Job ID = 11388791 sra ファイルのダウンロード中... Completed: 1040317K bytes transferred in 16 seconds (520135K 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... Read 41243968 spots for /home/okishinya/chipatlas/results/rn6/SRX2867569/SRR5627022.sra Written 41243968 spots for /home/okishinya/chipatlas/results/rn6/SRX2867569/SRR5627022.sra 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: 02:09:39 41243968 reads; of these: 41243968 (100.00%) were unpaired; of these: 1615567 (3.92%) aligned 0 times 28694868 (69.57%) aligned exactly 1 time 10933533 (26.51%) aligned >1 times 96.08% overall alignment rate Time searching: 02:09:43 Overall time: 02:09:43 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] 1385224 / 39628401 = 0.0350 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, 13 Dec 2018 01:07:44: # Command line: callpeak -t SRX2867569.bam -f BAM -g 2.15e9 -n SRX2867569.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2867569.05 # format = BAM # ChIP-seq file = ['SRX2867569.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, 13 Dec 2018 01:07:44: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:07:44: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:07:44: # Command line: callpeak -t SRX2867569.bam -f BAM -g 2.15e9 -n SRX2867569.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2867569.20 # format = BAM # ChIP-seq file = ['SRX2867569.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, 13 Dec 2018 01:07:44: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:07:44: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:07:44: # Command line: callpeak -t SRX2867569.bam -f BAM -g 2.15e9 -n SRX2867569.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2867569.10 # format = BAM # ChIP-seq file = ['SRX2867569.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, 13 Dec 2018 01:07:44: #1 read tag files... INFO @ Thu, 13 Dec 2018 01:07:44: #1 read treatment tags... INFO @ Thu, 13 Dec 2018 01:07:54: 1000000 INFO @ Thu, 13 Dec 2018 01:07:56: 1000000 INFO @ Thu, 13 Dec 2018 01:07:56: 1000000 INFO @ Thu, 13 Dec 2018 01:08:03: 2000000 INFO @ Thu, 13 Dec 2018 01:08:06: 2000000 INFO @ Thu, 13 Dec 2018 01:08:10: 2000000 INFO @ Thu, 13 Dec 2018 01:08:13: 3000000 INFO @ Thu, 13 Dec 2018 01:08:17: 3000000 INFO @ Thu, 13 Dec 2018 01:08:23: 4000000 INFO @ Thu, 13 Dec 2018 01:08:24: 3000000 INFO @ Thu, 13 Dec 2018 01:08:28: 4000000 INFO @ Thu, 13 Dec 2018 01:08:32: 5000000 INFO @ Thu, 13 Dec 2018 01:08:35: 4000000 INFO @ Thu, 13 Dec 2018 01:08:40: 5000000 INFO @ Thu, 13 Dec 2018 01:08:43: 6000000 INFO @ Thu, 13 Dec 2018 01:08:46: 5000000 INFO @ Thu, 13 Dec 2018 01:08:50: 6000000 INFO @ Thu, 13 Dec 2018 01:08:54: 7000000 INFO @ Thu, 13 Dec 2018 01:08:56: 6000000 INFO @ Thu, 13 Dec 2018 01:09:01: 7000000 INFO @ Thu, 13 Dec 2018 01:09:05: 8000000 INFO @ Thu, 13 Dec 2018 01:09:06: 7000000 INFO @ Thu, 13 Dec 2018 01:09:13: 8000000 INFO @ Thu, 13 Dec 2018 01:09:17: 8000000 INFO @ Thu, 13 Dec 2018 01:09:18: 9000000 INFO @ Thu, 13 Dec 2018 01:09:23: 9000000 INFO @ Thu, 13 Dec 2018 01:09:28: 9000000 INFO @ Thu, 13 Dec 2018 01:09:29: 10000000 INFO @ Thu, 13 Dec 2018 01:09:34: 10000000 