Job ID = 1295460 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,567,281 reads read : 45,134,562 reads written : 45,134,562 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 01:04:59 22567281 reads; of these: 22567281 (100.00%) were paired; of these: 2611718 (11.57%) aligned concordantly 0 times 13119703 (58.14%) aligned concordantly exactly 1 time 6835860 (30.29%) aligned concordantly >1 times ---- 2611718 pairs aligned concordantly 0 times; of these: 147138 (5.63%) aligned discordantly 1 time ---- 2464580 pairs aligned 0 times concordantly or discordantly; of these: 4929160 mates make up the pairs; of these: 3745435 (75.99%) aligned 0 times 594557 (12.06%) aligned exactly 1 time 589168 (11.95%) aligned >1 times 91.70% overall alignment rate Time searching: 01:04:59 Overall time: 01:04:59 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1258304 / 20031079 = 0.0628 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 @ Mon, 03 Jun 2019 15:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.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 # Paired-End mode is off INFO @ Mon, 03 Jun 2019 15:18:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:18:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.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 # Paired-End mode is off INFO @ Mon, 03 Jun 2019 15:18:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:18:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.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 # Paired-End mode is off INFO @ Mon, 03 Jun 2019 15:18:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:18:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:18:10: 1000000 INFO @ Mon, 03 Jun 2019 15:18:11: 1000000 INFO @ Mon, 03 Jun 2019 15:18:11: 1000000 INFO @ Mon, 03 Jun 2019 15:18:19: 2000000 INFO @ Mon, 03 Jun 2019 15:18:21: 2000000 INFO @ Mon, 03 Jun 2019 15:18:21: 2000000 INFO @ Mon, 03 Jun 2019 15:18:27: 3000000 INFO @ Mon, 03 Jun 2019 15:18:30: 3000000 INFO @ Mon, 03 Jun 2019 15:18:31: 3000000 INFO @ Mon, 03 Jun 2019 15:18:35: 4000000 INFO @ Mon, 03 Jun 2019 15:18:39: 4000000 INFO @ Mon, 03 Jun 2019 15:18:41: 4000000 INFO @ Mon, 03 Jun 2019 15:18:43: 5000000 INFO @ Mon, 03 Jun 2019 15:18:48: 5000000 INFO @ Mon, 03 Jun 2019 15:18:51: 5000000 INFO @ Mon, 03 Jun 2019 15:18:51: 6000000 INFO @ Mon, 03 Jun 2019 15:18:57: 6000000 INFO @ Mon, 03 Jun 2019 15:18:59: 7000000 INFO @ Mon, 03 Jun 2019 15:19:01: 6000000 INFO @ Mon, 03 Jun 2019 15:19:08: 7000000 INFO @ Mon, 03 Jun 2019 15:19:08: 8000000 INFO @ Mon, 03 Jun 2019 15:19:11: 7000000 INFO @ Mon, 03 Jun 2019 15:19:17: 9000000 INFO @ Mon, 03 Jun 2019 15:19:17: 8000000 INFO @ Mon, 03 Jun 2019 15:19:21: 8000000 INFO @ Mon, 03 Jun 2019 15:19:25: 10000000 INFO @ Mon, 03 Jun 2019 15:19:26: 9000000 INFO @ Mon, 03 Jun 2019 15:19:31: 9000000 INFO @ Mon, 03 Jun 2019 15:19:34: 11000000 INFO @ Mon, 03 Jun 2019 15:19:35: 10000000 INFO @ Mon, 03 Jun 2019 15:19:42: 10000000 INFO @ Mon, 03 Jun 2019 15:19:43: 12000000 INFO @ Mon, 03 Jun 2019 15:19:44: 11000000 INFO @ Mon, 03 Jun 2019 15:19:51: 11000000 INFO @ Mon, 03 Jun 2019 15:19:52: 13000000 INFO @ Mon, 03 Jun 2019 15:19:53: 12000000 INFO @ Mon, 03 Jun 2019 15:20:01: 14000000 INFO @ Mon, 03 Jun 2019 15:20:02: 12000000 INFO @ Mon, 03 Jun 2019 15:20:02: 13000000 INFO @ Mon, 03 Jun 2019 15:20:10: 15000000 INFO @ Mon, 03 Jun 2019 15:20:11: 14000000 INFO @ Mon, 03 Jun 2019 15:20:12: 13000000 INFO @ Mon, 03 Jun 2019 15:20:19: 16000000 INFO @ Mon, 03 Jun 2019 15:20:19: 15000000 INFO @ Mon, 03 Jun 2019 15:20:21: 14000000 INFO @ Mon, 03 Jun 2019 15:20:28: 17000000 INFO @ Mon, 03 Jun 2019 15:20:28: 16000000 INFO @ Mon, 03 Jun 2019 15:20:31: 