Job ID = 10194846 sra ファイルのダウンロード中... Completed: 817034K bytes transferred in 14 seconds (464057K 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 41735368 spots for /home/okishinya/chipatlas/results/rn6/SRX1977135/SRR3952267.sra Written 41735368 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: 01:20:46 41735368 reads; of these: 41735368 (100.00%) were unpaired; of these: 5857055 (14.03%) aligned 0 times 17520518 (41.98%) aligned exactly 1 time 18357795 (43.99%) aligned >1 times 85.97% overall alignment rate Time searching: 01:20:49 Overall time: 01:20:49 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] 4779027 / 35878313 = 0.1332 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 03:18:38: # Command line: callpeak -t SRX1977135.bam -f BAM -g 2.15e9 -n SRX1977135.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1977135.05 # format = BAM # ChIP-seq file = ['SRX1977135.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 03:18:38: # Command line: callpeak -t SRX1977135.bam -f BAM -g 2.15e9 -n SRX1977135.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1977135.20 # format = BAM # ChIP-seq file = ['SRX1977135.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 03:18:38: # Command line: callpeak -t SRX1977135.bam -f BAM -g 2.15e9 -n SRX1977135.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1977135.10 # format = BAM # ChIP-seq file = ['SRX1977135.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 03:18:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:18:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:18:38: #1 read tag files... INFO @ Sat, 11 Nov 2017 03:18:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:18:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:18:38: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 03:18:45: 1000000 INFO @ Sat, 11 Nov 2017 03:18:45: 1000000 INFO @ Sat, 11 Nov 2017 03:18:46: 1000000 INFO @ Sat, 11 Nov 2017 03:18:53: 2000000 INFO @ Sat, 11 Nov 2017 03:18:53: 2000000 INFO @ Sat, 11 Nov 2017 03:18:53: 2000000 INFO @ Sat, 11 Nov 2017 03:19:00: 3000000 INFO @ Sat, 11 Nov 2017 03:19:00: 3000000 INFO @ Sat, 11 Nov 2017 03:19:00: 3000000 INFO @ Sat, 11 Nov 2017 03:19:07: 4000000 INFO @ Sat, 11 Nov 2017 03:19:07: 4000000 INFO @ Sat, 11 Nov 2017 03:19:08: 4000000 INFO @ Sat, 11 Nov 2017 03:19:14: 5000000 INFO @ Sat, 11 Nov 2017 03:19:14: 5000000 INFO @ Sat, 11 Nov 2017 03:19:15: 5000000 INFO @ Sat, 11 Nov 2017 03:19:21: 6000000 INFO @ Sat, 11 Nov 2017 03:19:21: 6000000 INFO @ Sat, 11 Nov 2017 03:19:22: 6000000 INFO @ Sat, 11 Nov 2017 03:19:29: 7000000 INFO @ Sat, 11 Nov 2017 03:19:29: 7000000 INFO @ Sat, 11 Nov 2017 03:19:30: 7000000 INFO @ Sat, 11 Nov 2017 03:19:36: 8000000 INFO @ Sat, 11 Nov 2017 03:19:36: 8000000 INFO @ Sat, 11 Nov 2017 03:19:37: 8000000 INFO @ Sat, 11 Nov 2017 03:19:43: 9000000 INFO @ Sat, 11 Nov 2017 03:19:43: 9000000 INFO @ Sat, 11 Nov 2017 03:19:44: 9000000 INFO @ Sat, 11 Nov 2017 03:19:50: 10000000 INFO @ Sat, 11 Nov 2017 03:19:50: 10000000 INFO @ Sat, 11 Nov 2017 03:19:51: 10000000 INFO @ Sat, 11 Nov 2017 03:19:57: 11000000 INFO @ Sat, 11 Nov 2017 03:19:57: 11000000 INFO @ Sat, 11 Nov 2017 03:19:59: 11000000 INFO @ Sat, 11 Nov 2017 03:20:05: 12000000 INFO @ Sat, 11 Nov 2017 03:20:05: 12000000 INFO @ Sat, 11 Nov 2017 03:20:06: 12000000 INFO @ Sat, 11 Nov 2017 03:20:12: 13000000 INFO @ Sat, 11 Nov 2017 03:20:12: 13000000 INFO @ Sat, 11 Nov 2017 03:20:13: 13000000 INFO @ Sat, 11 Nov 2017 03:20:19: 14000000 INFO @ Sat, 11 Nov 2017 03:20:19: 14000000 INFO @ Sat, 11 Nov 2017 03:20:20: 14000000 INFO @ Sat, 11 Nov 2017 03:20:26: 15000000 INFO @ Sat, 11 Nov 2017 03:20:26: 15000000 INFO @ Sat, 11 Nov 2017 03:20:28: 15000000 INFO @ Sat, 11 Nov 2017 03:20:33: 16000000 INFO @ Sat, 11 Nov 2017 03:20:33: 16000000 INFO @ Sat, 11 Nov 2017 03:20:35: 16000000 INFO @ Sat, 11 Nov 2017 03:20:41: 17000000 INFO @ Sat, 11 Nov 2017 03:20:41: 17000000 INFO @ Sat, 11 Nov 2017 03:20:42: 17000000 INFO @ Sat, 11 Nov 2017 03:20:48: 18000000 INFO @ Sat, 11 Nov 2017 03:20:48: 18000000 INFO @ Sat, 11 Nov 2017 03:20:50: 18000000 INFO @ Sat, 11 Nov 2017 03:20:55: 19000000 INFO @ Sat, 11 Nov 2017 03:20:55: 19000000 INFO @ Sat, 11 Nov 2017 03:20:57: 19000000 INFO @ Sat, 11 Nov 2017 03:21:02: 20000000 INFO @ Sat, 11 Nov 2017 03:21:02: 20000000 INFO @ Sat, 11 Nov 2017 03:21:04: 20000000 INFO @ Sat, 11 Nov 2017 03:21:09: 21000000 INFO @ Sat, 11 Nov 2017 03:21:09: 21000000 INFO @ Sat, 11 Nov 2017 03:21:11: 21000000 INFO @ Sat, 11 Nov 2017 03:21:17: 22000000 INFO @ Sat, 11 Nov 2017 03:21:17: 22000000 INFO @ Sat, 11 Nov 2017 03:21:19: 22000000 INFO @ Sat, 11 Nov 2017 03:21:24: 23000000 INFO @ Sat, 11 Nov 2017 03:21:24: 23000000 INFO @ Sat, 11 Nov 2017 03:21:26: 23000000 INFO @ Sat, 11 Nov 2017 03:21:31: 24000000 INFO @ Sat, 11 Nov 2017 03:21:31: 24000000 INFO @ Sat, 11 Nov 2017 03:21:33: 24000000 INFO @ Sat, 11 Nov 2017 03:21:38: 25000000 INFO @ Sat, 11 Nov 2017 03:21:38: 25000000 INFO @ Sat, 11 Nov 2017 03:21:40: 25000000 INFO @ Sat, 11 Nov 2017 03:21:45: 26000000 INFO @ Sat, 11 Nov 2017 03:21:45: 26000000 INFO @ Sat, 11 Nov 2017 03:21:48: 26000000 INFO @ Sat, 11 Nov 2017 03:21:53: 27000000 INFO @ Sat, 11 Nov 2017 03:21:53: 27000000 INFO @ Sat, 11 Nov 2017 03:21:55: 27000000 INFO @ Sat, 11 Nov 2017 03:22:00: 28000000 INFO @ Sat, 11 Nov 2017 03:22:00: 28000000 INFO @ Sat, 11 Nov 2017 03:22:02: 28000000 INFO @ Sat, 11 Nov 2017 03:22:07: 29000000 INFO @ Sat, 11 Nov 2017 03:22:07: 29000000 INFO @ Sat, 11 Nov 2017 03:22:09: 29000000 INFO @ Sat, 11 Nov 2017 03:22:15: 30000000 INFO @ Sat, 11 Nov 2017 03:22:15: 30000000 INFO @ Sat, 11 Nov 2017 03:22:17: 30000000 INFO @ Sat, 11 Nov 2017 03:22:22: 31000000 INFO @ Sat, 11 Nov 2017 03:22:22: 31000000 INFO @ Sat, 11 Nov 2017 03:22:23: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:22:23: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:22:23: #1 total tags in treatment: 31099286 INFO @ Sat, 11 Nov 2017 03:22:23: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:22:23: #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 03:22:23: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:22:23: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:22:23: #1 total tags in treatment: 31099286 INFO @ Sat, 11 Nov 2017 03:22:23: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:22:23: #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 03:22:24: #1 tags after filtering in treatment: 31099207 INFO @ Sat, 11 Nov 2017 03:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:22:24: #1 finished! INFO @ Sat, 11 Nov 2017 03:22:24: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:22:24: #1 tags after filtering in treatment: 31099207 INFO @ Sat, 11 Nov 2017 03:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:22:24: #1 finished! INFO @ Sat, 11 Nov 2017 03:22:24: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:22:24: 31000000 INFO @ Sat, 11 Nov 2017 03:22:25: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 03:22:25: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 03:22:25: #1 total tags in treatment: 31099286 INFO @ Sat, 11 Nov 2017 03:22:25: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 03:22:25: #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 03:22:26: #1 tags after filtering in treatment: 31099207 INFO @ Sat, 11 Nov 