Job ID = 10194845 sra ファイルのダウンロード中... Completed: 952629K bytes transferred in 15 seconds (492662K 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 47825858 spots for /home/okishinya/chipatlas/results/rn6/SRX1977134/SRR3952266.sra Written 47825858 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:19:56 47825858 reads; of these: 47825858 (100.00%) were unpaired; of these: 14524170 (30.37%) aligned 0 times 19434661 (40.64%) aligned exactly 1 time 13867027 (28.99%) aligned >1 times 69.63% overall alignment rate Time searching: 01:19:59 Overall time: 01:19:59 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] 5155627 / 33301688 = 0.1548 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 03:17:51: # Command line: callpeak -t SRX1977134.bam -f BAM -g 2.15e9 -n SRX1977134.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977134.20 # format = BAM # ChIP-seq file = ['SRX1977134.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 03:17:51: # Command line: callpeak -t SRX1977134.bam -f BAM -g 2.15e9 -n SRX1977134.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977134.05 # format = BAM # ChIP-seq file = ['SRX1977134.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 03:17:51: # Command line: callpeak -t SRX1977134.bam -f BAM -g 2.15e9 -n SRX1977134.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977134.10 # format = BAM # ChIP-seq file = ['SRX1977134.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 03:17:51: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:17:51: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:17:51: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:17:51: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:17:51: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:17:51: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:17:57: 1000000 INFO @ Sat, 11 Nov 2017 03:17:57: 1000000 INFO @ Sat, 11 Nov 2017 03:17:57: 1000000 INFO @ Sat, 11 Nov 2017 03:18:04: 2000000 INFO @ Sat, 11 Nov 2017 03:18:04: 2000000 INFO @ Sat, 11 Nov 2017 03:18:04: 2000000 INFO @ Sat, 11 Nov 2017 03:18:11: 3000000 INFO @ Sat, 11 Nov 2017 03:18:11: 3000000 INFO @ Sat, 11 Nov 2017 03:18:11: 3000000 INFO @ Sat, 11 Nov 2017 03:18:17: 4000000 INFO @ Sat, 11 Nov 2017 03:18:18: 4000000 INFO @ Sat, 11 Nov 2017 03:18:18: 4000000 INFO @ Sat, 11 Nov 2017 03:18:24: 5000000 INFO @ Sat, 11 Nov 2017 03:18:24: 5000000 INFO @ Sat, 11 Nov 2017 03:18:24: 5000000 INFO @ Sat, 11 Nov 2017 03:18:31: 6000000 INFO @ Sat, 11 Nov 2017 03:18:31: 6000000 INFO @ Sat, 11 Nov 2017 03:18:31: 6000000 INFO @ Sat, 11 Nov 2017 03:18:37: 7000000 INFO @ Sat, 11 Nov 2017 03:18:38: 7000000 INFO @ Sat, 11 Nov 2017 03:18:38: 7000000 INFO @ Sat, 11 Nov 2017 03:18:44: 8000000 INFO @ Sat, 11 Nov 2017 03:18:45: 8000000 INFO @ Sat, 11 Nov 2017 03:18:45: 8000000 INFO @ Sat, 11 Nov 2017 03:18:51: 9000000 INFO @ Sat, 11 Nov 2017 03:18:52: 9000000 INFO @ Sat, 11 Nov 2017 03:18:52: 9000000 INFO @ Sat, 11 Nov 2017 03:18:57: 10000000 INFO @ Sat, 11 Nov 2017 03:18:58: 10000000 INFO @ Sat, 11 Nov 2017 03:18:58: 10000000 INFO @ Sat, 11 Nov 2017 03:19:04: 11000000 INFO @ Sat, 11 Nov 2017 03:19:05: 11000000 INFO @ Sat, 11 Nov 2017 03:19:05: 11000000 INFO @ Sat, 11 Nov 2017 03:19:11: 12000000 INFO @ Sat, 11 Nov 2017 03:19:12: 12000000 INFO @ Sat, 11 Nov 2017 03:19:12: 12000000 INFO @ Sat, 11 Nov 2017 03:19:17: 13000000 INFO @ Sat, 11 Nov 2017 03:19:19: 13000000 INFO @ Sat, 11 Nov 2017 03:19:19: 13000000 INFO @ Sat, 11 Nov 2017 03:19:24: 14000000 INFO @ Sat, 11 Nov 2017 03:19:25: 14000000 INFO @ Sat, 11 Nov 2017 