15000000 INFO @ Mon, 03 Jun 2019 15:20:37: 18000000 INFO @ Mon, 03 Jun 2019 15:20:37: 17000000 INFO @ Mon, 03 Jun 2019 15:20:42: 16000000 INFO @ Mon, 03 Jun 2019 15:20:46: 19000000 INFO @ Mon, 03 Jun 2019 15:20:46: 18000000 INFO @ Mon, 03 Jun 2019 15:20:52: 17000000 INFO @ Mon, 03 Jun 2019 15:20:54: 20000000 INFO @ Mon, 03 Jun 2019 15:20:55: 19000000 INFO @ Mon, 03 Jun 2019 15:21:02: 21000000 INFO @ Mon, 03 Jun 2019 15:21:03: 18000000 INFO @ Mon, 03 Jun 2019 15:21:05: 20000000 INFO @ Mon, 03 Jun 2019 15:21:11: 22000000 INFO @ Mon, 03 Jun 2019 15:21:13: 19000000 INFO @ Mon, 03 Jun 2019 15:21:15: 21000000 INFO @ Mon, 03 Jun 2019 15:21:19: 23000000 INFO @ Mon, 03 Jun 2019 15:21:23: 20000000 INFO @ Mon, 03 Jun 2019 15:21:25: 22000000 INFO @ Mon, 03 Jun 2019 15:21:27: 24000000 INFO @ Mon, 03 Jun 2019 15:21:34: 21000000 INFO @ Mon, 03 Jun 2019 15:21:34: 23000000 INFO @ Mon, 03 Jun 2019 15:21:36: 25000000 INFO @ Mon, 03 Jun 2019 15:21:43: 26000000 INFO @ Mon, 03 Jun 2019 15:21:43: 24000000 INFO @ Mon, 03 Jun 2019 15:21:44: 22000000 INFO @ Mon, 03 Jun 2019 15:21:51: 27000000 INFO @ Mon, 03 Jun 2019 15:21:52: 25000000 INFO @ Mon, 03 Jun 2019 15:21:56: 23000000 INFO @ Mon, 03 Jun 2019 15:21:59: 28000000 INFO @ Mon, 03 Jun 2019 15:22:01: 26000000 INFO @ Mon, 03 Jun 2019 15:22:07: 29000000 INFO @ Mon, 03 Jun 2019 15:22:07: 24000000 INFO @ Mon, 03 Jun 2019 15:22:10: 27000000 INFO @ Mon, 03 Jun 2019 15:22:15: 30000000 INFO @ Mon, 03 Jun 2019 15:22:18: 25000000 INFO @ Mon, 03 Jun 2019 15:22:19: 28000000 INFO @ Mon, 03 Jun 2019 15:22:23: 31000000 INFO @ Mon, 03 Jun 2019 15:22:28: 29000000 INFO @ Mon, 03 Jun 2019 15:22:28: 26000000 INFO @ Mon, 03 Jun 2019 15:22:30: 32000000 INFO @ Mon, 03 Jun 2019 15:22:37: 30000000 INFO @ Mon, 03 Jun 2019 15:22:38: 33000000 INFO @ Mon, 03 Jun 2019 15:22:39: 27000000 INFO @ Mon, 03 Jun 2019 15:22:45: 34000000 INFO @ Mon, 03 Jun 2019 15:22:46: 31000000 INFO @ Mon, 03 Jun 2019 15:22:49: 28000000 INFO @ Mon, 03 Jun 2019 15:22:53: 35000000 INFO @ Mon, 03 Jun 2019 15:22:56: 32000000 INFO @ Mon, 03 Jun 2019 15:23:00: 29000000 INFO @ Mon, 03 Jun 2019 15:23:00: 36000000 INFO @ Mon, 03 Jun 2019 15:23:06: 33000000 INFO @ Mon, 03 Jun 2019 15:23:08: 37000000 INFO @ Mon, 03 Jun 2019 15:23:11: 30000000 INFO @ Mon, 03 Jun 2019 15:23:15: 34000000 INFO @ Mon, 03 Jun 2019 15:23:15: 38000000 INFO @ Mon, 03 Jun 2019 15:23:22: 31000000 INFO @ Mon, 03 Jun 2019 15:23:22: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:23:22: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:23:22: #1 total tags in treatment: 18698453 INFO @ Mon, 03 Jun 2019 15:23:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:23:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:23:23: #1 tags after filtering in treatment: 16936378 INFO @ Mon, 03 Jun 2019 15:23:23: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:23:23: #1 finished! INFO @ Mon, 03 Jun 2019 15:23:23: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:23:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:23:23: 35000000 INFO @ Mon, 03 Jun 2019 15:23:24: #2 number of paired peaks: 1312 INFO @ Mon, 03 Jun 2019 15:23:24: start model_add_line... INFO @ Mon, 03 Jun 2019 15:23:24: start X-correlation... INFO @ Mon, 03 Jun 2019 15:23:24: end of X-cor INFO @ Mon, 03 Jun 2019 15:23:24: #2 finished! INFO @ Mon, 03 Jun 2019 15:23:24: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:23:24: #2 alternative fragment length(s) may be 4,159 bps INFO @ Mon, 03 Jun 2019 15:23:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.05_model.r INFO @ Mon, 03 Jun 2019 15:23:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:23:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:23:32: 