Job ID = 10453667 sra ファイルのダウンロード中... Completed: 724563K bytes transferred in 19 seconds (297838K 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 41964739 spots for /home/okishinya/chipatlas/results/rn6/SRX3478272/SRR6384651.sra Written 41964739 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: 01:15:03 41964739 reads; of these: 41964739 (100.00%) were unpaired; of these: 1010396 (2.41%) aligned 0 times 28448915 (67.79%) aligned exactly 1 time 12505428 (29.80%) aligned >1 times 97.59% overall alignment rate Time searching: 01:15:07 Overall time: 01:15:07 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 20 files... [bam_rmdupse_core] 1187946 / 40954343 = 0.0290 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 @ Thu, 08 Feb 2018 18:06:01: # Command line: callpeak -t SRX3478272.bam -f BAM -g 2.15e9 -n SRX3478272.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3478272.10 # format = BAM # ChIP-seq file = ['SRX3478272.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 @ Thu, 08 Feb 2018 18:06:01: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:06:01: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:06:01: # Command line: callpeak -t SRX3478272.bam -f BAM -g 2.15e9 -n SRX3478272.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3478272.05 # format = BAM # ChIP-seq file = ['SRX3478272.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 @ Thu, 08 Feb 2018 18:06:01: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:06:01: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:06:01: # Command line: callpeak -t SRX3478272.bam -f BAM -g 2.15e9 -n SRX3478272.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3478272.20 # format = BAM # ChIP-seq file = ['SRX3478272.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 @ Thu, 08 Feb 2018 18:06:01: #1 read tag files... INFO @ Thu, 08 Feb 2018 18:06:01: #1 read treatment tags... INFO @ Thu, 08 Feb 2018 18:06:12: 1000000 INFO @ Thu, 08 Feb 2018 18:06:13: 1000000 INFO @ Thu, 08 Feb 2018 18:06:17: 1000000 INFO @ Thu, 08 Feb 2018 18:06:25: 2000000 INFO @ Thu, 08 Feb 2018 18:06:27: 2000000 INFO @ Thu, 08 Feb 2018 18:06:36: 2000000 INFO @ Thu, 08 Feb 2018 18:06:37: 3000000 INFO @ Thu, 08 Feb 2018 18:06:42: 3000000 INFO @ Thu, 08 Feb 2018 18:06:49: 4000000 INFO @ Thu, 08 Feb 2018 18:06:57: 4000000 INFO @ Thu, 08 Feb 2018 18:06:57: 3000000 INFO @ Thu, 08 Feb 2018 18:07:02: 5000000 INFO @ Thu, 08 Feb 2018 18:07:12: 5000000 INFO @ Thu, 08 Feb 2018 18:07:14: 6000000 INFO @ Thu, 08 Feb 2018 18:07:18: 4000000 INFO @ Thu, 08 Feb 2018 18:07:26: 7000000 INFO @ Thu, 08 Feb 2018 18:07:27: 6000000 INFO @ Thu, 08 Feb 2018 18:07:39: 5000000 INFO @ Thu, 08 Feb 2018 18:07:39: 8000000 INFO @ Thu, 08 Feb 2018 18:07:41: 7000000 INFO @ Thu, 08 Feb 2018 18:07:53: 9000000 INFO @ Thu, 08 Feb 2018 18:07:56: 8000000 INFO @ Thu, 08 Feb 2018 18:08:00: 6000000 INFO @ Thu, 08 Feb 2018 18:08:06: 10000000 INFO @ Thu, 08 Feb 2018 18:08:11: 9000000 INFO @ Thu, 08 Feb 2018 18:08:18: 11000000 INFO @ Thu, 08 Feb 2018 18:08:19: 7000000 INFO @ Thu, 08 Feb 2018 18:08:26: 10000000 INFO @ Thu, 08 Feb 2018 18:08:31: 12000000 INFO @ Thu, 08 Feb 2018 18:08:39: 8000000 INFO @ Thu, 08 Feb 2018 18:08:41: 11000000 INFO @ Thu, 08 Feb 2018 18:08:42: 13000000 INFO @ Thu, 08 Feb 2018 18:08:54: 14000000 INFO @ Thu, 08 Feb 2018 18:08:55: 12000000 INFO @ Thu, 08 Feb 2018 18:08:58: 9000000 INFO @ Thu, 08 Feb 2018 18:09:05: 15000000 INFO @ Thu, 08 Feb 2018 18:09:09: 13000000 INFO @ Thu, 08 Feb 2018 18:09:17: 16000000 INFO @ Thu, 08 Feb 2018 18:09:18: 10000000 INFO @ Thu, 08 Feb 2018 18:09:22: 14000000 INFO @ Thu, 08 Feb 2018 18:09:28: 17000000 INFO @ Thu, 08 Feb 2018 18:09:36: 15000000 INFO @ Thu, 08 Feb 2018 18:09:37: 11000000 INFO @ Thu, 08 Feb 2018 18:09:40: 18000000 INFO @ Thu, 08 Feb 2018 18:09:51: 16000000 INFO @ Thu, 08 Feb 2018 18:09:51: 19000000 INFO @ Thu, 08 Feb 2018 18:09:57: 12000000 INFO @ Thu, 08 Feb 2018 18:10:03: 20000000 INFO @ Thu, 08 Feb 2018 18:10:05: 17000000 INFO @ Thu, 08 Feb 2018 18:10:15: 21000000 INFO @ Thu, 08 Feb 2018 18:10:16: 13000000 INFO @ Thu, 08 Feb 2018 18:10:20: 18000000 INFO @ Thu, 08 Feb 2018 18:10:26: 22000000 INFO @ Thu, 08 Feb 2018 18:10:34: 19000000 INFO @ Thu, 08 Feb 2018 18:10:36: 14000000 INFO @ Thu, 08 Feb 2018 18:10:37: 23000000 INFO @ Thu, 08 Feb 2018 18:10:48: 20000000 INFO @ Thu, 08 Feb 2018 18:10:49: 24000000 INFO @ Thu, 08 Feb 2018 18:10:55: 15000000 INFO @ Thu, 08 Feb 2018 18:11:01: 25000000 INFO @ Thu, 08 Feb 2018 18:11:02: 21000000 INFO @ Thu, 08 Feb 2018 18:11:12: 26000000 INFO @ Thu, 08 Feb 2018 18:11:14: 22000000 INFO @ Thu, 08 Feb 2018 18:11:15: 16000000 INFO @ Thu, 08 Feb 2018 18:11:23: 27000000 INFO @ Thu, 08 Feb 2018 18:11:25: 23000000 INFO @ Thu, 08 Feb 2018 18:11:34: 17000000 INFO @ Thu, 08 Feb 2018 18:11:34: 28000000 INFO @ Thu, 08 Feb 2018 18:11:36: 24000000 INFO @ Thu, 08 Feb 2018 18:11:46: 29000000 INFO @ Thu, 08 Feb 2018 18:11:48: 25000000 INFO @ Thu, 08 Feb 2018 18:11:54: 18000000 INFO @ Thu, 08 Feb 2018 18:11:57: 30000000 INFO @ Thu, 08 Feb 2018 18:11:59: 26000000 INFO @ Thu, 08 Feb 2018 18:12:08: 31000000 INFO @ Thu, 08 Feb 2018 18:12:10: 27000000 INFO @ Thu, 08 Feb 2018 18:12:13: 19000000 INFO @ Thu, 08 Feb 2018 18:12:19: 32000000 INFO @ Thu, 08 Feb 2018 18:12:21: 28000000 INFO @ Thu, 08 Feb 2018 18:12:31: 33000000 INFO @ Thu, 08 Feb 2018 18:12:33: 29000000 INFO @ Thu, 08 Feb 2018 18:12:33: 20000000 INFO @ Thu, 08 Feb 2018 18:12:42: 34000000 INFO @ Thu, 08 Feb 2018 18:12:44: 30000000 INFO @ Thu, 08 Feb 2018 18:12:52: 21000000 INFO @ Thu, 08 Feb 2018 18:12:54: 35000000 INFO @ Thu, 08 Feb 2018 18:12:56: 31000000 INFO @ Thu, 08 Feb 2018 18:13:06: 36000000 INFO @ Thu, 08 Feb 2018 18:13:08: 32000000 INFO @ Thu, 08 Feb 2018 18:13:11: 22000000 INFO @ Thu, 08 Feb 2018 18:13:18: 37000000 INFO @ Thu, 08 Feb 2018 18:13:21: 33000000 INFO @ Thu, 08 Feb 2018 18:13:30: 38000000 INFO @ Thu, 08 Feb 2018 18:13:31: 23000000 INFO @ Thu, 08 Feb 2018 18:13:32: 34000000 INFO @ Thu, 08 Feb 2018 18:13:41: 39000000 INFO @ Thu, 08 Feb 2018 18:13:44: 35000000 INFO @ Thu, 08 Feb 2018 18:13:50: 24000000 INFO @ Thu, 08 Feb 2018 18:13:50: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:13:50: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:13:50: #1 total tags in treatment: 39766397 INFO @ Thu, 08 Feb 2018 