03:19:26: 14000000 INFO @ Sat, 11 Nov 2017 03:19:31: 15000000 INFO @ Sat, 11 Nov 2017 03:19:32: 15000000 INFO @ Sat, 11 Nov 2017 03:19:34: 15000000 INFO @ Sat, 11 Nov 2017 03:19:38: 16000000 INFO @ Sat, 11 Nov 2017 03:19:38: 16000000 INFO @ Sat, 11 Nov 2017 03:19:41: 16000000 INFO @ Sat, 11 Nov 2017 03:19:45: 17000000 INFO @ Sat, 11 Nov 2017 03:19:45: 17000000 INFO @ Sat, 11 Nov 2017 03:19:48: 17000000 INFO @ Sat, 11 Nov 2017 03:19:52: 18000000 INFO @ Sat, 11 Nov 2017 03:19:52: 18000000 INFO @ Sat, 11 Nov 2017 03:19:56: 18000000 INFO @ Sat, 11 Nov 2017 03:19:59: 19000000 INFO @ Sat, 11 Nov 2017 03:19:59: 19000000 INFO @ Sat, 11 Nov 2017 03:20:03: 19000000 INFO @ Sat, 11 Nov 2017 03:20:06: 20000000 INFO @ Sat, 11 Nov 2017 03:20:06: 20000000 INFO @ Sat, 11 Nov 2017 03:20:11: 20000000 INFO @ Sat, 11 Nov 2017 03:20:13: 21000000 INFO @ Sat, 11 Nov 2017 03:20:13: 21000000 INFO @ Sat, 11 Nov 2017 03:20:18: 21000000 INFO @ Sat, 11 Nov 2017 03:20:19: 22000000 INFO @ Sat, 11 Nov 2017 03:20:20: 22000000 INFO @ Sat, 11 Nov 2017 03:20:25: 22000000 INFO @ Sat, 11 Nov 2017 03:20:26: 23000000 INFO @ Sat, 11 Nov 2017 03:20:28: 23000000 INFO @ Sat, 11 Nov 2017 03:20:33: 24000000 INFO @ Sat, 11 Nov 2017 03:20:33: 23000000 INFO @ Sat, 11 Nov 2017 03:20:35: 24000000 INFO @ Sat, 11 Nov 2017 03:20:40: 25000000 INFO @ Sat, 11 Nov 2017 03:20:41: 24000000 INFO @ Sat, 11 Nov 2017 03:20:42: 25000000 INFO @ Sat, 11 Nov 2017 03:20:46: 26000000 INFO @ Sat, 11 Nov 2017 03:20:48: 25000000 INFO @ Sat, 11 Nov 2017 03:20:50: 26000000 INFO @ Sat, 11 Nov 2017 03:20:53: 27000000 INFO @ Sat, 11 Nov 2017 03:20:56: 26000000 INFO @ Sat, 11 Nov 2017 03:20:57: 27000000 INFO @ Sat, 11 Nov 2017 03:21:00: 28000000 INFO @ Sat, 11 Nov 2017 03:21:01: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:21:01: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:21:01: #1 total tags in treatment: 28146061 INFO @ Sat, 11 Nov 2017 03:21:01: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:21:01: #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 03:21:02: #1 tags after filtering in treatment: 28145961 INFO @ Sat, 11 Nov 2017 03:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:21:02: #1 finished! INFO @ Sat, 11 Nov 2017 03:21:02: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:21:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:21:04: 27000000 INFO @ Sat, 11 Nov 2017 03:21:05: 28000000 INFO @ Sat, 11 Nov 2017 03:21:06: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:21:06: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:21:06: #1 total tags in treatment: 28146061 INFO @ Sat, 11 Nov 2017 03:21:06: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:21:06: #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 03:21:07: #2 number of paired peaks: 53500 INFO @ Sat, 11 Nov 2017 03:21:07: start model_add_line... INFO @ Sat, 11 Nov 2017 03:21:07: #1 tags after filtering in treatment: 28145961 INFO @ Sat, 11 Nov 2017 03:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:21:07: #1 finished! INFO @ Sat, 11 Nov 2017 03:21:07: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:21:07: start X-correlation... INFO @ Sat, 11 Nov 2017 03:21:07: end of X-cor INFO @ Sat, 11 Nov 2017 03:21:07: #2 finished! INFO @ Sat, 11 Nov 2017 03:21:07: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Nov 2017 03:21:07: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Nov 2017 03:21:07: #2.2 Generate R script for model : SRX1977134.05_model.r INFO @ Sat, 11 Nov 2017 