INFO @ Thu, 13 Dec 2018 01:09:39: 10000000 INFO @ Thu, 13 Dec 2018 01:09:40: 11000000 INFO @ Thu, 13 Dec 2018 01:09:44: 11000000 INFO @ Thu, 13 Dec 2018 01:09:49: 12000000 INFO @ Thu, 13 Dec 2018 01:09:51: 11000000 INFO @ Thu, 13 Dec 2018 01:09:56: 12000000 INFO @ Thu, 13 Dec 2018 01:10:00: 13000000 INFO @ Thu, 13 Dec 2018 01:10:01: 12000000 INFO @ Thu, 13 Dec 2018 01:10:09: 14000000 INFO @ Thu, 13 Dec 2018 01:10:09: 13000000 INFO @ Thu, 13 Dec 2018 01:10:11: 13000000 INFO @ Thu, 13 Dec 2018 01:10:18: 15000000 INFO @ Thu, 13 Dec 2018 01:10:23: 14000000 INFO @ Thu, 13 Dec 2018 01:10:23: 14000000 INFO @ Thu, 13 Dec 2018 01:10:27: 16000000 INFO @ Thu, 13 Dec 2018 01:10:37: 17000000 INFO @ Thu, 13 Dec 2018 01:10:37: 15000000 INFO @ Thu, 13 Dec 2018 01:10:37: 15000000 INFO @ Thu, 13 Dec 2018 01:10:46: 18000000 INFO @ Thu, 13 Dec 2018 01:10:50: 16000000 INFO @ Thu, 13 Dec 2018 01:10:50: 16000000 INFO @ Thu, 13 Dec 2018 01:10:55: 19000000 INFO @ Thu, 13 Dec 2018 01:10:59: 17000000 INFO @ Thu, 13 Dec 2018 01:11:03: 17000000 INFO @ Thu, 13 Dec 2018 01:11:04: 20000000 INFO @ Thu, 13 Dec 2018 01:11:08: 18000000 INFO @ Thu, 13 Dec 2018 01:11:13: 21000000 INFO @ Thu, 13 Dec 2018 01:11:14: 18000000 INFO @ Thu, 13 Dec 2018 01:11:18: 19000000 INFO @ Thu, 13 Dec 2018 01:11:22: 22000000 INFO @ Thu, 13 Dec 2018 01:11:26: 19000000 INFO @ Thu, 13 Dec 2018 01:11:27: 20000000 INFO @ Thu, 13 Dec 2018 01:11:31: 23000000 INFO @ Thu, 13 Dec 2018 01:11:36: 21000000 INFO @ Thu, 13 Dec 2018 01:11:39: 20000000 INFO @ Thu, 13 Dec 2018 01:11:41: 24000000 INFO @ Thu, 13 Dec 2018 01:11:46: 22000000 INFO @ Thu, 13 Dec 2018 01:11:55: 25000000 INFO @ Thu, 13 Dec 2018 01:11:56: 21000000 INFO @ Thu, 13 Dec 2018 01:11:57: 23000000 INFO @ Thu, 13 Dec 2018 01:12:07: 24000000 INFO @ Thu, 13 Dec 2018 01:12:13: 26000000 INFO @ Thu, 13 Dec 2018 01:12:13: 22000000 INFO @ Thu, 13 Dec 2018 01:12:17: 25000000 INFO @ Thu, 13 Dec 2018 01:12:25: 23000000 INFO @ Thu, 13 Dec 2018 01:12:26: 27000000 INFO @ Thu, 13 Dec 2018 01:12:28: 26000000 INFO @ Thu, 13 Dec 2018 01:12:36: 24000000 INFO @ Thu, 13 Dec 2018 01:12:40: 28000000 INFO @ Thu, 13 Dec 2018 01:12:44: 27000000 INFO @ Thu, 13 Dec 2018 01:12:48: 25000000 INFO @ Thu, 13 Dec 2018 01:12:53: 29000000 INFO @ Thu, 13 Dec 2018 01:12:58: 28000000 INFO @ Thu, 13 Dec 2018 01:12:59: 26000000 INFO @ Thu, 13 Dec 2018 01:13:04: 30000000 INFO @ Thu, 13 Dec 2018 01:13:11: 27000000 INFO @ Thu, 13 Dec 2018 01:13:13: 29000000 INFO @ Thu, 13 Dec 2018 01:13:15: 31000000 INFO @ Thu, 13 Dec 2018 01:13:24: 28000000 INFO @ Thu, 13 Dec 2018 01:13:27: 32000000 INFO @ Thu, 13 Dec 2018 01:13:29: 30000000 INFO @ Thu, 13 Dec 2018 01:13:37: 29000000 INFO @ Thu, 13 Dec 2018 01:13:38: 33000000 INFO @ Thu, 13 Dec 2018 01:13:42: 31000000 INFO @ Thu, 13 Dec 2018 01:13:49: 34000000 INFO @ Thu, 13 Dec 2018 01:13:53: 32000000 INFO @ Thu, 13 Dec 2018 01:13:57: 30000000 INFO @ Thu, 13 Dec 2018 01:13:59: 35000000 INFO @ Thu, 13 Dec 2018 01:14:05: 33000000 INFO @ Thu, 13 Dec 2018 01:14:09: 36000000 INFO @ Thu, 13 Dec 2018 01:14:11: 31000000 INFO @ Thu, 13 Dec 2018 01:14:15: 34000000 INFO @ Thu, 13 Dec 2018 01:14:21: 