2017 03:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 03:22:26: #1 finished! INFO @ Sat, 11 Nov 2017 03:22:26: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 03:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 03:22:28: #2 number of paired peaks: 43256 INFO @ Sat, 11 Nov 2017 03:22:28: start model_add_line... INFO @ Sat, 11 Nov 2017 03:22:28: #2 number of paired peaks: 43256 INFO @ Sat, 11 Nov 2017 03:22:28: start model_add_line... INFO @ Sat, 11 Nov 2017 03:22:29: start X-correlation... INFO @ Sat, 11 Nov 2017 03:22:29: end of X-cor INFO @ Sat, 11 Nov 2017 03:22:29: #2 finished! INFO @ Sat, 11 Nov 2017 03:22:29: #2 predicted fragment length is 160 bps INFO @ Sat, 11 Nov 2017 03:22:29: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 11 Nov 2017 03:22:29: #2.2 Generate R script for model : SRX1977135.20_model.r INFO @ Sat, 11 Nov 2017 03:22:29: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:22:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:22:29: start X-correlation... INFO @ Sat, 11 Nov 2017 03:22:29: end of X-cor INFO @ Sat, 11 Nov 2017 03:22:29: #2 finished! INFO @ Sat, 11 Nov 2017 03:22:29: #2 predicted fragment length is 160 bps INFO @ Sat, 11 Nov 2017 03:22:29: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 11 Nov 2017 03:22:29: #2.2 Generate R script for model : SRX1977135.10_model.r INFO @ Sat, 11 Nov 2017 03:22:29: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:22:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:22:31: #2 number of paired peaks: 43256 INFO @ Sat, 11 Nov 2017 03:22:31: start model_add_line... INFO @ Sat, 11 Nov 2017 03:22:31: start X-correlation... INFO @ Sat, 11 Nov 2017 03:22:31: end of X-cor INFO @ Sat, 11 Nov 2017 03:22:31: #2 finished! INFO @ Sat, 11 Nov 2017 03:22:31: #2 predicted fragment length is 160 bps INFO @ Sat, 11 Nov 2017 03:22:31: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 11 Nov 2017 03:22:31: #2.2 Generate R script for model : SRX1977135.05_model.r INFO @ Sat, 11 Nov 2017 03:22:31: #3 Call peaks... INFO @ Sat, 11 Nov 2017 03:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 03:23:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:23:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:23:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 03:24:33: #4 Write output xls file... SRX1977135.10_peaks.xls INFO @ Sat, 11 Nov 2017 03:24:33: #4 Write peak in narrowPeak format file... SRX1977135.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:24:33: #4 Write summits bed file... SRX1977135.10_summits.bed INFO @ Sat, 11 Nov 2017 03:24:33: Done! pass1 - making usageList (131 chroms): 3 millis pass2 - checking and writing primary data (18192 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:24:33: #4 Write output xls file... SRX1977135.20_peaks.xls INFO @ Sat, 11 Nov 2017 03:24:33: #4 Write peak in narrowPeak format file... SRX1977135.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:24:33: #4 Write summits bed file... SRX1977135.20_summits.bed INFO @ Sat, 11 Nov 2017 03:24:33: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (3141 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 03:24:36: #4 Write output xls file... SRX1977135.05_peaks.xls INFO @ Sat, 11 Nov 2017 03:24:37: #4 Write peak in narrowPeak format file... SRX1977135.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 03:24:37: #4 Write summits bed file... SRX1977135.05_summits.bed INFO @ Sat, 11 Nov 2017 03:24:37: Done! pass1 - making usageList (218 chroms): 12 millis pass2 - checking and writing primary data (62505 records, 4 fields): 77 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。