03:21:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:21:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:21:11: 28000000 INFO @ Sat, 11 Nov 2017 03:21:12: #2 number of paired peaks: 53500 INFO @ Sat, 11 Nov 2017 03:21:12: start model_add_line... INFO @ Sat, 11 Nov 2017 03:21:12: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:21:12: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:21:12: #1 total tags in treatment: 28146061 INFO @ Sat, 11 Nov 2017 03:21:12: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:21:12: #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 03:21:12: start X-correlation... INFO @ Sat, 11 Nov 2017 03:21:12: end of X-cor INFO @ Sat, 11 Nov 2017 03:21:12: #2 finished! INFO @ Sat, 11 Nov 2017 03:21:12: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Nov 2017 03:21:12: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Nov 2017 03:21:12: #2.2 Generate R script for model : SRX1977134.10_model.r INFO @ Sat, 11 Nov 2017 03:21:12: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:21:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:21:13: #1 tags after filtering in treatment: 28145961 INFO @ Sat, 11 Nov 2017 03:21:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:21:13: #1 finished! INFO @ Sat, 11 Nov 2017 03:21:13: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:21:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:21:17: #2 number of paired peaks: 53500 INFO @ Sat, 11 Nov 2017 03:21:17: start model_add_line... INFO @ Sat, 11 Nov 2017 03:21:18: start X-correlation... INFO @ Sat, 11 Nov 2017 03:21:18: end of X-cor INFO @ Sat, 11 Nov 2017 03:21:18: #2 finished! INFO @ Sat, 11 Nov 2017 03:21:18: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Nov 2017 03:21:18: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Nov 2017 03:21:18: #2.2 Generate R script for model : SRX1977134.20_model.r INFO @ Sat, 11 Nov 2017 03:21:18: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:21:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:22:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:22:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:22:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:23:00: #4 Write output xls file... SRX1977134.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:23:01: #4 Write peak in narrowPeak format file... SRX1977134.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:23:01: #4 Write summits bed file... SRX1977134.05_summits.bed INFO @ Sat, 11 Nov 2017 03:23:01: Done! pass1 - making usageList (203 chroms): 8 millis pass2 - checking and writing primary data (42213 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:23:06: #4 Write output xls file... SRX1977134.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:23:06: #4 Write peak in narrowPeak format file... SRX1977134.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:23:06: #4 Write summits bed file... SRX1977134.10_summits.bed INFO @ Sat, 11 Nov 2017 03:23:06: Done! pass1 - making usageList (117 chroms): 3 millis pass2 - checking and writing primary data (10506 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:23:12: #4 Write output xls file... SRX1977134.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:23:12: #4 Write peak in narrowPeak format file... SRX1977134.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:23:12: #4 Write summits bed file... SRX1977134.20_summits.bed INFO @ Sat, 11 Nov 2017 03:23:12: Done! pass1 - making usageList (69 chroms): 1 millis pass2 - checking and writing primary data (2112 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。