Job ID = 10194940 sra ファイルのダウンロード中... Completed: 568102K bytes transferred in 16 seconds (282003K bits/sec), in 1 file. Completed: 631987K bytes transferred in 20 seconds (253127K 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 27257626 spots for /home/okishinya/chipatlas/results/rn6/SRX2512950/SRR5197466.sra Written 27257626 spots total Written 31411763 spots for /home/okishinya/chipatlas/results/rn6/SRX2512950/SRR5197467.sra Written 31411763 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:57:32 58669389 reads; of these: 58669389 (100.00%) were unpaired; of these: 19412524 (33.09%) aligned 0 times 26043192 (44.39%) aligned exactly 1 time 13213673 (22.52%) aligned >1 times 66.91% overall alignment rate Time searching: 00:57:38 Overall time: 00:57:38 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 12 files... [bam_rmdupse_core] 5405695 / 39256865 = 0.1377 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 01:14:23: # Command line: callpeak -t SRX2512950.bam -f BAM -g 2.15e9 -n SRX2512950.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512950.10 # format = BAM # ChIP-seq file = ['SRX2512950.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 01:14:23: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:14:23: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:14:23: # Command line: callpeak -t SRX2512950.bam -f BAM -g 2.15e9 -n SRX2512950.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512950.05 # format = BAM # ChIP-seq file = ['SRX2512950.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 01:14:23: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:14:23: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:14:23: # Command line: callpeak -t SRX2512950.bam -f BAM -g 2.15e9 -n SRX2512950.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512950.20 # format = BAM # ChIP-seq file = ['SRX2512950.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 01:14:23: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:14:23: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:14:33: 1000000 INFO @ Sat, 11 Nov 2017 01:14:34: 1000000 INFO @ Sat, 11 Nov 2017 01:14:35: 1000000 INFO @ Sat, 11 Nov 2017 01:14:43: 2000000 INFO @ Sat, 11 Nov 2017 01:14:45: 2000000 INFO @ Sat, 11 Nov 2017 01:14:48: 2000000 INFO @ Sat, 11 Nov 2017 01:14:53: 3000000 INFO @ Sat, 11 Nov 2017 01:14:55: 3000000 INFO @ Sat, 11 Nov 2017 01:15:00: 3000000 INFO @ Sat, 11 Nov 2017 01:15:03: 4000000 INFO @ Sat, 11 Nov 2017 01:15:04: 4000000 INFO @ Sat, 11 Nov 2017 01:15:14: 5000000 INFO @ Sat, 11 Nov 2017 01:15:16: 4000000 INFO @ Sat, 11 Nov 2017 01:15:20: 5000000 INFO @ Sat, 11 Nov 2017 01:15:23: 6000000 INFO @ Sat, 11 Nov 2017 01:15:34: 7000000 INFO @ Sat, 11 Nov 2017 01:15:44: 8000000 INFO @ Sat, 11 Nov 2017 01:15:55: 5000000 INFO @ Sat, 11 Nov 2017 01:15:55: 9000000 INFO @ Sat, 11 Nov 2017 01:16:01: 6000000 INFO @ Sat, 11 Nov 2017 01:16:06: 10000000 INFO @ Sat, 11 Nov 2017 01:16:17: 11000000 INFO @ Sat, 11 Nov 2017 01:16:28: 12000000 INFO @ Sat, 11 Nov 2017 01:16:31: 6000000 INFO @ Sat, 11 Nov 2017 01:16:35: 7000000 INFO @ Sat, 11 Nov 2017 01:16:39: 13000000 INFO @ Sat, 11 Nov 2017 01:16:49: 14000000 INFO @ Sat, 11 Nov 2017 01:16:58: 15000000 INFO @ Sat, 11 Nov 2017 01:17:09: 16000000 INFO @ Sat, 11 Nov 2017 01:17:09: 7000000 INFO @ Sat, 11 Nov 2017 01:17:15: 8000000 INFO @ Sat, 11 Nov 2017 01:17:20: 17000000 INFO @ Sat, 11 Nov 2017 01:17:30: 18000000 INFO @ Sat, 11 Nov 2017 01:17:41: 19000000 INFO @ Sat, 11 Nov 2017 01:17:51: 9000000 INFO @ Sat, 11 Nov 2017 01:17:52: 8000000 INFO @ Sat, 11 Nov 2017 01:17:52: 20000000 INFO @ Sat, 11 Nov 2017 01:18:03: 21000000 INFO @ Sat, 11 Nov 2017 01:18:14: 22000000 INFO @ Sat, 11 Nov 2017 01:18:24: 23000000 INFO @ Sat, 11 Nov 2017 01:18:28: 10000000 INFO @ Sat, 11 Nov 2017 01:18:35: 24000000 INFO @ Sat, 