Job ID = 2590795 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,183,688 reads read : 44,367,376 reads written : 22,183,688 reads 0-length : 22,183,688 rm: cannot remove ‘[DSE]RR*’: 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: 00:08:16 22183688 reads; of these: 22183688 (100.00%) were unpaired; of these: 871805 (3.93%) aligned 0 times 16485016 (74.31%) aligned exactly 1 time 4826867 (21.76%) aligned >1 times 96.07% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 7771778 / 21311883 = 0.3647 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 23:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.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 23:29:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.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 23:29:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.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 23:29:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:42: 1000000 INFO @ Mon, 12 Aug 2019 23:29:43: 1000000 INFO @ Mon, 12 Aug 2019 23:29:45: 1000000 INFO @ Mon, 12 Aug 2019 23:29:49: 2000000 INFO @ Mon, 12 Aug 2019 23:29:50: 2000000 INFO @ Mon, 12 Aug 2019 23:29:54: 2000000 INFO @ Mon, 12 Aug 2019 23:29:56: 3000000 INFO @ Mon, 12 Aug 2019 23:29:57: 3000000 INFO @ Mon, 12 Aug 2019 23:30:03: 3000000 INFO @ Mon, 12 Aug 2019 23:30:03: 4000000 INFO @ Mon, 12 Aug 2019 23:30:05: 4000000 INFO @ Mon, 12 Aug 2019 23:30:11: 5000000 INFO @ Mon, 12 Aug 2019 23:30:11: 4000000 INFO @ Mon, 12 Aug 2019 23:30:12: 5000000 INFO @ Mon, 12 Aug 2019 23:30:18: 6000000 INFO @ Mon, 12 Aug 2019 23:30:19: 6000000 INFO @ Mon, 12 Aug 2019 23:30:20: 5000000 INFO @ Mon, 12 Aug 2019 23:30:25: 7000000 INFO @ Mon, 12 Aug 2019 23:30:27: 7000000 INFO @ Mon, 12 Aug 2019 23:30:29: 6000000 INFO @ Mon, 12 Aug 2019 23:30:32: 8000000 INFO @ Mon, 12 Aug 2019 23:30:34: 8000000 INFO @ Mon, 12 Aug 2019 23:30:37: 7000000 INFO @ Mon, 12 Aug 2019 23:30:39: 9000000 INFO @ Mon, 12 Aug 2019 23:30:41: 9000000 INFO @ Mon, 12 Aug 2019 23:30:46: 8000000 INFO @ Mon, 12 Aug 2019 23:30:47: 10000000 INFO @ Mon, 12 Aug 2019 23:30:48: 10000000 INFO @ Mon, 12 Aug 2019 23:30:54: 11000000 INFO @ Mon, 12 Aug 2019 23:30:55: 9000000 INFO @ Mon, 12 Aug 2019 23:30:56: 11000000 INFO @ Mon, 12 Aug 2019 23:31:01: 12000000 INFO @ Mon, 12 Aug 2019 23:31:03: 12000000 INFO @ Mon, 12 Aug 2019 23:31:03: 10000000 INFO @ Mon, 12 Aug 2019 23:31:08: 13000000 INFO @ Mon, 12 Aug 2019 23:31:10: 13000000 INFO @ Mon, 12 Aug 2019 23:31:12: 11000000 INFO @ Mon, 12 Aug 2019 23:31:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:31:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:31:12: #1 total tags in treatment: 13540105 INFO @ Mon, 12 Aug 2019 23:31:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:31:12: #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 23:31:13: #1 tags after filtering in treatment: 13540105 INFO @ Mon, 12 Aug 2019 23:31:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:31:13: #1 finished! INFO @ Mon, 12 Aug 2019 23:31:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:31:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:31:14: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:31:14: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:31:14: #1 total tags in treatment: 13540105 INFO @ Mon, 12 Aug 2019 23:31:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:31:14: #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 23:31:14: #2 number of paired peaks: 3051 INFO @ Mon, 12 Aug 2019 23:31:14: start model_add_line... INFO @ Mon, 12 Aug 2019 23:31:14: #1 tags after filtering in treatment: 13540105 INFO @ Mon, 12 Aug 2019 23:31:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:31:14: #1 finished! INFO @ Mon, 12 Aug 2019 23:31:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:31:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:31:14: start X-correlation... INFO @ Mon, 12 Aug 2019 23:31:14: end of X-cor INFO @ Mon, 12 Aug 2019 23:31:14: #2 finished! INFO @ Mon, 12 Aug 2019 23:31:14: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 23:31:14: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 12 Aug 2019 23:31:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.05_model.r INFO @ Mon, 12 Aug 2019 23:31:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:31:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:16: #2 number of paired peaks: 3051 INFO @ Mon, 12 Aug 2019 23:31:16: start model_add_line... INFO @ Mon, 12 Aug 2019 23:31:16: start X-correlation... INFO @ Mon, 12 Aug 2019 23:31:16: end of X-cor INFO @ Mon, 12 Aug 2019 23:31:16: #2 finished! INFO @ Mon, 12 Aug 2019 23:31:16: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 23:31:16: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 12 Aug 2019 23:31:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.10_model.r INFO @ Mon, 12 Aug 2019 23:31:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:21: 12000000 INFO @ Mon, 12 Aug 2019 23:31:29: 13000000 INFO @ Mon, 12 Aug 2019 23:31:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:31:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:31:34: #1 total tags in treatment: 13540105 INFO @ Mon, 12 Aug 2019 23:31:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:31:34: #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 23:31:34: #1 tags after filtering in treatment: 13540105 INFO @ Mon, 12 Aug 2019 23:31:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:31:34: #1 finished! INFO @ Mon, 12 Aug 2019 23:31:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:31:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:31:35: #2 number of paired peaks: 3051 INFO @ Mon, 12 Aug 2019 23:31:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:31:36: start X-correlation... INFO @ Mon, 12 Aug 2019 23:31:36: end of X-cor INFO @ Mon, 12 Aug 2019 23:31:36: #2 finished! INFO @ Mon, 12 Aug 2019 23:31:36: #2 predicted fragment length is 212 bps INFO @ Mon, 12 Aug 2019 23:31:36: #2 alternative fragment length(s) may be 212 bps INFO @ Mon, 12 Aug 2019 23:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.20_model.r INFO @ Mon, 12 Aug 2019 23:31:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:32:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:32:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:32:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.05_summits.bed INFO @ Mon, 12 Aug 2019 23:32:19: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (13198 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:32:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:32:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:32:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:32:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.10_summits.bed INFO @ Mon, 12 Aug 2019 23:32:23: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9735 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:32:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:32:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011037/SRX5011037.20_summits.bed INFO @ Mon, 12 Aug 2019 23:32:40: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5893 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。