18:13:50: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:13:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:13:52: #1 tags after filtering in treatment: 39766329 INFO @ Thu, 08 Feb 2018 18:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:13:52: #1 finished! INFO @ Thu, 08 Feb 2018 18:13:52: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:13:55: 36000000 INFO @ Thu, 08 Feb 2018 18:13:56: #2 number of paired peaks: 5942 INFO @ Thu, 08 Feb 2018 18:13:56: start model_add_line... INFO @ Thu, 08 Feb 2018 18:13:57: start X-correlation... INFO @ Thu, 08 Feb 2018 18:13:57: end of X-cor INFO @ Thu, 08 Feb 2018 18:13:57: #2 finished! INFO @ Thu, 08 Feb 2018 18:13:57: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 18:13:57: #2 alternative fragment length(s) may be 50,398 bps INFO @ Thu, 08 Feb 2018 18:13:57: #2.2 Generate R script for model : SRX3478272.10_model.r WARNING @ Thu, 08 Feb 2018 18:13:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 18:13:57: #2 You may need to consider one of the other alternative d(s): 50,398 WARNING @ Thu, 08 Feb 2018 18:13:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 18:13:57: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:14:06: 37000000 INFO @ Thu, 08 Feb 2018 18:14:09: 25000000 INFO @ Thu, 08 Feb 2018 18:14:18: 38000000 INFO @ Thu, 08 Feb 2018 18:14:28: 26000000 INFO @ Thu, 08 Feb 2018 18:14:30: 39000000 INFO @ Thu, 08 Feb 2018 18:14:39: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:14:39: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:14:39: #1 total tags in treatment: 39766397 INFO @ Thu, 08 Feb 2018 18:14:39: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:14:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:14:40: #1 tags after filtering in treatment: 39766329 INFO @ Thu, 08 Feb 2018 18:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:14:40: #1 finished! INFO @ Thu, 08 Feb 2018 18:14:40: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:14:45: #2 number of paired peaks: 5942 INFO @ Thu, 08 Feb 2018 18:14:45: start model_add_line... INFO @ Thu, 08 Feb 2018 18:14:45: start X-correlation... INFO @ Thu, 08 Feb 2018 18:14:45: end of X-cor INFO @ Thu, 08 Feb 2018 18:14:45: #2 finished! INFO @ Thu, 08 Feb 2018 18:14:45: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 18:14:45: #2 alternative fragment length(s) may be 50,398 bps INFO @ Thu, 08 Feb 2018 18:14:45: #2.2 Generate R script for model : SRX3478272.05_model.r WARNING @ Thu, 08 Feb 2018 18:14:45: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 18:14:45: #2 You may need to consider one of the other alternative d(s): 50,398 WARNING @ Thu, 08 Feb 2018 18:14:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 18:14:45: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:14:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:14:48: 27000000 INFO @ Thu, 08 Feb 2018 18:15:08: 28000000 INFO @ Thu, 08 Feb 2018 18:15:27: 29000000 INFO @ Thu, 08 Feb 2018 18:15:46: 30000000 INFO @ Thu, 08 Feb 2018 18:15:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:16:05: 31000000 INFO @ Thu, 08 Feb 2018 18:16:24: 32000000 INFO @ Thu, 08 Feb 2018 