Job ID = 9039915 sra ファイルのダウンロード中... Completed: 1748611K bytes transferred in 34 seconds (412233K bits/sec), in 2 files, 3 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 23765 0 23765 0 0 2983 0 --:--:-- 0:00:07 --:--:-- 15204 100 59965 0 59965 0 0 6817 0 --:--:-- 0:00:08 --:--:-- 25058 100 90275 0 90275 0 0 9847 0 --:--:-- 0:00:09 --:--:-- 32649 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 21295859 spots for /home/okishinya/chipatlas/results/dm3/SRX1085380/SRR2090180.sra Written 21295859 spots total Written 25907828 spots for /home/okishinya/chipatlas/results/dm3/SRX1085380/SRR2090179.sra Written 25907828 spots total 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: 00:09:51 47203687 reads; of these: 47203687 (100.00%) were unpaired; of these: 20254214 (42.91%) aligned 0 times 23483866 (49.75%) aligned exactly 1 time 3465607 (7.34%) aligned >1 times 57.09% overall alignment rate Time searching: 00:09:51 Overall time: 00:09:51 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 16 files... [bam_rmdupse_core] 8068388 / 26949473 = 0.2994 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 23:29:51: # Command line: callpeak -t SRX1085380.bam -f BAM -g dm -n SRX1085380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1085380.10 # format = BAM # ChIP-seq file = ['SRX1085380.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 23:29:51: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:29:51: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:29:51: # Command line: callpeak -t SRX1085380.bam -f BAM -g dm -n SRX1085380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1085380.20 # format = BAM # ChIP-seq file = ['SRX1085380.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 23:29:51: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:29:51: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:29:51: # Command line: callpeak -t SRX1085380.bam -f BAM -g dm -n SRX1085380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1085380.05 # format = BAM # ChIP-seq file = ['SRX1085380.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 23:29:51: #1 read tag files... INFO @ Sun, 04 Jun 2017 23:29:51: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 23:29:58: 1000000 INFO @ Sun, 04 Jun 2017 23:29:58: 1000000 INFO @ Sun, 04 Jun 2017 23:29:59: 1000000 INFO @ Sun, 04 Jun 2017 23:30:06: 2000000 INFO @ Sun, 04 Jun 2017 23:30:06: 2000000 INFO @ Sun, 04 Jun 2017 23:30:07: 2000000 INFO @ Sun, 04 Jun 2017 23:30:14: 3000000 INFO @ Sun, 04 Jun 2017 23:30:14: 3000000 INFO @ Sun, 04 Jun 2017 23:30:14: 3000000 INFO @ Sun, 04 Jun 2017 23:30:21: 4000000 INFO @ Sun, 04 Jun 2017 23:30:21: 4000000 INFO @ Sun, 04 Jun 2017 23:30:22: 4000000 INFO @ Sun, 04 Jun 2017 23:30:29: 5000000 INFO @ Sun, 04 Jun 2017 23:30:29: 5000000 INFO @ Sun, 04 Jun 2017 23:30:30: 5000000 INFO @ Sun, 04 Jun 2017 23:30:37: 6000000 INFO @ Sun, 04 Jun 2017 23:30:37: 6000000 INFO @ Sun, 04 Jun 2017 23:30:38: 6000000 INFO @ Sun, 04 Jun 2017 23:30:44: 7000000 INFO @ Sun, 04 Jun 2017 23:30:44: 7000000 INFO @ Sun, 04 Jun 2017 23:30:46: 7000000 INFO @ Sun, 04 Jun 2017 23:30:52: 8000000 INFO @ Sun, 04 Jun 2017 23:30:52: 8000000 INFO @ Sun, 04 Jun 2017 23:30:53: 8000000 INFO @ Sun, 04 Jun 2017 23:31:00: 9000000 INFO @ Sun, 04 Jun 2017 23:31:00: 9000000 INFO @ Sun, 04 Jun 2017 23:31:01: 9000000 INFO @ Sun, 04 Jun 2017 23:31:07: 10000000 INFO @ Sun, 04 Jun 2017 23:31:07: 10000000 INFO @ Sun, 04 Jun 2017 23:31:09: 10000000 INFO @ Sun, 04 Jun 2017 23:31:15: 11000000 INFO @ Sun, 04 Jun 2017 23:31:15: 11000000 INFO @ Sun, 04 Jun 2017 23:31:17: 11000000 INFO @ Sun, 04 Jun 2017 23:31:23: 12000000 INFO @ Sun, 04 Jun 2017 23:31:23: 12000000 INFO @ Sun, 04 Jun 2017 23:31:25: 12000000 INFO @ Sun, 04 Jun 2017 23:31:30: 13000000 INFO @ Sun, 04 Jun 2017 23:31:30: 13000000 INFO @ Sun, 04 Jun 2017 23:31:33: 13000000 INFO @ Sun, 04 Jun 2017 23:31:39: 14000000 INFO @ Sun, 04 Jun 2017 23:31:39: 14000000 INFO @ Sun, 04 Jun 2017 23:31:43: 14000000 INFO @ Sun, 04 Jun 2017 23:31:47: 15000000 INFO @ Sun, 04 Jun 2017 23:31:47: 15000000 INFO @ Sun, 04 Jun 2017 23:31:53: 15000000 INFO @ Sun, 04 Jun 2017 23:31:56: 16000000 INFO @ Sun, 04 Jun 2017 23:31:56: 16000000 INFO @ Sun, 04 Jun 2017 23:32:02: 16000000 INFO @ Sun, 04 Jun 2017 23:32:04: 17000000 INFO @ Sun, 04 Jun 2017 23:32:04: 17000000 INFO @ Sun, 04 Jun 2017 23:32:12: 17000000 INFO @ Sun, 04 Jun 2017 23:32:13: 18000000 INFO @ Sun, 04 Jun 2017 23:32:13: 18000000 INFO @ Sun, 04 Jun 2017 23:32:20: #1 tag size is determined as 82 bps INFO @ Sun, 04 Jun 2017 23:32:20: #1 tag size = 82 INFO @ Sun, 04 Jun 2017 23:32:20: #1 total tags in treatment: 18881085 INFO @ Sun, 04 Jun 2017 23:32:20: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:32:20: #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 23:32:20: #1 tag size is determined as 82 bps INFO @ Sun, 04 Jun 2017 23:32:20: #1 tag size = 82 INFO @ Sun, 04 Jun 2017 23:32:20: #1 total tags in treatment: 18881085 INFO @ Sun, 04 Jun 2017 23:32:20: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:32:20: #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 23:32:21: 18000000 INFO @ Sun, 04 Jun 2017 23:32:24: #1 tags after filtering in treatment: 18814567 INFO @ Sun, 04 Jun 2017 23:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:32:24: #1 finished! INFO @ Sun, 04 Jun 2017 23:32:24: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:32:24: #1 tags after filtering in treatment: 18814567 INFO @ Sun, 04 Jun 2017 23:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:32:24: #1 finished! INFO @ Sun, 04 Jun 2017 23:32:24: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:32:27: #2 number of paired peaks: 3008 INFO @ Sun, 04 Jun 2017 23:32:27: start model_add_line... INFO @ Sun, 04 Jun 2017 23:32:28: #2 number of paired peaks: 3008 INFO @ Sun, 04 Jun 2017 23:32:28: start model_add_line... INFO @ Sun, 04 Jun 2017 23:32:28: #1 tag size is determined as 82 bps INFO @ Sun, 04 Jun 2017 23:32:28: #1 tag size = 82 INFO @ Sun, 04 Jun 2017 23:32:28: #1 total tags in treatment: 18881085 INFO @ Sun, 04 Jun 2017 23:32:28: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 23:32:28: #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 23:32:31: #1 tags after filtering in treatment: 18814567 INFO @ Sun, 04 Jun 2017 23:32:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 23:32:31: #1 finished! INFO @ Sun, 04 Jun 2017 23:32:31: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 23:32:35: #2 number of paired peaks: 3008 INFO @ Sun, 04 Jun 2017 23:32:35: start model_add_line... INFO @ Sun, 04 Jun 2017 23:32:57: start X-correlation... INFO @ Sun, 04 Jun 2017 23:32:57: end of X-cor INFO @ Sun, 04 Jun 2017 23:32:57: #2 finished! INFO @ Sun, 04 Jun 2017 23:32:57: #2 predicted fragment length is 187 bps INFO @ Sun, 04 Jun 2017 23:32:57: #2 alternative fragment length(s) may be 187 bps INFO @ Sun, 04 Jun 2017 23:32:57: #2.2 Generate R script for model : SRX1085380.05_model.r INFO @ Sun, 04 Jun 2017 23:32:57: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:32:57: start X-correlation... INFO @ Sun, 04 Jun 2017 23:32:57: end of X-cor INFO @ Sun, 04 Jun 2017 23:32:57: #2 finished! INFO @ Sun, 04 Jun 2017 23:32:57: #2 predicted fragment length is 187 bps INFO @ Sun, 04 Jun 2017 23:32:57: #2 alternative fragment length(s) may be 187 bps INFO @ Sun, 04 Jun 2017 23:32:57: #2.2 Generate R script for model : SRX1085380.10_model.r INFO @ Sun, 04 Jun 2017 23:32:57: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:33:05: start X-correlation... INFO @ Sun, 04 Jun 2017 23:33:05: end of X-cor INFO @ Sun, 04 Jun 2017 23:33:05: #2 finished! INFO @ Sun, 04 Jun 2017 23:33:05: #2 predicted fragment length is 187 bps INFO @ Sun, 04 Jun 2017 23:33:05: #2 alternative fragment length(s) may be 187 bps INFO @ Sun, 04 Jun 2017 23:33:05: #2.2 Generate R script for model : SRX1085380.20_model.r INFO @ Sun, 04 Jun 2017 23:33:05: #3 Call peaks... INFO @ Sun, 04 Jun 2017 23:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 23:34:41: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:34:47: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:34:49: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 23:36:04: #4 Write output xls file... SRX1085380.20_peaks.xls INFO @ Sun, 04 Jun 2017 23:36:05: #4 Write peak in narrowPeak format file... SRX1085380.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:36:05: #4 Write summits bed file... SRX1085380.20_summits.bed INFO @ Sun, 04 Jun 2017 23:36:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6941 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 23:36:14: #4 Write output xls file... SRX1085380.05_peaks.xls INFO @ Sun, 04 Jun 2017 23:36:15: #4 Write output xls file... SRX1085380.10_peaks.xls INFO @ Sun, 04 Jun 2017 23:36:15: #4 Write peak in narrowPeak format file... SRX1085380.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:36:15: #4 Write peak in narrowPeak format file... SRX1085380.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 23:36:15: #4 Write summits bed file... SRX1085380.10_summits.bed INFO @ Sun, 04 Jun 2017 23:36:15: Done! INFO @ Sun, 04 Jun 2017 23:36:15: #4 Write summits bed file... SRX1085380.05_summits.bed INFO @ Sun, 04 Jun 2017 23:36:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10293 records, 4 fields): 14 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14125 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。