37000000 INFO @ Thu, 13 Dec 2018 01:14:24: 32000000 INFO @ Thu, 13 Dec 2018 01:14:25: 35000000 INFO @ Thu, 13 Dec 2018 01:14:33: 38000000 INFO @ Thu, 13 Dec 2018 01:14:35: 36000000 INFO @ Thu, 13 Dec 2018 01:14:36: 33000000 INFO @ Thu, 13 Dec 2018 01:14:37: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:14:37: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:14:37: #1 total tags in treatment: 38243177 INFO @ Thu, 13 Dec 2018 01:14:37: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:14:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:14:38: #1 tags after filtering in treatment: 38243092 INFO @ Thu, 13 Dec 2018 01:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:14:38: #1 finished! INFO @ Thu, 13 Dec 2018 01:14:38: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:14:43: #2 number of paired peaks: 6159 INFO @ Thu, 13 Dec 2018 01:14:43: start model_add_line... INFO @ Thu, 13 Dec 2018 01:14:43: start X-correlation... INFO @ Thu, 13 Dec 2018 01:14:43: end of X-cor INFO @ Thu, 13 Dec 2018 01:14:43: #2 finished! INFO @ Thu, 13 Dec 2018 01:14:43: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 01:14:43: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 01:14:43: #2.2 Generate R script for model : SRX2867569.10_model.r WARNING @ Thu, 13 Dec 2018 01:14:43: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:14:43: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 01:14:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:14:43: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:14:45: 37000000 INFO @ Thu, 13 Dec 2018 01:14:48: 34000000 INFO @ Thu, 13 Dec 2018 01:14:55: 38000000 INFO @ Thu, 13 Dec 2018 01:14:59: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:14:59: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:14:59: #1 total tags in treatment: 38243177 INFO @ Thu, 13 Dec 2018 01:14:59: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:14:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:14:59: 35000000 INFO @ Thu, 13 Dec 2018 01:15:00: #1 tags after filtering in treatment: 38243092 INFO @ Thu, 13 Dec 2018 01:15:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:15:00: #1 finished! INFO @ Thu, 13 Dec 2018 01:15:00: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:15:05: #2 number of paired peaks: 6159 INFO @ Thu, 13 Dec 2018 01:15:05: start model_add_line... INFO @ Thu, 13 Dec 2018 01:15:05: start X-correlation... INFO @ Thu, 13 Dec 2018 01:15:05: end of X-cor INFO @ Thu, 13 Dec 2018 01:15:05: #2 finished! INFO @ Thu, 13 Dec 2018 01:15:05: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 01:15:05: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 01:15:05: #2.2 Generate R script for model : SRX2867569.20_model.r WARNING @ Thu, 13 Dec 2018 01:15:05: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:15:05: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 01:15:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:15:05: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:15:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:15:11: 36000000 INFO @ Thu, 13 Dec 2018 01:15:23: 37000000 INFO @ Thu, 13 Dec 2018 01:15:34: 