Job ID = 9033332 sra ファイルのダウンロード中... Completed: 384858K bytes transferred in 6 seconds (504524K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 22318 0 22318 0 0 2878 0 --:--:-- 0:00:07 --:--:-- 18707 100 66026 0 66026 0 0 7620 0 --:--:-- 0:00:08 --:--:-- 31381 100 67897 0 67897 0 0 7835 0 --:--:-- 0:00:08 --:--:-- 32255 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 17332179 spots for /home/okishinya/chipatlas/results/dm3/SRX969921/SRR1931637.sra Written 17332179 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: 00:00:00 Multiseed full-index search: 00:07:07 17332179 reads; of these: 17332179 (100.00%) were unpaired; of these: 566093 (3.27%) aligned 0 times 12569267 (72.52%) aligned exactly 1 time 4196819 (24.21%) aligned >1 times 96.73% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 3131873 / 16766086 = 0.1868 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 00:23:04: # Command line: callpeak -t SRX969921.bam -f BAM -g dm -n SRX969921.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969921.05 # format = BAM # ChIP-seq file = ['SRX969921.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 00:23:04: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:23:04: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:23:04: # Command line: callpeak -t SRX969921.bam -f BAM -g dm -n SRX969921.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969921.20 # format = BAM # ChIP-seq file = ['SRX969921.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 00:23:04: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:23:04: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:23:04: # Command line: callpeak -t SRX969921.bam -f BAM -g dm -n SRX969921.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969921.10 # format = BAM # ChIP-seq file = ['SRX969921.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 00:23:04: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:23:04: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:23:11: 1000000 INFO @ Sun, 04 Jun 2017 00:23:11: 1000000 INFO @ Sun, 04 Jun 2017 00:23:11: 1000000 INFO @ Sun, 04 Jun 2017 00:23:18: 2000000 INFO @ Sun, 04 Jun 2017 00:23:19: 2000000 INFO @ Sun, 04 Jun 2017 00:23:19: 2000000 INFO @ Sun, 04 Jun 2017 00:23:25: 3000000 INFO @ Sun, 04 Jun 2017 00:23:27: 3000000 INFO @ Sun, 04 Jun 2017 00:23:27: 3000000 INFO @ Sun, 04 Jun 2017 00:23:32: 4000000 INFO @ Sun, 04 Jun 2017 00:23:35: 4000000 INFO @ Sun, 04 Jun 2017 00:23:35: 4000000 INFO @ Sun, 04 Jun 2017 00:23:39: 5000000 INFO @ Sun, 04 Jun 2017 00:23:43: 5000000 INFO @ Sun, 04 Jun 2017 00:23:43: 5000000 INFO @ Sun, 04 Jun 2017 00:23:46: 6000000 INFO @ Sun, 04 Jun 2017 00:23:51: 6000000 INFO @ Sun, 04 Jun 2017 00:23:51: 6000000 INFO @ Sun, 04 Jun 2017 00:23:53: 7000000 INFO @ Sun, 04 Jun 2017 00:23:59: 7000000 INFO @ Sun, 04 Jun 2017 00:23:59: 7000000 INFO @ Sun, 04 Jun 2017 00:24:00: 8000000 INFO @ Sun, 04 Jun 2017 00:24:06: 8000000 INFO @ Sun, 04 Jun 2017 00:24:06: 8000000 INFO @ Sun, 04 Jun 2017 00:24:07: 9000000 INFO @ Sun, 04 Jun 2017 00:24:14: 10000000 INFO @ Sun, 04 Jun 2017 00:24:14: 9000000 INFO @ Sun, 04 Jun 2017 00:24:14: 9000000 INFO @ Sun, 04 Jun 2017 00:24:21: 11000000 INFO @ Sun, 04 Jun 2017 00:24:22: 10000000 INFO @ Sun, 04 Jun 2017 00:24:22: 10000000 INFO @ Sun, 04 Jun 2017 00:24:27: 12000000 INFO @ Sun, 04 Jun 2017 00:24:29: 11000000 INFO @ Sun, 04 Jun 2017 00:24:29: 11000000 INFO @ Sun, 04 Jun 2017 00:24:34: 13000000 INFO @ Sun, 04 Jun 2017 00:24:37: 12000000 INFO @ Sun, 04 Jun 2017 00:24:37: 12000000 INFO @ Sun, 04 Jun 2017 00:24:38: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:24:38: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:24:38: #1 total tags in treatment: 13634213 INFO @ Sun, 04 Jun 2017 00:24:38: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:24:38: #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 00:24:41: #1 tags after filtering in treatment: 13629066 INFO @ Sun, 04 Jun 2017 00:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:24:41: #1 finished! INFO @ Sun, 04 Jun 2017 00:24:41: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:24:44: #2 number of paired peaks: 2319 INFO @ Sun, 04 Jun 2017 00:24:44: start model_add_line... INFO @ Sun, 04 Jun 2017 00:24:44: 13000000 INFO @ Sun, 04 Jun 2017 00:24:44: 13000000 INFO @ Sun, 04 Jun 2017 00:24:49: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:24:49: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:24:49: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:24:49: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:24:49: #1 total tags in treatment: 13634213 INFO @ Sun, 04 Jun 2017 00:24:49: #1 total tags in treatment: 13634213 INFO @ Sun, 04 Jun 2017 00:24:49: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:24:49: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:24:49: #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 00:24:49: #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 00:24:52: #1 tags after filtering in treatment: 13629066 INFO @ Sun, 04 Jun 2017 00:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:24:52: #1 finished! INFO @ Sun, 04 Jun 2017 00:24:52: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:24:52: #1 tags after filtering in treatment: 13629066 INFO @ Sun, 04 Jun 2017 00:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:24:52: #1 finished! INFO @ Sun, 04 Jun 2017 00:24:52: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:24:54: #2 number of paired peaks: 2319 INFO @ Sun, 04 Jun 2017 00:24:54: start model_add_line... INFO @ Sun, 04 Jun 2017 00:24:55: #2 number of paired peaks: 2319 INFO @ Sun, 04 Jun 2017 00:24:55: start model_add_line... INFO @ Sun, 04 Jun 2017 00:25:00: start X-correlation... INFO @ Sun, 04 Jun 2017 00:25:00: end of X-cor INFO @ Sun, 04 Jun 2017 00:25:00: #2 finished! INFO @ Sun, 04 Jun 2017 00:25:00: #2 predicted fragment length is 275 bps INFO @ Sun, 04 Jun 2017 00:25:00: #2 alternative fragment length(s) may be 275 bps INFO @ Sun, 04 Jun 2017 00:25:00: #2.2 Generate R script for model : SRX969921.05_model.r INFO @ Sun, 04 Jun 2017 00:25:00: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:25:11: start X-correlation... INFO @ Sun, 04 Jun 2017 00:25:11: end of X-cor INFO @ Sun, 04 Jun 2017 00:25:11: #2 finished! INFO @ Sun, 04 Jun 2017 00:25:11: #2 predicted fragment length is 275 bps INFO @ Sun, 04 Jun 2017 00:25:11: #2 alternative fragment length(s) may be 275 bps INFO @ Sun, 04 Jun 2017 00:25:11: #2.2 Generate R script for model : SRX969921.20_model.r INFO @ Sun, 04 Jun 2017 00:25:11: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:25:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:25:11: start X-correlation... INFO @ Sun, 04 Jun 2017 00:25:11: end of X-cor INFO @ Sun, 04 Jun 2017 00:25:11: #2 finished! INFO @ Sun, 04 Jun 2017 00:25:11: #2 predicted fragment length is 275 bps INFO @ Sun, 04 Jun 2017 00:25:11: #2 alternative fragment length(s) may be 275 bps INFO @ Sun, 04 Jun 2017 00:25:11: #2.2 Generate R script for model : SRX969921.10_model.r INFO @ Sun, 04 Jun 2017 00:25:11: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:25:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:26:23: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:26:33: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:26:34: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:27:33: #4 Write output xls file... SRX969921.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:27:33: #4 Write peak in narrowPeak format file... SRX969921.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:27:33: #4 Write summits bed file... SRX969921.05_summits.bed INFO @ Sun, 04 Jun 2017 00:27:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6901 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:27:38: #4 Write output xls file... SRX969921.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:27:38: #4 Write peak in narrowPeak format file... SRX969921.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:27:38: #4 Write summits bed file... SRX969921.20_summits.bed INFO @ Sun, 04 Jun 2017 00:27:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4687 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:27:46: #4 Write output xls file... SRX969921.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:27:46: #4 Write peak in narrowPeak format file... SRX969921.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:27:46: #4 Write summits bed file... SRX969921.10_summits.bed INFO @ Sun, 04 Jun 2017 00:27:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5836 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。