11 Nov 2017 01:18:36: 9000000 INFO @ Sat, 11 Nov 2017 01:18:46: 25000000 INFO @ Sat, 11 Nov 2017 01:18:56: 26000000 INFO @ Sat, 11 Nov 2017 01:19:05: 11000000 INFO @ Sat, 11 Nov 2017 01:19:05: 27000000 INFO @ Sat, 11 Nov 2017 01:19:15: 28000000 INFO @ Sat, 11 Nov 2017 01:19:17: 10000000 INFO @ Sat, 11 Nov 2017 01:19:25: 29000000 INFO @ Sat, 11 Nov 2017 01:19:35: 30000000 INFO @ Sat, 11 Nov 2017 01:19:41: 12000000 INFO @ Sat, 11 Nov 2017 01:19:45: 31000000 INFO @ Sat, 11 Nov 2017 01:19:48: 11000000 INFO @ Sat, 11 Nov 2017 01:19:56: 32000000 INFO @ Sat, 11 Nov 2017 01:20:06: 33000000 INFO @ Sat, 11 Nov 2017 01:20:14: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:20:14: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:20:14: #1 total tags in treatment: 33851170 INFO @ Sat, 11 Nov 2017 01:20:14: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:20:14: #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 01:20:15: 13000000 INFO @ Sat, 11 Nov 2017 01:20:16: #1 tags after filtering in treatment: 33851096 INFO @ Sat, 11 Nov 2017 01:20:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:20:16: #1 finished! INFO @ Sat, 11 Nov 2017 01:20:16: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:20:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:20:18: 12000000 INFO @ Sat, 11 Nov 2017 01:20:20: #2 number of paired peaks: 11841 INFO @ Sat, 11 Nov 2017 01:20:20: start model_add_line... INFO @ Sat, 11 Nov 2017 01:20:21: start X-correlation... INFO @ Sat, 11 Nov 2017 01:20:21: end of X-cor INFO @ Sat, 11 Nov 2017 01:20:21: #2 finished! INFO @ Sat, 11 Nov 2017 01:20:21: #2 predicted fragment length is 150 bps INFO @ Sat, 11 Nov 2017 01:20:21: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 11 Nov 2017 01:20:21: #2.2 Generate R script for model : SRX2512950.10_model.r INFO @ Sat, 11 Nov 2017 01:20:21: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:20:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:20:49: 14000000 INFO @ Sat, 11 Nov 2017 01:20:54: 13000000 INFO @ Sat, 11 Nov 2017 01:21:21: 14000000 INFO @ Sat, 11 Nov 2017 01:21:22: 15000000 INFO @ Sat, 11 Nov 2017 01:21:46: 15000000 INFO @ Sat, 11 Nov 2017 01:21:51: 16000000 INFO @ Sat, 11 Nov 2017 01:22:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:22:11: 17000000 INFO @ Sat, 11 Nov 2017 01:22:12: 16000000 INFO @ Sat, 11 Nov 2017 01:22:22: 18000000 INFO @ Sat, 11 Nov 2017 01:22:34: 19000000 INFO @ Sat, 11 Nov 2017 01:22:39: 17000000 INFO @ Sat, 11 Nov 2017 01:22:46: 20000000 INFO @ Sat, 11 Nov 2017 01:22:58: 21000000 INFO @ Sat, 11 Nov 2017 01:23:04: 18000000 INFO @ Sat, 11 Nov 2017 01:23:05: #4 Write output xls file... SRX2512950.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:23:05: #4 Write peak in narrowPeak format file... SRX2512950.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:23:05: #4 Write summits bed file... SRX2512950.10_summits.bed INFO @ Sat, 11 Nov 2017 01:23:05: Done! pass1 - making usageList (99 chroms): 3 millis pass2 - checking and writing primary data (5804 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:23:09: 22000000 INFO @ Sat, 11 Nov 2017 01:23:20: 23000000 INFO @ Sat, 11 Nov 2017 01:23:22: 19000000 INFO @ Sat, 11 Nov 2017 01:23:30: 24000000 INFO @ Sat, 11 Nov 2017 01:23:40: 20000000 INFO @ Sat, 11 Nov 2017 01:23:41: 25000000 INFO @ Sat, 11 Nov 2017 01:23:52: 26000000 INFO @ Sat, 11 Nov 2017 01:23:58: 21000000 INFO @ Sat, 11 Nov 2017 01:24:02: 27000000 INFO @ Sat, 11 Nov 2017 01:24:13: 28000000 INFO @ Sat, 11 Nov 2017 01:24:17: 22000000 INFO @ Sat, 11 Nov 2017 01:24:23: 29000000 INFO @ Sat, 11 Nov 2017 01:24:36: 23000000 INFO @ Sat, 11 Nov 2017 01:24:43: 30000000 INFO @ Sat, 11 Nov 2017 01:25:03: 24000000 INFO @ Sat, 11 Nov 2017 01:25:06: 31000000 INFO @ Sat, 11 Nov 2017 01:25:31: 32000000 INFO @ Sat, 11 Nov 2017 