38000000 INFO @ Thu, 13 Dec 2018 01:15:38: #1 tag size is determined as 76 bps INFO @ Thu, 13 Dec 2018 01:15:38: #1 tag size = 76 INFO @ Thu, 13 Dec 2018 01:15:38: #1 total tags in treatment: 38243177 INFO @ Thu, 13 Dec 2018 01:15:38: #1 user defined the maximum tags... INFO @ Thu, 13 Dec 2018 01:15:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 13 Dec 2018 01:15:39: #1 tags after filtering in treatment: 38243092 INFO @ Thu, 13 Dec 2018 01:15:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 13 Dec 2018 01:15:39: #1 finished! INFO @ Thu, 13 Dec 2018 01:15:39: #2 Build Peak Model... INFO @ Thu, 13 Dec 2018 01:15:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 13 Dec 2018 01:15:44: #2 number of paired peaks: 6159 INFO @ Thu, 13 Dec 2018 01:15:44: start model_add_line... INFO @ Thu, 13 Dec 2018 01:15:44: start X-correlation... INFO @ Thu, 13 Dec 2018 01:15:44: end of X-cor INFO @ Thu, 13 Dec 2018 01:15:44: #2 finished! INFO @ Thu, 13 Dec 2018 01:15:44: #2 predicted fragment length is 78 bps INFO @ Thu, 13 Dec 2018 01:15:44: #2 alternative fragment length(s) may be 78 bps INFO @ Thu, 13 Dec 2018 01:15:44: #2.2 Generate R script for model : SRX2867569.05_model.r WARNING @ Thu, 13 Dec 2018 01:15:44: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 13 Dec 2018 01:15:44: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Thu, 13 Dec 2018 01:15:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 13 Dec 2018 01:15:44: #3 Call peaks... INFO @ Thu, 13 Dec 2018 01:15:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 13 Dec 2018 01:16:52: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:17:12: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:17:43: #3 Call peaks for each chromosome... INFO @ Thu, 13 Dec 2018 01:18:08: #4 Write output xls file... SRX2867569.10_peaks.xls INFO @ Thu, 13 Dec 2018 01:18:08: #4 Write peak in narrowPeak format file... SRX2867569.10_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:18:08: #4 Write summits bed file... SRX2867569.10_summits.bed INFO @ Thu, 13 Dec 2018 01:18:08: Done! pass1 - making usageList (55 chroms): 5 millis pass2 - checking and writing primary data (1426 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:18:33: #4 Write output xls file... SRX2867569.20_peaks.xls INFO @ Thu, 13 Dec 2018 01:18:33: #4 Write peak in narrowPeak format file... SRX2867569.20_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:18:33: #4 Write summits bed file... SRX2867569.20_summits.bed INFO @ Thu, 13 Dec 2018 01:18:33: Done! pass1 - making usageList (39 chroms): 4 millis pass2 - checking and writing primary data (671 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 13 Dec 2018 01:19:01: #4 Write output xls file... SRX2867569.05_peaks.xls INFO @ Thu, 13 Dec 2018 01:19:01: #4 Write peak in narrowPeak format file... SRX2867569.05_peaks.narrowPeak INFO @ Thu, 13 Dec 2018 01:19:01: #4 Write summits bed file... SRX2867569.05_summits.bed INFO @ Thu, 13 Dec 2018 01:19:01: Done! pass1 - making usageList (69 chroms): 5 millis pass2 - checking and writing primary data (3083 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。