Job ID = 2590821 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 35,673,391 reads read : 71,346,782 reads written : 35,673,391 reads 0-length : 35,673,391 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: 00:12:34 35673391 reads; of these: 35673391 (100.00%) were unpaired; of these: 3075247 (8.62%) aligned 0 times 25950240 (72.74%) aligned exactly 1 time 6647904 (18.64%) aligned >1 times 91.38% overall alignment rate Time searching: 00:12:34 Overall time: 00:12:34 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] 17140427 / 32598144 = 0.5258 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 23:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.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 23:47:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.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 23:47:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.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 23:47:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:48:00: 1000000 INFO @ Mon, 12 Aug 2019 23:48:03: 1000000 INFO @ Mon, 12 Aug 2019 23:48:04: 1000000 INFO @ Mon, 12 Aug 2019 23:48:07: 2000000 INFO @ Mon, 12 Aug 2019 23:48:10: 2000000 INFO @ Mon, 12 Aug 2019 23:48:12: 2000000 INFO @ Mon, 12 Aug 2019 23:48:13: 3000000 INFO @ Mon, 12 Aug 2019 23:48:18: 3000000 INFO @ Mon, 12 Aug 2019 23:48:19: 4000000 INFO @ Mon, 12 Aug 2019 23:48:19: 3000000 INFO @ Mon, 12 Aug 2019 23:48:25: 5000000 INFO @ Mon, 12 Aug 2019 23:48:26: 4000000 INFO @ Mon, 12 Aug 2019 23:48:27: 4000000 INFO @ Mon, 12 Aug 2019 23:48:32: 6000000 INFO @ Mon, 12 Aug 2019 23:48:34: 5000000 INFO @ Mon, 12 Aug 2019 23:48:35: 5000000 INFO @ Mon, 12 Aug 2019 23:48:38: 7000000 INFO @ Mon, 12 Aug 2019 23:48:41: 6000000 INFO @ Mon, 12 Aug 2019 23:48:43: 6000000 INFO @ Mon, 12 Aug 2019 23:48:44: 8000000 INFO @ Mon, 12 Aug 2019 23:48:49: 7000000 INFO @ Mon, 12 Aug 2019 23:48:50: 9000000 INFO @ Mon, 12 Aug 2019 23:48:51: 7000000 INFO @ Mon, 12 Aug 2019 23:48:57: 10000000 INFO @ Mon, 12 Aug 2019 23:48:57: 8000000 INFO @ Mon, 12 Aug 2019 23:48:58: 8000000 INFO @ Mon, 12 Aug 2019 23:49:03: 11000000 INFO @ Mon, 12 Aug 2019 23:49:04: 9000000 INFO @ Mon, 12 Aug 2019 23:49:06: 9000000 INFO @ Mon, 12 Aug 2019 23:49:09: 12000000 INFO @ Mon, 12 Aug 2019 23:49:12: 10000000 INFO @ Mon, 12 Aug 2019 23:49:14: 10000000 INFO @ Mon, 12 Aug 2019 23:49:15: 13000000 INFO @ Mon, 12 Aug 2019 23:49:20: 11000000 INFO @ Mon, 12 Aug 2019 23:49:22: 14000000 INFO @ Mon, 12 Aug 2019 23:49:22: 11000000 INFO @ Mon, 12 Aug 2019 23:49:28: 12000000 INFO @ Mon, 12 Aug 2019 23:49:28: 15000000 INFO @ Mon, 12 Aug 2019 23:49:29: 12000000 INFO @ Mon, 12 Aug 2019 23:49:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:49:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:49:31: #1 total tags in treatment: 15457717 INFO @ Mon, 12 Aug 2019 23:49:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:49:31: #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 23:49:31: #1 tags after filtering in treatment: 15457717 INFO @ Mon, 12 Aug 2019 23:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:49:31: #1 finished! INFO @ Mon, 12 Aug 2019 23:49:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:49:33: #2 number of paired peaks: 5573 INFO @ Mon, 12 Aug 2019 23:49:33: start model_add_line... INFO @ Mon, 12 Aug 2019 23:49:34: start X-correlation... INFO @ Mon, 12 Aug 2019 23:49:34: end of X-cor INFO @ Mon, 12 Aug 2019 23:49:34: #2 finished! INFO @ Mon, 12 Aug 2019 23:49:34: #2 predicted fragment length is 252 bps INFO @ Mon, 12 Aug 2019 23:49:34: #2 alternative fragment length(s) may be 252 bps INFO @ Mon, 12 Aug 2019 23:49:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.05_model.r INFO @ Mon, 12 Aug 2019 23:49:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:49:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:49:36: 13000000 INFO @ Mon, 12 Aug 2019 23:49:37: 13000000 INFO @ Mon, 12 Aug 2019 23:49:44: 14000000 INFO @ Mon, 12 Aug 2019 23:49:45: 14000000 INFO @ Mon, 12 Aug 2019 23:49:51: 15000000 INFO @ Mon, 12 Aug 2019 23:49:52: 15000000 INFO @ Mon, 12 Aug 2019 23:49:55: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:49:55: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:49:55: #1 total tags in treatment: 15457717 INFO @ Mon, 12 Aug 2019 23:49:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:49:55: #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 23:49:56: #1 tags after filtering in treatment: 15457717 INFO @ Mon, 12 Aug 2019 23:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:49:56: #1 finished! INFO @ Mon, 12 Aug 2019 23:49:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:49:56: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:49:56: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:49:56: #1 total tags in treatment: 15457717 INFO @ Mon, 12 Aug 2019 23:49:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:49:56: #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 23:49:56: #1 tags after filtering in treatment: 15457717 INFO @ Mon, 12 Aug 2019 23:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:49:56: #1 finished! INFO @ Mon, 12 Aug 2019 23:49:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:49:58: #2 number of paired peaks: 5573 INFO @ Mon, 12 Aug 2019 23:49:58: start model_add_line... INFO @ Mon, 12 Aug 2019 23:49:58: start X-correlation... INFO @ Mon, 12 Aug 2019 23:49:58: end of X-cor INFO @ Mon, 12 Aug 2019 23:49:58: #2 finished! INFO @ Mon, 12 Aug 2019 23:49:58: #2 predicted fragment length is 252 bps INFO @ Mon, 12 Aug 2019 23:49:58: #2 alternative fragment length(s) may be 252 bps INFO @ Mon, 12 Aug 2019 23:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.10_model.r INFO @ Mon, 12 Aug 2019 23:49:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:49:58: #2 number of paired peaks: 5573 INFO @ Mon, 12 Aug 2019 23:49:58: start model_add_line... INFO @ Mon, 12 Aug 2019 23:49:58: start X-correlation... INFO @ Mon, 12 Aug 2019 23:49:59: end of X-cor INFO @ Mon, 12 Aug 2019 23:49:59: #2 finished! INFO @ Mon, 12 Aug 2019 23:49:59: #2 predicted fragment length is 252 bps INFO @ Mon, 12 Aug 2019 23:49:59: #2 alternative fragment length(s) may be 252 bps INFO @ Mon, 12 Aug 2019 23:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.20_model.r INFO @ Mon, 12 Aug 2019 23:49:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.05_summits.bed INFO @ Mon, 12 Aug 2019 23:50:54: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (13817 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:50:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:50:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:19: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8351 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011060/SRX5011060.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:22: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11360 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。