36000000 INFO @ Mon, 03 Jun 2019 15:23:32: 32000000 INFO @ Mon, 03 Jun 2019 15:23:41: 37000000 INFO @ Mon, 03 Jun 2019 15:23:43: 33000000 INFO @ Mon, 03 Jun 2019 15:23:49: 38000000 INFO @ Mon, 03 Jun 2019 15:23:53: 34000000 INFO @ Mon, 03 Jun 2019 15:23:57: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:23:57: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:23:57: #1 total tags in treatment: 18698453 INFO @ Mon, 03 Jun 2019 15:23:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:23:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:23:57: #1 tags after filtering in treatment: 16936378 INFO @ Mon, 03 Jun 2019 15:23:57: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:23:57: #1 finished! INFO @ Mon, 03 Jun 2019 15:23:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:23:59: #2 number of paired peaks: 1312 INFO @ Mon, 03 Jun 2019 15:23:59: start model_add_line... INFO @ Mon, 03 Jun 2019 15:23:59: start X-correlation... INFO @ Mon, 03 Jun 2019 15:23:59: end of X-cor INFO @ Mon, 03 Jun 2019 15:23:59: #2 finished! INFO @ Mon, 03 Jun 2019 15:23:59: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:23:59: #2 alternative fragment length(s) may be 4,159 bps INFO @ Mon, 03 Jun 2019 15:23:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.10_model.r INFO @ Mon, 03 Jun 2019 15:23:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:23:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:24:03: 35000000 INFO @ Mon, 03 Jun 2019 15:24:14: 36000000 INFO @ Mon, 03 Jun 2019 15:24:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:24:24: 37000000 INFO @ Mon, 03 Jun 2019 15:24:34: 38000000 INFO @ Mon, 03 Jun 2019 15:24:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:24:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:24:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.05_summits.bed INFO @ Mon, 03 Jun 2019 15:24:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3068 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:24:42: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:24:42: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:24:42: #1 total tags in treatment: 18698453 INFO @ Mon, 03 Jun 2019 15:24:42: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:24:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:24:43: #1 tags after filtering in treatment: 16936378 INFO @ Mon, 03 Jun 2019 15:24:43: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:24:43: #1 finished! INFO @ Mon, 03 Jun 2019 15:24:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:24:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:24:45: #2 number of paired peaks: 1312 INFO @ Mon, 03 Jun 2019 15:24:45: start model_add_line... INFO @ Mon, 03 Jun 2019 15:24:45: start X-correlation... INFO @ Mon, 03 Jun 2019 15:24:45: end of X-cor INFO @ Mon, 03 Jun 2019 15:24:45: #2 finished! INFO @ Mon, 03 Jun 2019 15:24:45: #2 predicted fragment length is 159 bps INFO @ Mon, 03 Jun 2019 15:24:45: #2 alternative fragment length(s) may be 4,159 bps INFO @ Mon, 03 Jun 2019 15:24:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.20_model.r INFO @ Mon, 03 Jun 2019 15:24:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:24:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:24:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.10_summits.bed INFO @ Mon, 03 Jun 2019 15:25:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1872 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:25:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393663/SRX3393663.20_summits.bed INFO @ Mon, 03 Jun 2019 15:26:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1032 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。