Job ID = 10487592 sra ファイルのダウンロード中... Completed: 4921115K bytes transferred in 163 seconds (245874K 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 73484849 spots for /home/okishinya/chipatlas/results/rn6/SRX2611115/SRR5311159.sra Written 73484849 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: 04:03:25 73484849 reads; of these: 73484849 (100.00%) were unpaired; of these: 19969794 (27.18%) aligned 0 times 40229550 (54.75%) aligned exactly 1 time 13285505 (18.08%) aligned >1 times 72.82% overall alignment rate Time searching: 04:03:29 Overall time: 04:03:29 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 40 files... [bam_rmdupse_core] 14725051 / 53515055 = 0.2752 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 @ Sun, 18 Mar 2018 14:22:03: # Command line: callpeak -t SRX2611115.bam -f BAM -g 2.15e9 -n SRX2611115.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611115.20 # format = BAM # ChIP-seq file = ['SRX2611115.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 @ Sun, 18 Mar 2018 14:22:03: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:22:03: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:22:03: # Command line: callpeak -t SRX2611115.bam -f BAM -g 2.15e9 -n SRX2611115.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611115.05 # format = BAM # ChIP-seq file = ['SRX2611115.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 @ Sun, 18 Mar 2018 14:22:03: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:22:03: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:22:03: # Command line: callpeak -t SRX2611115.bam -f BAM -g 2.15e9 -n SRX2611115.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611115.10 # format = BAM # ChIP-seq file = ['SRX2611115.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 @ Sun, 18 Mar 2018 14:22:03: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:22:03: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:22:13: 1000000 INFO @ Sun, 18 Mar 2018 14:22:13: 1000000 INFO @ Sun, 18 Mar 2018 14:22:13: 1000000 INFO @ Sun, 18 Mar 2018 14:22:23: 2000000 INFO @ Sun, 18 Mar 2018 14:22:23: 2000000 INFO @ Sun, 18 Mar 2018 14:22:23: 2000000 INFO @ Sun, 18 Mar 2018 14:22:32: 3000000 INFO @ Sun, 18 Mar 2018 14:22:33: 3000000 INFO @ Sun, 18 Mar 2018 14:22:33: 3000000 INFO @ Sun, 18 Mar 2018 14:22:42: 4000000 INFO @ Sun, 18 Mar 2018 14:22:43: 4000000 INFO @ Sun, 18 Mar 2018 14:22:43: 4000000 INFO @ Sun, 18 Mar 2018 14:22:51: 5000000 INFO @ Sun, 18 Mar 2018 14:22:53: 5000000 INFO @ Sun, 18 Mar 2018 14:22:54: 5000000 INFO @ Sun, 18 Mar 2018 14:23:01: 6000000 INFO @ Sun, 18 Mar 2018 14:23:03: 6000000 INFO @ Sun, 18 Mar 2018 14:23:04: 6000000 INFO @ Sun, 18 Mar 2018 14:23:10: 7000000 INFO @ Sun, 18 Mar 2018 14:23:13: 7000000 INFO @ Sun, 18 Mar 2018 14:23:14: 7000000 INFO @ Sun, 18 Mar 2018 14:23:20: 8000000 INFO @ Sun, 18 Mar 2018 14:23:23: 8000000 INFO @ Sun, 18 Mar 2018 14:23:24: 8000000 INFO @ Sun, 18 Mar 2018 14:23:29: 9000000 INFO @ Sun, 18 Mar 2018 14:23:33: 9000000 INFO @ Sun, 18 Mar 2018 14:23:35: 9000000 INFO @ Sun, 18 Mar 2018 14:23:39: 10000000 INFO @ Sun, 18 Mar 2018 14:23:43: 10000000 INFO @ Sun, 18 Mar 2018 14:23:45: 10000000 INFO @ Sun, 18 Mar 2018 14:23:48: 11000000 INFO @ Sun, 18 Mar 2018 14:23:53: 11000000 INFO @ Sun, 18 Mar 2018 14:23:55: 11000000 INFO @ Sun, 18 Mar 2018 14:23:57: 12000000 INFO @ Sun, 18 Mar 2018 14:24:04: 12000000 INFO @ Sun, 18 Mar 2018 14:24:06: 12000000 INFO @ Sun, 18 Mar 2018 14:24:07: 13000000 INFO @ Sun, 18 Mar 2018 14:24:14: 13000000 INFO @ Sun, 18 Mar 2018 14:24:16: 14000000 INFO @ Sun, 18 Mar 2018 14:24:16: 13000000 INFO @ Sun, 18 Mar 2018 14:24:24: 14000000 INFO @ Sun, 18 Mar 2018 14:24:25: 15000000 INFO @ Sun, 18 Mar 2018 14:24:27: 14000000 INFO @ Sun, 18 Mar 2018 14:24:34: 15000000 INFO @ Sun, 18 Mar 2018 14:24:35: 16000000 INFO @ Sun, 18 Mar 2018 14:24:37: 15000000 INFO @ Sun, 18 Mar 2018 14:24:44: 17000000 INFO @ Sun, 18 Mar 2018 14:24:45: 16000000 INFO @ Sun, 18 Mar 2018 14:24:48: 16000000 INFO @ Sun, 18 Mar 2018 14:24:54: 18000000 INFO @ Sun, 18 Mar 2018 14:24:55: 17000000 INFO @ Sun, 18 Mar 2018 14:24:58: 