Job ID = 2590794 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,136,444 reads read : 66,272,888 reads written : 33,136,444 reads 0-length : 33,136,444 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: 00:11:56 33136444 reads; of these: 33136444 (100.00%) were unpaired; of these: 1566620 (4.73%) aligned 0 times 24763269 (74.73%) aligned exactly 1 time 6806555 (20.54%) aligned >1 times 95.27% overall alignment rate Time searching: 00:11:56 Overall time: 00:11:56 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] 11534763 / 31569824 = 0.3654 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 23:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.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 23:37:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:37:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:37:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.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 23:37:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:37:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:37:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.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 23:37:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:37:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:38:07: 1000000 INFO @ Mon, 12 Aug 2019 23:38:08: 1000000 INFO @ Mon, 12 Aug 2019 23:38:09: 1000000 INFO @ Mon, 12 Aug 2019 23:38:18: 2000000 INFO @ Mon, 12 Aug 2019 23:38:19: 2000000 INFO @ Mon, 12 Aug 2019 23:38:20: 2000000 INFO @ Mon, 12 Aug 2019 23:38:29: 3000000 INFO @ Mon, 12 Aug 2019 23:38:30: 3000000 INFO @ Mon, 12 Aug 2019 23:38:31: 3000000 INFO @ Mon, 12 Aug 2019 23:38:40: 4000000 INFO @ Mon, 12 Aug 2019 23:38:41: 4000000 INFO @ Mon, 12 Aug 2019 23:38:42: 4000000 INFO @ Mon, 12 Aug 2019 23:38:51: 5000000 INFO @ Mon, 12 Aug 2019 23:38:52: 5000000 INFO @ Mon, 12 Aug 2019 23:38:53: 5000000 INFO @ Mon, 12 Aug 2019 23:39:02: 6000000 INFO @ Mon, 12 Aug 2019 23:39:03: 6000000 INFO @ Mon, 12 Aug 2019 23:39:04: 6000000 INFO @ Mon, 12 Aug 2019 23:39:13: 7000000 INFO @ Mon, 12 Aug 2019 23:39:14: 7000000 INFO @ Mon, 12 Aug 2019 23:39:15: 7000000 INFO @ Mon, 12 Aug 2019 23:39:24: 8000000 INFO @ Mon, 12 Aug 2019 23:39:25: 8000000 INFO @ Mon, 12 Aug 2019 23:39:26: 8000000 INFO @ Mon, 12 Aug 2019 23:39:35: 9000000 INFO @ Mon, 12 Aug 2019 23:39:36: 9000000 INFO @ Mon, 12 Aug 2019 23:39:37: 9000000 INFO @ Mon, 12 Aug 2019 23:39:45: 10000000 INFO @ Mon, 12 Aug 2019 23:39:45: 10000000 INFO @ Mon, 12 Aug 2019 23:39:46: 10000000 INFO @ Mon, 12 Aug 2019 23:39:53: 11000000 INFO @ Mon, 12 Aug 2019 23:39:53: 11000000 INFO @ Mon, 12 Aug 2019 23:39:56: 11000000 INFO @ Mon, 12 Aug 2019 23:40:00: 12000000 INFO @ Mon, 12 Aug 2019 23:40:01: 12000000 INFO @ Mon, 12 Aug 2019 23:40:07: 12000000 INFO @ Mon, 12 Aug 2019 23:40:08: 13000000 INFO @ Mon, 12 Aug 2019 23:40:09: 13000000 INFO @ Mon, 12 Aug 2019 23:40:16: 14000000 INFO @ Mon, 12 Aug 2019 23:40:16: 14000000 INFO @ Mon, 12 Aug 2019 23:40:17: 13000000 INFO @ Mon, 12 Aug 2019 23:40:23: 15000000 INFO @ Mon, 12 Aug 2019 23:40:24: 15000000 INFO @ Mon, 12 Aug 2019 23:40:27: 14000000 INFO @ Mon, 12 Aug 2019 23:40:31: 16000000 INFO @ Mon, 12 Aug 2019 23:40:32: 16000000 INFO @ Mon, 12 Aug 2019 23:40:38: 15000000 INFO @ Mon, 12 Aug 2019 23:40:39: 17000000 INFO @ Mon, 12 Aug 2019 23:40:39: 17000000 INFO @ Mon, 12 Aug 2019 23:40:46: 18000000 INFO @ Mon, 12 Aug 2019 23:40:47: 18000000 INFO @ Mon, 12 Aug 2019 23:40:48: 16000000 INFO @ Mon, 12 Aug 2019 23:40:54: 19000000 INFO @ Mon, 12 Aug 2019 23:40:54: 19000000 INFO @ Mon, 12 Aug 2019 23:40:58: 17000000 INFO @ Mon, 12 Aug 2019 23:41:01: 20000000 INFO @ Mon, 12 Aug 2019 23:41:01: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:41:01: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:41:01: #1 total tags in treatment: 20035061 INFO @ Mon, 12 Aug 2019 23:41:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:41:01: #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 23:41:02: 20000000 INFO @ Mon, 12 Aug 2019 23:41:02: #1 tags