Job ID = 1294164 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 39,268,447 reads read : 39,268,447 reads written : 39,268,447 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: 00:11:28 39268447 reads; of these: 39268447 (100.00%) were unpaired; of these: 1396552 (3.56%) aligned 0 times 31975854 (81.43%) aligned exactly 1 time 5896041 (15.01%) aligned >1 times 96.44% overall alignment rate Time searching: 00:11:28 Overall time: 00:11:28 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] 9874024 / 37871895 = 0.2607 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 05:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.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 05:35:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.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 05:35:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:35:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:35:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.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 05:35:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:35:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:35:48: 1000000 INFO @ Mon, 03 Jun 2019 05:35:50: 1000000 INFO @ Mon, 03 Jun 2019 05:35:50: 1000000 INFO @ Mon, 03 Jun 2019 05:35:57: 2000000 INFO @ Mon, 03 Jun 2019 05:36:02: 2000000 INFO @ Mon, 03 Jun 2019 05:36:02: 2000000 INFO @ Mon, 03 Jun 2019 05:36:05: 3000000 INFO @ Mon, 03 Jun 2019 05:36:13: 3000000 INFO @ Mon, 03 Jun 2019 05:36:13: 4000000 INFO @ Mon, 03 Jun 2019 05:36:13: 3000000 INFO @ Mon, 03 Jun 2019 05:36:21: 5000000 INFO @ Mon, 03 Jun 2019 05:36:22: 4000000 INFO @ Mon, 03 Jun 2019 05:36:22: 4000000 INFO @ Mon, 03 Jun 2019 05:36:28: 6000000 INFO @ Mon, 03 Jun 2019 05:36:31: 5000000 INFO @ Mon, 03 Jun 2019 05:36:31: 5000000 INFO @ Mon, 03 Jun 2019 05:36:36: 7000000 INFO @ Mon, 03 Jun 2019 05:36:41: 6000000 INFO @ Mon, 03 Jun 2019 05:36:41: 6000000 INFO @ Mon, 03 Jun 2019 05:36:44: 8000000 INFO @ Mon, 03 Jun 2019 05:36:50: 7000000 INFO @ Mon, 03 Jun 2019 05:36:51: 7000000 INFO @ Mon, 03 Jun 2019 05:36:51: 9000000 INFO @ Mon, 03 Jun 2019 05:36:59: 10000000 INFO @ Mon, 03 Jun 2019 05:36:59: 8000000 INFO @ Mon, 03 Jun 2019 05:37:00: 8000000 INFO @ Mon, 03 Jun 2019 05:37:06: 11000000 INFO @ Mon, 03 Jun 2019 05:37:09: 9000000 INFO @ Mon, 03 Jun 2019 05:37:09: 9000000 INFO @ Mon, 03 Jun 2019 05:37:14: 12000000 INFO @ Mon, 03 Jun 2019 05:37:18: 10000000 INFO @ Mon, 03 Jun 2019 05:37:19: 10000000 INFO @ Mon, 03 Jun 2019 05:37:21: 13000000 INFO @ Mon, 03 Jun 2019 05:37:27: 11000000 INFO @ Mon, 03 Jun 2019 05:37:28: 11000000 INFO @ Mon, 03 Jun 2019 05:37:29: 14000000 INFO @ Mon, 03 Jun 2019 05:37:36: 12000000 INFO @ Mon, 03 Jun 2019 05:37:37: 15000000 INFO @ Mon, 03 Jun 2019 05:37:37: 12000000 INFO @ Mon, 03 Jun 2019 05:37:44: 16000000 INFO @ Mon, 03 Jun 2019 05:37:45: 13000000 INFO @ Mon, 03 Jun 2019 05:37:47: 13000000 INFO @ Mon, 03 Jun 2019 05:37:52: 17000000 INFO @ Mon, 03 Jun 2019 05:37:55: 14000000 INFO @ Mon, 03 Jun 2019 05:37:57: 14000000 INFO @ Mon, 03 Jun 2019 05:37:59: 18000000 INFO @ Mon, 03 Jun 2019 05:38:05: 15000000 INFO @ Mon, 03 Jun 2019 05:38:07: 19000000 INFO @ Mon, 03 Jun 2019 05:38:07: 15000000 INFO @ Mon, 03 Jun 2019 05:38:14: 20000000 INFO @ Mon, 03 Jun 2019 05:38:15: 16000000 INFO @ Mon, 03 Jun 2019 05:38:18: 16000000 INFO @ Mon, 03 Jun 2019 05:38:22: 21000000 INFO @ Mon, 03 Jun 2019 05:38:26: 17000000 INFO @ Mon, 03 Jun 2019 05:38:28: 17000000 INFO @ Mon, 03 Jun 2019 05:38:29: 22000000 INFO @ Mon, 03 Jun 2019 05:38:36: 18000000 INFO @ Mon, 03 Jun 2019 05:38:36: 23000000 INFO @ Mon, 03 Jun 2019 05:38:38: 18000000 INFO @ Mon, 03 Jun 2019 05:38:44: 24000000 INFO @ Mon, 03 Jun 2019 05:38:47: 19000000 INFO @ Mon, 03 Jun 2019 05:38:49: 19000000 INFO @ Mon, 03 Jun 2019 05:38:51: 25000000 INFO @ Mon, 03 Jun 2019 05:38:57: 20000000 INFO @ Mon, 03 Jun 2019 05:38:59: 20000000 INFO @ Mon, 03 Jun 2019 05:38:59: 26000000 INFO @ Mon, 03 Jun 2019 05:39:06: 21000000 INFO @ Mon, 03 Jun 2019 05:39:07: 27000000 INFO @ Mon, 03 Jun 2019 05:39:08: 21000000 INFO @ Mon, 03 Jun 2019 05:39:15: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:39:15: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:39:15: #1 total tags in treatment: 27997871 INFO @ Mon, 03 Jun 2019 05:39:15: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:39:15: #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 05:39:15: #1 tags after filtering in treatment: 27997871 INFO @ Mon, 03 Jun 2019 