Job ID = 1293615 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,099,620 reads read : 28,099,620 reads written : 28,099,620 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: 00:10:12 28099620 reads; of these: 28099620 (100.00%) were unpaired; of these: 902960 (3.21%) aligned 0 times 21663029 (77.09%) aligned exactly 1 time 5533631 (19.69%) aligned >1 times 96.79% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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 12 files... [bam_rmdupse_core] 7045190 / 27196660 = 0.2590 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 01:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.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 01:23:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:23:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.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 01:23:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:23:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.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 01:23:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:23:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:23:36: 1000000 INFO @ Mon, 03 Jun 2019 01:23:38: 1000000 INFO @ Mon, 03 Jun 2019 01:23:38: 1000000 INFO @ Mon, 03 Jun 2019 01:23:43: 2000000 INFO @ Mon, 03 Jun 2019 01:23:46: 2000000 INFO @ Mon, 03 Jun 2019 01:23:47: 2000000 INFO @ Mon, 03 Jun 2019 01:23:50: 3000000 INFO @ Mon, 03 Jun 2019 01:23:54: 3000000 INFO @ Mon, 03 Jun 2019 01:23:55: 3000000 INFO @ Mon, 03 Jun 2019 01:23:57: 4000000 INFO @ Mon, 03 Jun 2019 01:24:02: 4000000 INFO @ Mon, 03 Jun 2019 01:24:03: 4000000 INFO @ Mon, 03 Jun 2019 01:24:04: 5000000 INFO @ Mon, 03 Jun 2019 01:24:10: 5000000 INFO @ Mon, 03 Jun 2019 01:24:11: 6000000 INFO @ Mon, 03 Jun 2019 01:24:12: 5000000 INFO @ Mon, 03 Jun 2019 01:24:18: 7000000 INFO @ Mon, 03 Jun 2019 01:24:18: 6000000 INFO @ Mon, 03 Jun 2019 01:24:20: 6000000 INFO @ Mon, 03 Jun 2019 01:24:24: 8000000 INFO @ Mon, 03 Jun 2019 01:24:25: 7000000 INFO @ Mon, 03 Jun 2019 01:24:28: 7000000 INFO @ Mon, 03 Jun 2019 01:24:31: 9000000 INFO @ Mon, 03 Jun 2019 01:24:33: 8000000 INFO @ Mon, 03 Jun 2019 01:24:36: 8000000 INFO @ Mon, 03 Jun 2019 01:24:38: 10000000 INFO @ Mon, 03 Jun 2019 01:24:41: 9000000 INFO @ Mon, 03 Jun 2019 01:24:44: 9000000 INFO @ Mon, 03 Jun 2019 01:24:45: 11000000 INFO @ Mon, 03 Jun 2019 01:24:49: 10000000 INFO @ Mon, 03 Jun 2019 01:24:52: 12000000 INFO @ Mon, 03 Jun 2019 01:24:53: 10000000 INFO @ Mon, 03 Jun 2019 01:24:57: 11000000 INFO @ Mon, 03 Jun 2019 01:24:59: 13000000 INFO @ Mon, 03 Jun 2019 01:25:01: 11000000 INFO @ Mon, 03 Jun 2019 01:25:05: 12000000 INFO @ Mon, 03 Jun 2019 01:25:05: 14000000 INFO @ Mon, 03 Jun 2019 01:25:09: 12000000 INFO @ Mon, 03 Jun 2019 01:25:12: 15000000 INFO @ Mon, 03 Jun 2019 01:25:12: 13000000 INFO @ Mon, 03 Jun 2019 01:25:17: 13000000 INFO @ Mon, 03 Jun 2019 01:25:19: 16000000 INFO @ Mon, 03 Jun 2019 01:25:20: 14000000 INFO @ Mon, 03 Jun 2019 01:25:25: 14000000 INFO @ Mon, 03 Jun 2019 01:25:27: 17000000 INFO @ Mon, 03 Jun 2019 01:25:28: 15000000 INFO @ Mon, 03 Jun 2019 01:25:33: 15000000 INFO @ Mon, 03 Jun 2019 01:25:34: 18000000 INFO @ Mon, 03 Jun 2019 01:25:37: 16000000 INFO @ Mon, 03 Jun 2019 01:25:40: 19000000 INFO @ Mon, 03 Jun 2019 01:25:42: 16000000 INFO @ Mon, 03 Jun 2019 01:25:45: 17000000 INFO @ Mon, 03 Jun 2019 01:25:47: 20000000 INFO @ Mon, 03 Jun 2019 01:25:49: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:25:49: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:25:49: #1 total tags in treatment: 20151470 INFO @ Mon, 03 Jun 2019 01:25:49: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:25:49: #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 01:25:49: #1 tags after filtering in treatment: 20151470 INFO @ Mon, 03 Jun 2019 01:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:25:49: #1 finished! INFO @ Mon, 03 Jun 2019 01:25:49: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:25:51: #2 number of paired peaks: 3496 INFO @ Mon, 03 Jun 2019 01:25:51: start model_add_line... INFO @ Mon, 03 Jun 2019 01:25:51: 