Job ID = 2590446 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,374,688 reads read : 24,749,376 reads written : 12,374,688 reads 0-length : 12,374,688 spots read : 12,354,759 reads read : 24,709,518 reads written : 12,354,759 reads 0-length : 12,354,759 spots read : 12,284,127 reads read : 24,568,254 reads written : 12,284,127 reads 0-length : 12,284,127 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: 00:11:04 37013574 reads; of these: 37013574 (100.00%) were unpaired; of these: 1368017 (3.70%) aligned 0 times 29899637 (80.78%) aligned exactly 1 time 5745920 (15.52%) aligned >1 times 96.30% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 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] 9171580 / 35645557 = 0.2573 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, 12 Aug 2019 22:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.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, 12 Aug 2019 22:12:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:12:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.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, 12 Aug 2019 22:12:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:12:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:12:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.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, 12 Aug 2019 22:12:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:12:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:12:11: 1000000 INFO @ Mon, 12 Aug 2019 22:12:12: 1000000 INFO @ Mon, 12 Aug 2019 22:12:13: 1000000 INFO @ Mon, 12 Aug 2019 22:12:18: 2000000 INFO @ Mon, 12 Aug 2019 22:12:18: 2000000 INFO @ Mon, 12 Aug 2019 22:12:20: 2000000 INFO @ Mon, 12 Aug 2019 22:12:25: 3000000 INFO @ Mon, 12 Aug 2019 22:12:25: 3000000 INFO @ Mon, 12 Aug 2019 22:12:26: 3000000 INFO @ Mon, 12 Aug 2019 22:12:32: 4000000 INFO @ Mon, 12 Aug 2019 22:12:32: 4000000 INFO @ Mon, 12 Aug 2019 22:12:33: 4000000 INFO @ Mon, 12 Aug 2019 22:12:38: 5000000 INFO @ Mon, 12 Aug 2019 22:12:38: 5000000 INFO @ Mon, 12 Aug 2019 22:12:40: 5000000 INFO @ Mon, 12 Aug 2019 22:12:45: 6000000 INFO @ Mon, 12 Aug 2019 22:12:45: 6000000 INFO @ Mon, 12 Aug 2019 22:12:47: 6000000 INFO @ Mon, 12 Aug 2019 22:12:52: 7000000 INFO @ Mon, 12 Aug 2019 22:12:52: 7000000 INFO @ Mon, 12 Aug 2019 22:12:53: 7000000 INFO @ Mon, 12 Aug 2019 22:12:59: 8000000 INFO @ Mon, 12 Aug 2019 22:12:59: 8000000 INFO @ Mon, 12 Aug 2019 22:13:00: 8000000 INFO @ Mon, 12 Aug 2019 22:13:07: 9000000 INFO @ Mon, 12 Aug 2019 22:13:07: 9000000 INFO @ Mon, 12 Aug 2019 22:13:08: 9000000 INFO @ Mon, 12 Aug 2019 22:13:14: 10000000 INFO @ Mon, 12 Aug 2019 22:13:15: 10000000 INFO @ Mon, 12 Aug 2019 22:13:15: 10000000 INFO @ Mon, 12 Aug 2019 22:13:22: 11000000 INFO @ Mon, 12 Aug 2019 22:13:22: 11000000 INFO @ Mon, 12 Aug 2019 22:13:23: 11000000 INFO @ Mon, 12 Aug 2019 22:13:30: 12000000 INFO @ Mon, 12 Aug 2019 22:13:30: 12000000 INFO @ Mon, 12 Aug 2019 22:13:31: 12000000 INFO @ Mon, 12 Aug 2019 22:13:37: 13000000 INFO @ Mon, 12 Aug 2019 22:13:38: 13000000 INFO @ Mon, 12 Aug 2019 22:13:38: 13000000 INFO @ Mon, 12 Aug 2019 22:13:45: 14000000 INFO @ Mon, 12 Aug 2019 22:13:46: 14000000 INFO @ Mon, 12 Aug 2019 22:13:46: 14000000 INFO @ Mon, 12 Aug 2019 22:13:53: 15000000 INFO @ Mon, 12 Aug 2019 22:13:53: 15000000 INFO @ Mon, 12 Aug 2019 22:13:54: 15000000 INFO @ Mon, 12 Aug 2019 22:14:01: 16000000 INFO @ Mon, 12 Aug 2019 22:14:01: 16000000 INFO @ Mon, 12 Aug 2019 22:14:02: 16000000 INFO @ Mon, 12 Aug 2019 22:14:09: 17000000 INFO @ Mon, 12 Aug 2019 22:14:09: 17000000 INFO @ Mon, 12 Aug 2019 22:14:09: 17000000 INFO @ Mon, 12 Aug 2019 22:14:16: 18000000 INFO @ Mon, 12 Aug 2019 22:14:17: 18000000 INFO @ Mon, 12 Aug 2019 22:14:17: 18000000 INFO @ Mon, 12 Aug 2019 22:14:24: 19000000 INFO @ Mon, 12 Aug 2019 22:14:24: 19000000 INFO @ Mon, 12 Aug 2019 22:14:25: 19000000 INFO @ Mon, 12 Aug 2019 22:14:31: 20000000 INFO @ Mon, 12 Aug 2019 22:14:32: 20000000 INFO @ Mon, 12 Aug 2019 22:14:33: 20000000 INFO @ Mon, 12 Aug 2019 22:14:38: 21000000 INFO @ Mon, 12 Aug 2019 22:14:40: 21000000 INFO @ Mon, 12 Aug 2019 22:14:41: 21000000 INFO @ Mon, 12 Aug 2019 22:14:46: 22000000 INFO @ Mon, 12 Aug 2019 22:14:48: 22000000 INFO @ Mon, 12 Aug 2019 22:14:48: 22000000 INFO @ Mon, 12 Aug 2019 22:14:53: 23000000 INFO @ Mon, 12 Aug 2019 22:14:56: 23000000 INFO @ Mon, 12 Aug 2019 22:14:56: 23000000 INFO @ Mon, 12 Aug 2019 22:15:00: 24000000 INFO @ Mon, 12 Aug 2019 22:15:03: 24000000 INFO @ Mon, 12 Aug 2019 22:15:04: 24000000 INFO @ Mon, 12 Aug 2019 22:15:08: 25000000 INFO @ Mon, 12 Aug 2019 22:15:11: 25000000 INFO @ Mon, 12 Aug 2019 22:15:11: 25000000 INFO @ Mon, 12 Aug 2019 22:15:15: 26000000 INFO @ Mon, 12 Aug 2019 22:15:19: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:15:19: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:15:19: #1 total tags in treatment: 26473977 INFO @ Mon, 12 Aug 2019 22:15:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:15:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:15:19: 26000000 INFO @ Mon, 12 Aug 2019 22:15:19: 26000000 INFO @ Mon, 12 Aug 2019 22:15:19: #1 tags after filtering in treatment: 26473977 INFO @ Mon, 12 Aug 2019 22:15:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:15:19: #1 finished! INFO @ Mon, 12 Aug 2019 22:15:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:15:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:15:22: #2 number of paired peaks: 5648 INFO @ Mon, 12 Aug 2019 22:15:22: start model_add_line... INFO @ Mon, 12 Aug 2019 22:15:23: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:15:23: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:15:23: #1 total tags in treatment: 26473977 INFO @ Mon, 12 Aug 2019 22:15:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:15:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:15:23: start X-correlation... INFO @ Mon, 12 Aug 2019 22:15:23: end of X-cor INFO @ Mon, 12 Aug 2019 22:15:23: #2 finished! INFO @ Mon, 12 Aug 2019 22:15:23: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 22:15:23: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 22:15:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.10_model.r INFO @ Mon, 12 Aug 2019 22:15:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:15:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:15:23: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:15:23: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:15:23: #1 total tags in treatment: 26473977 INFO @ Mon, 12 Aug 2019 22:15:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:15:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:15:23: #1 tags after filtering in treatment: 26473977 INFO @ Mon, 12 Aug 2019 22:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:15:23: #1 finished! INFO @ Mon, 12 Aug 2019 22:15:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:15:23: #1 tags after filtering in treatment: 26473977 INFO @ Mon, 12 Aug 2019 22:15:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:15:23: #1 finished! INFO @ Mon, 12 Aug 2019 22:15:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:15:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:15:26: #2 number of paired peaks: 5648 INFO @ Mon, 12 Aug 2019 22:15:26: start model_add_line... INFO @ Mon, 12 Aug 2019 22:15:26: #2 number of paired peaks: 5648 INFO @ Mon, 12 Aug 2019 22:15:26: start model_add_line... INFO @ Mon, 12 Aug 2019 22:15:27: start X-correlation... INFO @ Mon, 12 Aug 2019 22:15:27: end of X-cor INFO @ Mon, 12 Aug 2019 22:15:27: #2 finished! INFO @ Mon, 12 Aug 2019 22:15:27: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 22:15:27: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 22:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.20_model.r INFO @ Mon, 12 Aug 2019 22:15:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:15:27: start X-correlation... INFO @ Mon, 12 Aug 2019 22:15:27: end of X-cor INFO @ Mon, 12 Aug 2019 22:15:27: #2 finished! INFO @ Mon, 12 Aug 2019 22:15:27: #2 predicted fragment length is 162 bps INFO @ Mon, 12 Aug 2019 22:15:27: #2 alternative fragment length(s) may be 162 bps INFO @ Mon, 12 Aug 2019 22:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.05_model.r INFO @ Mon, 12 Aug 2019 22:15:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:16:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:16:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:16:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.10_summits.bed INFO @ Mon, 12 Aug 2019 22:17:12: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9390 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.20_summits.bed INFO @ Mon, 12 Aug 2019 22:17:16: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7442 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981680/SRX3981680.05_summits.bed INFO @ Mon, 12 Aug 2019 22:17:17: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10696 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。