05:39:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:39:15: #1 finished! INFO @ Mon, 03 Jun 2019 05:39:15: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:39:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:39:16: 22000000 INFO @ Mon, 03 Jun 2019 05:39:18: 22000000 INFO @ Mon, 03 Jun 2019 05:39:18: #2 number of paired peaks: 2703 INFO @ Mon, 03 Jun 2019 05:39:18: start model_add_line... INFO @ Mon, 03 Jun 2019 05:39:19: start X-correlation... INFO @ Mon, 03 Jun 2019 05:39:19: end of X-cor INFO @ Mon, 03 Jun 2019 05:39:19: #2 finished! INFO @ Mon, 03 Jun 2019 05:39:19: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 05:39:19: #2 alternative fragment length(s) may be 3,112 bps INFO @ Mon, 03 Jun 2019 05:39:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.10_model.r INFO @ Mon, 03 Jun 2019 05:39:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:39:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:39:26: 23000000 INFO @ Mon, 03 Jun 2019 05:39:27: 23000000 INFO @ Mon, 03 Jun 2019 05:39:35: 24000000 INFO @ Mon, 03 Jun 2019 05:39:36: 24000000 INFO @ Mon, 03 Jun 2019 05:39:44: 25000000 INFO @ Mon, 03 Jun 2019 05:39:45: 25000000 INFO @ Mon, 03 Jun 2019 05:39:53: 26000000 INFO @ Mon, 03 Jun 2019 05:39:55: 26000000 INFO @ Mon, 03 Jun 2019 05:40:02: 27000000 INFO @ Mon, 03 Jun 2019 05:40:05: 27000000 INFO @ Mon, 03 Jun 2019 05:40:12: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:40:12: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:40:12: #1 total tags in treatment: 27997871 INFO @ Mon, 03 Jun 2019 05:40:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:12: #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 05:40:13: #1 tags after filtering in treatment: 27997871 INFO @ Mon, 03 Jun 2019 05:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:13: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:16: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 05:40:16: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 05:40:16: #1 total tags in treatment: 27997871 INFO @ Mon, 03 Jun 2019 05:40:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:40:16: #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 05:40:16: #2 number of paired peaks: 2703 INFO @ Mon, 03 Jun 2019 05:40:16: start model_add_line... INFO @ Mon, 03 Jun 2019 05:40:16: start X-correlation... INFO @ Mon, 03 Jun 2019 05:40:16: end of X-cor INFO @ Mon, 03 Jun 2019 05:40:16: #2 finished! INFO @ Mon, 03 Jun 2019 05:40:16: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 05:40:16: #2 alternative fragment length(s) may be 3,112 bps INFO @ Mon, 03 Jun 2019 05:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.05_model.r INFO @ Mon, 03 Jun 2019 05:40:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:40:16: #1 tags after filtering in treatment: 27997871 INFO @ Mon, 03 Jun 2019 05:40:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:40:16: #1 finished! INFO @ Mon, 03 Jun 2019 05:40:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:40:19: #2 number of paired peaks: 2703 INFO @ Mon, 03 Jun 2019 05:40:19: start model_add_line... INFO @ Mon, 03 Jun 2019 05:40:19: start X-correlation... INFO @ Mon, 03 Jun 2019 05:40:19: end of X-cor INFO @ Mon, 03 Jun 2019 05:40:19: #2 finished! INFO @ Mon, 03 Jun 2019 05:40:19: #2 predicted fragment length is 112 bps INFO @ Mon, 03 Jun 2019 05:40:19: #2 alternative fragment length(s) may be 3,112 bps INFO @ Mon, 03 Jun 2019 05:40:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.20_model.r INFO @ Mon, 03 Jun 2019 05:40:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:40:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:40:30: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.10_summits.bed INFO @ Mon, 03 Jun 2019 05:41:02: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11730 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:41:28: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:41:31: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:42:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:42:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.05_summits.bed INFO @ Mon, 03 Jun 2019 05:42:00: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (18647 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:42:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:42:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193340/SRX193340.20_summits.bed INFO @ Mon, 03 Jun 2019 05:42:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4590 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。