17000000 INFO @ Mon, 03 Jun 2019 01:25:51: start X-correlation... INFO @ Mon, 03 Jun 2019 01:25:51: end of X-cor INFO @ Mon, 03 Jun 2019 01:25:51: #2 finished! INFO @ Mon, 03 Jun 2019 01:25:51: #2 predicted fragment length is 151 bps INFO @ Mon, 03 Jun 2019 01:25:51: #2 alternative fragment length(s) may be 4,151 bps INFO @ Mon, 03 Jun 2019 01:25:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.10_model.r INFO @ Mon, 03 Jun 2019 01:25:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:25:53: 18000000 INFO @ Mon, 03 Jun 2019 01:25:59: 18000000 INFO @ Mon, 03 Jun 2019 01:26:01: 19000000 INFO @ Mon, 03 Jun 2019 01:26:08: 19000000 INFO @ Mon, 03 Jun 2019 01:26:09: 20000000 INFO @ Mon, 03 Jun 2019 01:26:10: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:26:10: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:26:10: #1 total tags in treatment: 20151470 INFO @ Mon, 03 Jun 2019 01:26:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:26:10: #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 01:26:10: #1 tags after filtering in treatment: 20151470 INFO @ Mon, 03 Jun 2019 01:26:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:26:10: #1 finished! INFO @ Mon, 03 Jun 2019 01:26:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:26:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:26:13: #2 number of paired peaks: 3496 INFO @ Mon, 03 Jun 2019 01:26:13: start model_add_line... INFO @ Mon, 03 Jun 2019 01:26:13: start X-correlation... INFO @ Mon, 03 Jun 2019 01:26:13: end of X-cor INFO @ Mon, 03 Jun 2019 01:26:13: #2 finished! INFO @ Mon, 03 Jun 2019 01:26:13: #2 predicted fragment length is 151 bps INFO @ Mon, 03 Jun 2019 01:26:13: #2 alternative fragment length(s) may be 4,151 bps INFO @ Mon, 03 Jun 2019 01:26:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.05_model.r INFO @ Mon, 03 Jun 2019 01:26:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:26:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:26:15: 20000000 INFO @ Mon, 03 Jun 2019 01:26:17: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:26:17: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:26:17: #1 total tags in treatment: 20151470 INFO @ Mon, 03 Jun 2019 01:26:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:26:17: #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 01:26:17: #1 tags after filtering in treatment: 20151470 INFO @ Mon, 03 Jun 2019 01:26:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:26:17: #1 finished! INFO @ Mon, 03 Jun 2019 01:26:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:26:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:26:19: #2 number of paired peaks: 3496 INFO @ Mon, 03 Jun 2019 01:26:19: start model_add_line... INFO @ Mon, 03 Jun 2019 01:26:20: start X-correlation... INFO @ Mon, 03 Jun 2019 01:26:20: end of X-cor INFO @ Mon, 03 Jun 2019 01:26:20: #2 finished! INFO @ Mon, 03 Jun 2019 01:26:20: #2 predicted fragment length is 151 bps INFO @ Mon, 03 Jun 2019 01:26:20: #2 alternative fragment length(s) may be 4,151 bps INFO @ Mon, 03 Jun 2019 01:26:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.20_model.r INFO @ Mon, 03 Jun 2019 01:26:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:26:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:26:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:27:17: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.10_summits.bed INFO @ Mon, 03 Jun 2019 01:27:19: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2717 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:27:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:27:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:27:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:27:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.05_summits.bed INFO @ Mon, 03 Jun 2019 01:27:41: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6694 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032392/SRX1032392.20_summits.bed INFO @ Mon, 03 Jun 2019 01:27:49: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (873 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。