01:25:31: 25000000 INFO @ Sat, 11 Nov 2017 01:25:55: 33000000 INFO @ Sat, 11 Nov 2017 01:25:58: 26000000 INFO @ Sat, 11 Nov 2017 01:26:17: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:26:17: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:26:17: #1 total tags in treatment: 33851170 INFO @ Sat, 11 Nov 2017 01:26:17: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:26:17: #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 01:26:19: #1 tags after filtering in treatment: 33851096 INFO @ Sat, 11 Nov 2017 01:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:26:19: #1 finished! INFO @ Sat, 11 Nov 2017 01:26:19: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:26:24: #2 number of paired peaks: 11841 INFO @ Sat, 11 Nov 2017 01:26:24: start model_add_line... INFO @ Sat, 11 Nov 2017 01:26:24: start X-correlation... INFO @ Sat, 11 Nov 2017 01:26:24: end of X-cor INFO @ Sat, 11 Nov 2017 01:26:24: #2 finished! INFO @ Sat, 11 Nov 2017 01:26:24: #2 predicted fragment length is 150 bps INFO @ Sat, 11 Nov 2017 01:26:24: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 11 Nov 2017 01:26:24: #2.2 Generate R script for model : SRX2512950.05_model.r INFO @ Sat, 11 Nov 2017 01:26:24: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:26:26: 27000000 INFO @ Sat, 11 Nov 2017 01:26:54: 28000000 INFO @ Sat, 11 Nov 2017 01:27:17: 29000000 INFO @ Sat, 11 Nov 2017 01:27:39: 30000000 INFO @ Sat, 11 Nov 2017 01:28:01: 31000000 INFO @ Sat, 11 Nov 2017 01:28:22: 32000000 INFO @ Sat, 11 Nov 2017 01:28:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:28:45: 33000000 INFO @ Sat, 11 Nov 2017 01:29:05: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:29:05: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:29:05: #1 total tags in treatment: 33851170 INFO @ Sat, 11 Nov 2017 01:29:05: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:29:05: #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 01:29:07: #1 tags after filtering in treatment: 33851096 INFO @ Sat, 11 Nov 2017 01:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:29:07: #1 finished! INFO @ Sat, 11 Nov 2017 01:29:07: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:29:12: #2 number of paired peaks: 11841 INFO @ Sat, 11 Nov 2017 01:29:12: start model_add_line... INFO @ Sat, 11 Nov 2017 01:29:13: start X-correlation... INFO @ Sat, 11 Nov 2017 01:29:13: end of X-cor INFO @ Sat, 11 Nov 2017 01:29:13: #2 finished! INFO @ Sat, 11 Nov 2017 01:29:13: #2 predicted fragment length is 150 bps INFO @ Sat, 11 Nov 2017 01:29:13: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 11 Nov 2017 01:29:13: #2.2 Generate R script for model : SRX2512950.20_model.r INFO @ Sat, 11 Nov 2017 01:29:13: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:29:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:29:41: #4 Write output xls file... SRX2512950.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:29:41: #4 Write peak in narrowPeak format file... SRX2512950.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:29:41: #4 Write summits bed file... SRX2512950.05_summits.bed INFO @ Sat, 11 Nov 2017 01:29:41: Done! pass1 - making usageList (145 chroms): 5 millis pass2 - checking and writing primary data (15724 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:31:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:32:21: #4 Write output xls file... SRX2512950.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:32:21: #4 Write peak in narrowPeak format file... SRX2512950.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:32:21: #4 Write summits bed file... SRX2512950.20_summits.bed INFO @ Sat, 11 Nov 2017 01:32:21: Done! pass1 - making usageList (66 chroms): 2 millis pass2 - checking and writing primary data (2106 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。