Job ID = 2590680 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,711,964 reads read : 91,423,928 reads written : 45,711,964 reads 0-length : 45,711,964 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: 00:17:39 45711964 reads; of these: 45711964 (100.00%) were unpaired; of these: 4658572 (10.19%) aligned 0 times 29811414 (65.22%) aligned exactly 1 time 11241978 (24.59%) aligned >1 times 89.81% overall alignment rate Time searching: 00:17:39 Overall time: 00:17:39 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 20 files... [bam_rmdupse_core] 22455370 / 41053392 = 0.5470 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 23:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.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 23:42:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.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 23:42:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:42:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.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 23:42:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:42:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:43:07: 1000000 INFO @ Mon, 12 Aug 2019 23:43:08: 1000000 INFO @ Mon, 12 Aug 2019 23:43:09: 1000000 INFO @ Mon, 12 Aug 2019 23:43:17: 2000000 INFO @ Mon, 12 Aug 2019 23:43:18: 2000000 INFO @ Mon, 12 Aug 2019 23:43:20: 2000000 INFO @ Mon, 12 Aug 2019 23:43:26: 3000000 INFO @ Mon, 12 Aug 2019 23:43:29: 3000000 INFO @ Mon, 12 Aug 2019 23:43:30: 3000000 INFO @ Mon, 12 Aug 2019 23:43:36: 4000000 INFO @ Mon, 12 Aug 2019 23:43:38: 4000000 INFO @ Mon, 12 Aug 2019 23:43:39: 4000000 INFO @ Mon, 12 Aug 2019 23:43:45: 5000000 INFO @ Mon, 12 Aug 2019 23:43:48: 5000000 INFO @ Mon, 12 Aug 2019 23:43:49: 5000000 INFO @ Mon, 12 Aug 2019 23:43:54: 6000000 INFO @ Mon, 12 Aug 2019 23:43:58: 6000000 INFO @ Mon, 12 Aug 2019 23:43:58: 6000000 INFO @ Mon, 12 Aug 2019 23:44:03: 7000000 INFO @ Mon, 12 Aug 2019 23:44:07: 7000000 INFO @ Mon, 12 Aug 2019 23:44:08: 7000000 INFO @ Mon, 12 Aug 2019 23:44:12: 8000000 INFO @ Mon, 12 Aug 2019 23:44:17: 8000000 INFO @ Mon, 12 Aug 2019 23:44:17: 8000000 INFO @ Mon, 12 Aug 2019 23:44:21: 9000000 INFO @ Mon, 12 Aug 2019 23:44:26: 9000000 INFO @ Mon, 12 Aug 2019 23:44:27: 9000000 INFO @ Mon, 12 Aug 2019 23:44:31: 10000000 INFO @ Mon, 12 Aug 2019 23:44:36: 10000000 INFO @ Mon, 12 Aug 2019 23:44:36: 10000000 INFO @ Mon, 12 Aug 2019 23:44:40: 11000000 INFO @ Mon, 12 Aug 2019 23:44:45: 11000000 INFO @ Mon, 12 Aug 2019 23:44:46: 11000000 INFO @ Mon, 12 Aug 2019 23:44:49: 12000000 INFO @ Mon, 12 Aug 2019 23:44:54: 12000000 INFO @ Mon, 12 Aug 2019 23:44:55: 12000000 INFO @ Mon, 12 Aug 2019 23:44:58: 13000000 INFO @ Mon, 12 Aug 2019 23:45:03: 13000000 INFO @ Mon, 12 Aug 2019 23:45:04: 13000000 INFO @ Mon, 12 Aug 2019 23:45:07: 14000000 INFO @ Mon, 12 Aug 2019 23:45:12: 14000000 INFO @ Mon, 12 Aug 2019 23:45:14: 14000000 INFO @ Mon, 12 Aug 2019 23:45:16: 15000000 INFO @ Mon, 12 Aug 2019 23:45:21: 15000000 INFO @ Mon, 12 Aug 2019 23:45:23: 15000000 INFO @ Mon, 12 Aug 2019 23:45:26: 16000000 INFO @ Mon, 12 Aug 2019 23:45:31: 16000000 INFO @ Mon, 12 Aug 2019 23:45:33: 16000000 INFO @ Mon, 12 Aug 2019 23:45:35: 17000000 INFO @ Mon, 12 Aug 2019 23:45:40: 17000000 INFO @ Mon, 12 Aug 2019 23:45:42: 17000000 INFO @ Mon, 12 Aug 2019 23:45:44: 18000000 INFO @ Mon, 12 Aug 2019 23:45:49: 18000000 INFO @ Mon, 12 Aug 2019 23:45:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:49: #1 total tags in treatment: 18598022 INFO @ Mon, 12 Aug 2019 23:45:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:49: #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 23:45:50: #1 tags after filtering in treatment: 18598022 INFO @ Mon, 12 Aug 2019 23:45:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:50: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:51: #2 number of paired peaks: 1027 INFO @ Mon, 12 Aug 2019 23:45:51: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:51: 18000000 INFO @ Mon, 12 Aug 2019 23:45:52: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:52: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:52: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:52: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 23:45:52: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 23:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.05_model.r INFO @ Mon, 12 Aug 2019 23:45:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:55: #1 total tags in treatment: 18598022 INFO @ Mon, 12 Aug 2019 23:45:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:55: #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 23:45:55: #1 tags after filtering in treatment: 18598022 INFO @ Mon, 12 Aug 2019 23:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:55: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:57: #2 number of paired peaks: 1027 INFO @ Mon, 12 Aug 2019 23:45:57: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:57: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:57: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:45:57: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:45:57: #1 total tags in treatment: 18598022 INFO @ Mon, 12 Aug 2019 23:45:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:45:57: #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 23:45:57: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:57: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:57: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 23:45:57: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 23:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.20_model.r INFO @ Mon, 12 Aug 2019 23:45:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:45:57: #1 tags after filtering in treatment: 18598022 INFO @ Mon, 12 Aug 2019 23:45:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:45:57: #1 finished! INFO @ Mon, 12 Aug 2019 23:45:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:45:59: #2 number of paired peaks: 1027 INFO @ Mon, 12 Aug 2019 23:45:59: start model_add_line... INFO @ Mon, 12 Aug 2019 23:45:59: start X-correlation... INFO @ Mon, 12 Aug 2019 23:45:59: end of X-cor INFO @ Mon, 12 Aug 2019 23:45:59: #2 finished! INFO @ Mon, 12 Aug 2019 23:45:59: #2 predicted fragment length is 135 bps INFO @ Mon, 12 Aug 2019 23:45:59: #2 alternative fragment length(s) may be 135 bps INFO @ Mon, 12 Aug 2019 23:45:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.10_model.r INFO @ Mon, 12 Aug 2019 23:45:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:46:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:46:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.05_summits.bed INFO @ Mon, 12 Aug 2019 23:47:10: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (11094 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.20_summits.bed INFO @ Mon, 12 Aug 2019 23:47:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3010 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:47:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:47:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011027/SRX5011027.10_summits.bed INFO @ Mon, 12 Aug 2019 23:47:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6479 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。