Job ID = 9033147 sra ファイルのダウンロード中... Completed: 660893K bytes transferred in 9 seconds (566602K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 13455 0 13455 0 0 1804 0 --:--:-- 0:00:07 --:--:-- 14850 100 46174 0 46174 0 0 5463 0 --:--:-- 0:00:08 --:--:-- 24289 100 65334 0 65334 0 0 7580 0 --:--:-- 0:00:08 --:--:-- 31592 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 25903929 spots for /home/okishinya/chipatlas/results/dm3/SRX914961/SRR1873271.sra Written 25903929 spots total 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:50 25903929 reads; of these: 25903929 (100.00%) were unpaired; of these: 3187990 (12.31%) aligned 0 times 19992211 (77.18%) aligned exactly 1 time 2723728 (10.51%) aligned >1 times 87.69% overall alignment rate Time searching: 00:06:51 Overall time: 00:06:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 10373782 / 22715939 = 0.4567 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, 04 Jun 2017 00:17:18: # Command line: callpeak -t SRX914961.bam -f BAM -g dm -n SRX914961.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX914961.20 # format = BAM # ChIP-seq file = ['SRX914961.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sun, 04 Jun 2017 00:17:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:17:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:17:18: # Command line: callpeak -t SRX914961.bam -f BAM -g dm -n SRX914961.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX914961.05 # format = BAM # ChIP-seq file = ['SRX914961.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sun, 04 Jun 2017 00:17:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:17:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:17:18: # Command line: callpeak -t SRX914961.bam -f BAM -g dm -n SRX914961.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX914961.10 # format = BAM # ChIP-seq file = ['SRX914961.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sun, 04 Jun 2017 00:17:18: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:17:18: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:17:24: 1000000 INFO @ Sun, 04 Jun 2017 00:17:24: 1000000 INFO @ Sun, 04 Jun 2017 00:17:24: 1000000 INFO @ Sun, 04 Jun 2017 00:17:29: 2000000 INFO @ Sun, 04 Jun 2017 00:17:30: 2000000 INFO @ Sun, 04 Jun 2017 00:17:30: 2000000 INFO @ Sun, 04 Jun 2017 00:17:35: 3000000 INFO @ Sun, 04 Jun 2017 00:17:36: 3000000 INFO @ Sun, 04 Jun 2017 00:17:37: 3000000 INFO @ Sun, 04 Jun 2017 00:17:42: 4000000 INFO @ Sun, 04 Jun 2017 00:17:42: 4000000 INFO @ Sun, 04 Jun 2017 00:17:43: 4000000 INFO @ Sun, 04 Jun 2017 00:17:48: 5000000 INFO @ Sun, 04 Jun 2017 00:17:49: 5000000 INFO @ Sun, 04 Jun 2017 00:17:49: 5000000 INFO @ Sun, 04 Jun 2017 00:17:54: 6000000 INFO @ Sun, 04 Jun 2017 00:17:55: 6000000 INFO @ Sun, 04 Jun 2017 00:17:55: 6000000 INFO @ Sun, 04 Jun 2017 00:18:00: 7000000 INFO @ Sun, 04 Jun 2017 00:18:01: 7000000 INFO @ Sun, 04 Jun 2017 00:18:02: 7000000 INFO @ Sun, 04 Jun 2017 00:18:05: 8000000 INFO @ Sun, 04 Jun 2017 00:18:08: 8000000 INFO @ Sun, 04 Jun 2017 00:18:08: 8000000 INFO @ Sun, 04 Jun 2017 00:18:11: 9000000 INFO @ Sun, 04 Jun 2017 00:18:14: 9000000 INFO @ Sun, 04 Jun 2017 00:18:14: 9000000 INFO @ Sun, 04 Jun 2017 00:18:17: 10000000 INFO @ Sun, 04 Jun 2017 00:18:21: 10000000 INFO @ Sun, 04 Jun 2017 00:18:21: 10000000 INFO @ Sun, 04 Jun 2017 00:18:22: 11000000 INFO @ Sun, 04 Jun 2017 00:18:27: 11000000 INFO @ Sun, 04 Jun 2017 00:18:28: 11000000 INFO @ Sun, 04 Jun 2017 00:18:28: 12000000 INFO @ Sun, 04 Jun 2017 00:18:30: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:18:30: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:18:30: #1 total tags in treatment: 12342157 INFO @ Sun, 04 Jun 2017 00:18:30: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:33: #1 tags after filtering in treatment: 12339719 INFO @ Sun, 04 Jun 2017 00:18:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:33: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:33: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:33: 12000000 INFO @ Sun, 04 Jun 2017 00:18:34: 12000000 INFO @ Sun, 04 Jun 2017 00:18:35: #2 number of paired peaks: 1411 INFO @ Sun, 04 Jun 2017 