18:16:40: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:16:43: 33000000 INFO @ Thu, 08 Feb 2018 18:17:03: 34000000 INFO @ Thu, 08 Feb 2018 18:17:08: #4 Write output xls file... SRX3478272.10_peaks.xls INFO @ Thu, 08 Feb 2018 18:17:08: #4 Write peak in narrowPeak format file... SRX3478272.10_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:17:08: #4 Write summits bed file... SRX3478272.10_summits.bed INFO @ Thu, 08 Feb 2018 18:17:08: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (1274 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:17:22: 35000000 INFO @ Thu, 08 Feb 2018 18:17:42: 36000000 INFO @ Thu, 08 Feb 2018 18:17:46: #4 Write output xls file... SRX3478272.05_peaks.xls INFO @ Thu, 08 Feb 2018 18:17:46: #4 Write peak in narrowPeak format file... SRX3478272.05_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:17:46: #4 Write summits bed file... SRX3478272.05_summits.bed INFO @ Thu, 08 Feb 2018 18:17:46: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (2339 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 08 Feb 2018 18:18:01: 37000000 INFO @ Thu, 08 Feb 2018 18:18:21: 38000000 INFO @ Thu, 08 Feb 2018 18:18:41: 39000000 INFO @ Thu, 08 Feb 2018 18:18:56: #1 tag size is determined as 51 bps INFO @ Thu, 08 Feb 2018 18:18:56: #1 tag size = 51 INFO @ Thu, 08 Feb 2018 18:18:56: #1 total tags in treatment: 39766397 INFO @ Thu, 08 Feb 2018 18:18:56: #1 user defined the maximum tags... INFO @ Thu, 08 Feb 2018 18:18:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Feb 2018 18:18:57: #1 tags after filtering in treatment: 39766329 INFO @ Thu, 08 Feb 2018 18:18:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Feb 2018 18:18:57: #1 finished! INFO @ Thu, 08 Feb 2018 18:18:57: #2 Build Peak Model... INFO @ Thu, 08 Feb 2018 18:18:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Feb 2018 18:19:02: #2 number of paired peaks: 5942 INFO @ Thu, 08 Feb 2018 18:19:02: start model_add_line... INFO @ Thu, 08 Feb 2018 18:19:02: start X-correlation... INFO @ Thu, 08 Feb 2018 18:19:02: end of X-cor INFO @ Thu, 08 Feb 2018 18:19:02: #2 finished! INFO @ Thu, 08 Feb 2018 18:19:02: #2 predicted fragment length is 50 bps INFO @ Thu, 08 Feb 2018 18:19:02: #2 alternative fragment length(s) may be 50,398 bps INFO @ Thu, 08 Feb 2018 18:19:02: #2.2 Generate R script for model : SRX3478272.20_model.r WARNING @ Thu, 08 Feb 2018 18:19:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Feb 2018 18:19:02: #2 You may need to consider one of the other alternative d(s): 50,398 WARNING @ Thu, 08 Feb 2018 18:19:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Feb 2018 18:19:02: #3 Call peaks... INFO @ Thu, 08 Feb 2018 18:19:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Feb 2018 18:20:54: #3 Call peaks for each chromosome... INFO @ Thu, 08 Feb 2018 18:21:58: #4 Write output xls file... SRX3478272.20_peaks.xls INFO @ Thu, 08 Feb 2018 18:21:58: #4 Write peak in narrowPeak format file... SRX3478272.20_peaks.narrowPeak INFO @ Thu, 08 Feb 2018 18:21:58: #4 Write summits bed file... SRX3478272.20_summits.bed INFO @ Thu, 08 Feb 2018 18:21:58: Done! pass1 - making usageList (36 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。