filtering in treatment: 50797112 INFO @ Sat, 11 Nov 2017 01:10:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:10:00: #1 finished! INFO @ Sat, 11 Nov 2017 01:10:00: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:10:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:10:03: #2 number of paired peaks: 7659 INFO @ Sat, 11 Nov 2017 01:10:03: start model_add_line... INFO @ Sat, 11 Nov 2017 01:10:04: start X-correlation... INFO @ Sat, 11 Nov 2017 01:10:04: end of X-cor INFO @ Sat, 11 Nov 2017 01:10:04: #2 finished! INFO @ Sat, 11 Nov 2017 01:10:04: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Nov 2017 01:10:04: #2 alternative fragment length(s) may be 42,106 bps INFO @ Sat, 11 Nov 2017 01:10:04: #2.2 Generate R script for model : SRX2512946.05_model.r WARNING @ Sat, 11 Nov 2017 01:10:04: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:10:04: #2 You may need to consider one of the other alternative d(s): 42,106 WARNING @ Sat, 11 Nov 2017 01:10:04: #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 01:10:04: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:10:05: #2 number of paired peaks: 7659 INFO @ Sat, 11 Nov 2017 01:10:05: start model_add_line... INFO @ Sat, 11 Nov 2017 01:10:06: start X-correlation... INFO @ Sat, 11 Nov 2017 01:10:06: end of X-cor INFO @ Sat, 11 Nov 2017 01:10:06: #2 finished! INFO @ Sat, 11 Nov 2017 01:10:06: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Nov 2017 01:10:06: #2 alternative fragment length(s) may be 42,106 bps INFO @ Sat, 11 Nov 2017 01:10:06: #2.2 Generate R script for model : SRX2512946.10_model.r WARNING @ Sat, 11 Nov 2017 01:10:06: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:10:06: #2 You may need to consider one of the other alternative d(s): 42,106 WARNING @ Sat, 11 Nov 2017 01:10:06: #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 01:10:06: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:11:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:12:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:12:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:13:15: #4 Write output xls file... SRX2512946.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:13:15: #4 Write peak in narrowPeak format file... SRX2512946.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:13:15: #4 Write summits bed file... SRX2512946.20_summits.bed INFO @ Sat, 11 Nov 2017 01:13:15: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (993 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:13:42: #4 Write output xls file... SRX2512946.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:13:42: #4 Write peak in narrowPeak format file... SRX2512946.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:13:42: #4 Write summits bed file... SRX2512946.05_summits.bed INFO @ Sat, 11 Nov 2017 01:13:42: Done! pass1 - making usageList (91 chroms): 2 millis pass2 - checking and writing primary data (5141 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:13:47: #4 Write output xls file... SRX2512946.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:13:47: #4 Write peak in narrowPeak format file... SRX2512946.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:13:47: #4 Write summits bed file... SRX2512946.10_summits.bed INFO @ Sat, 11 Nov 2017 01:13:47: Done! pass1 - making usageList (72 chroms): 2 millis pass2 - checking and writing primary data (2336 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。