00:18:35: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:36: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:18:36: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:18:36: #1 total tags in treatment: 12342157 INFO @ Sun, 04 Jun 2017 00:18:36: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:36: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 00:18:36: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 00:18:36: #1 total tags in treatment: 12342157 INFO @ Sun, 04 Jun 2017 00:18:36: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:18:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:18:38: #1 tags after filtering in treatment: 12339719 INFO @ Sun, 04 Jun 2017 00:18:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:38: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:38: #1 tags after filtering in treatment: 12339719 INFO @ Sun, 04 Jun 2017 00:18:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:18:38: #1 finished! INFO @ Sun, 04 Jun 2017 00:18:38: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:18:40: #2 number of paired peaks: 1411 INFO @ Sun, 04 Jun 2017 00:18:40: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:41: #2 number of paired peaks: 1411 INFO @ Sun, 04 Jun 2017 00:18:41: start model_add_line... INFO @ Sun, 04 Jun 2017 00:18:46: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:46: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:46: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:46: #2 predicted fragment length is 242 bps INFO @ Sun, 04 Jun 2017 00:18:46: #2 alternative fragment length(s) may be 2,242 bps INFO @ Sun, 04 Jun 2017 00:18:46: #2.2 Generate R script for model : SRX914961.20_model.r INFO @ Sun, 04 Jun 2017 00:18:46: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:18:52: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:52: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:52: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:52: #2 predicted fragment length is 242 bps INFO @ Sun, 04 Jun 2017 00:18:52: #2 alternative fragment length(s) may be 2,242 bps INFO @ Sun, 04 Jun 2017 00:18:52: #2.2 Generate R script for model : SRX914961.10_model.r INFO @ Sun, 04 Jun 2017 00:18:52: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:18:53: start X-correlation... INFO @ Sun, 04 Jun 2017 00:18:53: end of X-cor INFO @ Sun, 04 Jun 2017 00:18:53: #2 finished! INFO @ Sun, 04 Jun 2017 00:18:53: #2 predicted fragment length is 242 bps INFO @ Sun, 04 Jun 2017 00:18:53: #2 alternative fragment length(s) may be 2,242 bps INFO @ Sun, 04 Jun 2017 00:18:53: #2.2 Generate R script for model : SRX914961.05_model.r INFO @ Sun, 04 Jun 2017 00:18:53: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:18:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:19:58: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:03: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:06: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:20:45: #4 Write output xls file... SRX914961.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:20:45: #4 Write peak in narrowPeak format file... SRX914961.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:20:45: #4 Write summits bed file... SRX914961.20_summits.bed INFO @ Sun, 04 Jun 2017 00:20:45: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:21:00: #4 Write output xls file... SRX914961.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:21:00: #4 Write peak in narrowPeak format file... SRX914961.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:21:00: #4 Write summits bed file... SRX914961.10_summits.bed INFO @ Sun, 04 Jun 2017 00:21:00: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (2310 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:21:03: #4 Write output xls file... SRX914961.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:21:03: #4 Write peak in narrowPeak format file... SRX914961.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:21:03: #4 Write summits bed file... SRX914961.05_summits.bed INFO @ Sun, 04 Jun 2017 00:21:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4885 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。