after filtering in treatment: 20035061 INFO @ Mon, 12 Aug 2019 23:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:41:02: #1 finished! INFO @ Mon, 12 Aug 2019 23:41:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:41:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:41:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:41:02: #1 total tags in treatment: 20035061 INFO @ Mon, 12 Aug 2019 23:41:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:41:02: #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 23:41:03: #1 tags after filtering in treatment: 20035061 INFO @ Mon, 12 Aug 2019 23:41:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:41:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:41:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:41:04: #2 number of paired peaks: 3148 INFO @ Mon, 12 Aug 2019 23:41:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:41:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:41:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:41:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:41:04: #2 predicted fragment length is 214 bps INFO @ Mon, 12 Aug 2019 23:41:04: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 12 Aug 2019 23:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.10_model.r INFO @ Mon, 12 Aug 2019 23:41:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:41:05: #2 number of paired peaks: 3148 INFO @ Mon, 12 Aug 2019 23:41:05: start model_add_line... INFO @ Mon, 12 Aug 2019 23:41:05: start X-correlation... INFO @ Mon, 12 Aug 2019 23:41:05: end of X-cor INFO @ Mon, 12 Aug 2019 23:41:05: #2 finished! INFO @ Mon, 12 Aug 2019 23:41:05: #2 predicted fragment length is 214 bps INFO @ Mon, 12 Aug 2019 23:41:05: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 12 Aug 2019 23:41:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.05_model.r INFO @ Mon, 12 Aug 2019 23:41:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:41:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:41:08: 18000000 INFO @ Mon, 12 Aug 2019 23:41:17: 19000000 INFO @ Mon, 12 Aug 2019 23:41:26: 20000000 INFO @ Mon, 12 Aug 2019 23:41:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:41:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:41:27: #1 total tags in treatment: 20035061 INFO @ Mon, 12 Aug 2019 23:41:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:41:27: #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 23:41:27: #1 tags after filtering in treatment: 20035061 INFO @ Mon, 12 Aug 2019 23:41:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:41:27: #1 finished! INFO @ Mon, 12 Aug 2019 23:41:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:41:29: #2 number of paired peaks: 3148 INFO @ Mon, 12 Aug 2019 23:41:29: start model_add_line... INFO @ Mon, 12 Aug 2019 23:41:30: start X-correlation... INFO @ Mon, 12 Aug 2019 23:41:30: end of X-cor INFO @ Mon, 12 Aug 2019 23:41:30: #2 finished! INFO @ Mon, 12 Aug 2019 23:41:30: #2 predicted fragment length is 214 bps INFO @ Mon, 12 Aug 2019 23:41:30: #2 alternative fragment length(s) may be 214 bps INFO @ Mon, 12 Aug 2019 23:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.20_model.r INFO @ Mon, 12 Aug 2019 23:41:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:42:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:42:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:42:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.10_summits.bed INFO @ Mon, 12 Aug 2019 23:42:35: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (12456 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.05_summits.bed INFO @ Mon, 12 Aug 2019 23:42:36: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (15549 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:42:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:42:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011036/SRX5011036.20_summits.bed INFO @ Mon, 12 Aug 2019 23:42:59: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8558 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。