Job ID = 2590757 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 39,832,402 reads read : 79,664,804 reads written : 39,832,402 reads 0-length : 39,832,402 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: 00:13:39 39832402 reads; of these: 39832402 (100.00%) were unpaired; of these: 1934008 (4.86%) aligned 0 times 30103262 (75.57%) aligned exactly 1 time 7795132 (19.57%) aligned >1 times 95.14% overall alignment rate Time searching: 00:13:39 Overall time: 00:13:39 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] 16030646 / 37898394 = 0.4230 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 23:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.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 23:40:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:40:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.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 23:40:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:40:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.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 23:40:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:40:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:40:26: 1000000 INFO @ Mon, 12 Aug 2019 23:40:27: 1000000 INFO @ Mon, 12 Aug 2019 23:40:27: 1000000 INFO @ Mon, 12 Aug 2019 23:40:36: 2000000 INFO @ Mon, 12 Aug 2019 23:40:37: 2000000 INFO @ Mon, 12 Aug 2019 23:40:37: 2000000 INFO @ Mon, 12 Aug 2019 23:40:45: 3000000 INFO @ Mon, 12 Aug 2019 23:40:46: 3000000 INFO @ Mon, 12 Aug 2019 23:40:47: 3000000 INFO @ Mon, 12 Aug 2019 23:40:55: 4000000 INFO @ Mon, 12 Aug 2019 23:40:55: 4000000 INFO @ Mon, 12 Aug 2019 23:40:56: 4000000 INFO @ Mon, 12 Aug 2019 23:41:04: 5000000 INFO @ Mon, 12 Aug 2019 23:41:05: 5000000 INFO @ Mon, 12 Aug 2019 23:41:06: 5000000 INFO @ Mon, 12 Aug 2019 23:41:13: 6000000 INFO @ Mon, 12 Aug 2019 23:41:14: 6000000 INFO @ Mon, 12 Aug 2019 23:41:16: 6000000 INFO @ Mon, 12 Aug 2019 23:41:22: 7000000 INFO @ Mon, 12 Aug 2019 23:41:24: 7000000 INFO @ Mon, 12 Aug 2019 23:41:25: 7000000 INFO @ Mon, 12 Aug 2019 23:41:31: 8000000 INFO @ Mon, 12 Aug 2019 23:41:34: 8000000 INFO @ Mon, 12 Aug 2019 23:41:35: 8000000 INFO @ Mon, 12 Aug 2019 23:41:40: 9000000 INFO @ Mon, 12 Aug 2019 23:41:43: 9000000 INFO @ Mon, 12 Aug 2019 23:41:44: 9000000 INFO @ Mon, 12 Aug 2019 23:41:49: 10000000 INFO @ Mon, 12 Aug 2019 23:41:53: 10000000 INFO @ Mon, 12 Aug 2019 23:41:54: 10000000 INFO @ Mon, 12 Aug 2019 23:41:58: 11000000 INFO @ Mon, 12 Aug 2019 23:42:02: 11000000 INFO @ Mon, 12 Aug 2019 23:42:03: 11000000 INFO @ Mon, 12 Aug 2019 23:42:07: 12000000 INFO @ Mon, 12 Aug 2019 23:42:12: 12000000 INFO @ Mon, 12 Aug 2019 23:42:13: 12000000 INFO @ Mon, 12 Aug 2019 23:42:16: 13000000 INFO @ Mon, 12 Aug 2019 23:42:21: 13000000 INFO @ Mon, 12 Aug 2019 23:42:22: 13000000 INFO @ Mon, 12 Aug 2019 23:42:25: 14000000 INFO @ Mon, 12 Aug 2019 23:42:31: 14000000 INFO @ Mon, 12 Aug 2019 23:42:32: 14000000 INFO @ Mon, 12 Aug 2019 23:42:34: 15000000 INFO @ Mon, 12 Aug 2019 23:42:40: 15000000 INFO @ Mon, 12 Aug 2019 23:42:41: 15000000 INFO @ Mon, 12 Aug 2019 23:42:42: 16000000 INFO @ Mon, 12 Aug 2019 23:42:50: 16000000 INFO @ Mon, 12 Aug 2019 23:42:51: 16000000 INFO @ Mon, 12 Aug 2019 23:42:52: 17000000 INFO @ Mon, 12 Aug 2019 23:42:59: 17000000 INFO @ Mon, 12 Aug 2019 23:43:01: 17000000 INFO @ Mon, 12 Aug 2019 23:43:01: 18000000 INFO @ Mon, 12 Aug 2019 23:43:09: 18000000 INFO @ Mon, 12 Aug 2019 23:43:10: 18000000 INFO @ Mon, 12 Aug 2019 23:43:11: 19000000 INFO @ Mon, 12 Aug 2019 23:43:20: 19000000 INFO @ Mon, 12 Aug 2019 23:43:21: 20000000 INFO @ Mon, 12 Aug 2019 23:43:21: 19000000 INFO @ Mon, 12 Aug 2019 23:43:31: 21000000 INFO @ Mon, 12 Aug 2019 23:43:32: 20000000 INFO @ Mon, 12 Aug 2019 23:43:33: 20000000 INFO @ Mon, 12 Aug 2019 23:43:39: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:39: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:39: #1 total tags in treatment: 21867748 INFO @ Mon, 12 Aug 2019 23:43:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:39: #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 23:43:40: #1 tags after filtering in treatment: 21867748 INFO @ Mon, 12 Aug 2019 23:43:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:40: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:42: #2 number of paired peaks: 3651 INFO @ Mon, 12 Aug 2019 23:43:42: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:42: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:42: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:42: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:42: #2 predicted fragment length is 226 bps INFO @ Mon, 12 Aug 2019 23:43:42: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 12 Aug 2019 23:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.20_model.r INFO @ Mon, 12 Aug 2019 23:43:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:43:43: 21000000 INFO @ Mon, 12 Aug 2019 23:43:44: 21000000 INFO @ Mon, 12 Aug 2019 23:43:53: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:53: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:53: #1 total tags in treatment: 21867748 INFO @ Mon, 12 Aug 2019 23:43:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:53: #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 23:43:53: #1 tags after filtering in treatment: 21867748 INFO @ Mon, 12 Aug 2019 23:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:53: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:54: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:54: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:54: #1 total tags in treatment: 21867748 INFO @ Mon, 12 Aug 2019 23:43:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:54: #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 23:43:54: #1 tags after filtering in treatment: 21867748 INFO @ Mon, 12 Aug 2019 23:43:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:54: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:56: #2 number of paired peaks: 3651 INFO @ Mon, 12 Aug 2019 23:43:56: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:56: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:56: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:56: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:56: #2 predicted fragment length is 226 bps INFO @ Mon, 12 Aug 2019 23:43:56: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 12 Aug 2019 23:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.05_model.r INFO @ Mon, 12 Aug 2019 23:43:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:43:56: #2 number of paired peaks: 3651 INFO @ Mon, 12 Aug 2019 23:43:56: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:57: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:57: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:57: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:57: #2 predicted fragment length is 226 bps INFO @ Mon, 12 Aug 2019 23:43:57: #2 alternative fragment length(s) may be 226 bps INFO @ Mon, 12 Aug 2019 23:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.10_model.r INFO @ Mon, 12 Aug 2019 23:43:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:44:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.20_summits.bed INFO @ Mon, 12 Aug 2019 23:45:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9232 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.10_summits.bed INFO @ Mon, 12 Aug 2019 23:45:39: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (12740 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011033/SRX5011033.05_summits.bed INFO @ Mon, 12 Aug 2019 23:45:45: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (15634 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。