17000000 INFO @ Sun, 18 Mar 2018 14:25:03: 19000000 INFO @ Sun, 18 Mar 2018 14:25:05: 18000000 INFO @ Sun, 18 Mar 2018 14:25:08: 18000000 INFO @ Sun, 18 Mar 2018 14:25:12: 20000000 INFO @ Sun, 18 Mar 2018 14:25:15: 19000000 INFO @ Sun, 18 Mar 2018 14:25:19: 19000000 INFO @ Sun, 18 Mar 2018 14:25:22: 21000000 INFO @ Sun, 18 Mar 2018 14:25:25: 20000000 INFO @ Sun, 18 Mar 2018 14:25:29: 20000000 INFO @ Sun, 18 Mar 2018 14:25:31: 22000000 INFO @ Sun, 18 Mar 2018 14:25:36: 21000000 INFO @ Sun, 18 Mar 2018 14:25:40: 21000000 INFO @ Sun, 18 Mar 2018 14:25:41: 23000000 INFO @ Sun, 18 Mar 2018 14:25:46: 22000000 INFO @ Sun, 18 Mar 2018 14:25:50: 24000000 INFO @ Sun, 18 Mar 2018 14:25:50: 22000000 INFO @ Sun, 18 Mar 2018 14:25:56: 23000000 INFO @ Sun, 18 Mar 2018 14:25:59: 25000000 INFO @ Sun, 18 Mar 2018 14:26:01: 23000000 INFO @ Sun, 18 Mar 2018 14:26:07: 24000000 INFO @ Sun, 18 Mar 2018 14:26:09: 26000000 INFO @ Sun, 18 Mar 2018 14:26:11: 24000000 INFO @ Sun, 18 Mar 2018 14:26:17: 25000000 INFO @ Sun, 18 Mar 2018 14:26:18: 27000000 INFO @ Sun, 18 Mar 2018 14:26:22: 25000000 INFO @ Sun, 18 Mar 2018 14:26:27: 26000000 INFO @ Sun, 18 Mar 2018 14:26:28: 28000000 INFO @ Sun, 18 Mar 2018 14:26:32: 26000000 INFO @ Sun, 18 Mar 2018 14:26:37: 29000000 INFO @ Sun, 18 Mar 2018 14:26:38: 27000000 INFO @ Sun, 18 Mar 2018 14:26:43: 27000000 INFO @ Sun, 18 Mar 2018 14:26:47: 30000000 INFO @ Sun, 18 Mar 2018 14:26:48: 28000000 INFO @ Sun, 18 Mar 2018 14:26:53: 28000000 INFO @ Sun, 18 Mar 2018 14:26:56: 31000000 INFO @ Sun, 18 Mar 2018 14:26:58: 29000000 INFO @ Sun, 18 Mar 2018 14:27:03: 29000000 INFO @ Sun, 18 Mar 2018 14:27:06: 32000000 INFO @ Sun, 18 Mar 2018 14:27:08: 30000000 INFO @ Sun, 18 Mar 2018 14:27:14: 30000000 INFO @ Sun, 18 Mar 2018 14:27:15: 33000000 INFO @ Sun, 18 Mar 2018 14:27:19: 31000000 INFO @ Sun, 18 Mar 2018 14:27:24: 31000000 INFO @ Sun, 18 Mar 2018 14:27:25: 34000000 INFO @ Sun, 18 Mar 2018 14:27:29: 32000000 INFO @ Sun, 18 Mar 2018 14:27:34: 32000000 INFO @ Sun, 18 Mar 2018 14:27:34: 35000000 INFO @ Sun, 18 Mar 2018 14:27:39: 33000000 INFO @ Sun, 18 Mar 2018 14:27:44: 36000000 INFO @ Sun, 18 Mar 2018 14:27:45: 33000000 INFO @ Sun, 18 Mar 2018 14:27:49: 34000000 INFO @ Sun, 18 Mar 2018 14:27:53: 37000000 INFO @ Sun, 18 Mar 2018 14:27:55: 34000000 INFO @ Sun, 18 Mar 2018 14:28:00: 35000000 INFO @ Sun, 18 Mar 2018 14:28:03: 38000000 INFO @ Sun, 18 Mar 2018 14:28:06: 35000000 INFO @ Sun, 18 Mar 2018 14:28:10: 36000000 INFO @ Sun, 18 Mar 2018 14:28:11: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:28:11: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:28:11: #1 total tags in treatment: 38790004 INFO @ Sun, 18 Mar 2018 14:28:11: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:28:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:28:12: #1 tags after filtering in treatment: 38789932 INFO @ Sun, 18 Mar 2018 14:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:28:12: #1 finished! INFO @ Sun, 18 Mar 2018 14:28:12: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:28:15: #2 number of paired peaks: 7871 INFO @ Sun, 18 Mar 2018 14:28:15: start model_add_line... INFO @ Sun, 18 Mar 2018 14:28:16: start X-correlation... INFO @ Sun, 18 Mar 2018 14:28:16: end of X-cor INFO @ Sun, 18 Mar 2018 14:28:16: #2 finished! INFO @ Sun, 18 Mar 2018 14:28:16: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 14:28:16: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 14:28:16: #2.2 Generate R script for model : SRX2611115.20_model.r WARNING @ Sun, 18 Mar 2018 14:28:16: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:28:16: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 14:28:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:28:16: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:28:16: 36000000 INFO @ Sun, 18 Mar 2018 14:28:21: 37000000 INFO @ Sun, 18 Mar 2018 14:28:27: 37000000 INFO @ Sun, 18 Mar 2018 14:28:31: 38000000 INFO @ Sun, 18 Mar 2018 14:28:37: 38000000 INFO @ Sun, 18 Mar 2018 14:28:40: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:28:40: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:28:40: #1 total tags in treatment: 38790004 INFO @ Sun, 18 Mar 2018 14:28:40: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:28:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:28:41: #1 tags after filtering in treatment: 38789932 INFO @ Sun, 18 Mar 2018 14:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:28:41: #1 finished! INFO @ Sun, 18 Mar 2018 14:28:41: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:28:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:28:45: #2 number of paired peaks: 7871 INFO @ Sun, 18 Mar 2018 14:28:45: start model_add_line... INFO @ Sun, 18 Mar 2018 14:28:45: start X-correlation... INFO @ Sun, 18 Mar 2018 14:28:45: end of X-cor INFO @ Sun, 18 Mar 2018 14:28:45: #2 finished! INFO @ Sun, 18 Mar 2018 14:28:45: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 14:28:45: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 14:28:45: #2.2 Generate R script for model : SRX2611115.10_model.r WARNING @ Sun, 18 Mar 2018 14:28:45: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:28:45: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 14:28:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:28:45: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:28:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:28:46: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:28:46: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:28:46: #1 total tags in treatment: 38790004 INFO @ Sun, 18 Mar 2018 14:28:46: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:28:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 14:28:47: #1 tags after filtering in treatment: 38789932 INFO @ Sun, 18 Mar 2018 14:28:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:28:47: #1 finished! INFO @ Sun, 18 Mar 2018 14:28:47: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:28:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:28:51: #2 number of paired peaks: 7871 INFO @ Sun, 18 Mar 2018 14:28:51: start model_add_line... INFO @ Sun, 18 Mar 2018 14:28:51: start X-correlation... INFO @ Sun, 18 Mar 2018 14:28:51: end of X-cor INFO @ Sun, 18 Mar 2018 14:28:51: #2 finished! INFO @ Sun, 18 Mar 2018 14:28:51: #2 predicted fragment length is 148 bps INFO @ Sun, 18 Mar 2018 14:28:51: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 18 Mar 2018 14:28:51: #2.2 Generate R script for model : SRX2611115.05_model.r WARNING @ Sun, 18 Mar 2018 14:28:51: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:28:51: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Sun, 18 Mar 2018 14:28:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 14:28:51: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:29:54: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:30:17: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:30:22: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:30:59: #4 Write output xls file... SRX2611115.20_peaks.xls INFO @ Sun, 18 Mar 2018 14:30:59: #4 Write peak in narrowPeak format file... SRX2611115.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:30:59: #4 Write summits bed file... SRX2611115.20_summits.bed INFO @ Sun, 18 Mar 2018 14:30:59: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (872 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:31:22: #4 Write output xls file... SRX2611115.10_peaks.xls INFO @ Sun, 18 Mar 2018 14:31:22: #4 Write peak in narrowPeak format file... SRX2611115.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:31:22: #4 Write summits bed file... SRX2611115.10_summits.bed INFO @ Sun, 18 Mar 2018 14:31:22: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (1933 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:31:25: #4 Write output xls file... SRX2611115.05_peaks.xls INFO @ Sun, 18 Mar 2018 14:31:25: #4 Write peak in narrowPeak format file... SRX2611115.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:31:25: #4 Write summits bed file... SRX2611115.05_summits.bed INFO @ Sun, 18 Mar 2018 14:31:25: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (5157 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。