Job ID = 2590792 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 72,131,533 reads read : 144,263,066 reads written : 72,131,533 reads 0-length : 72,131,533 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: 00:22:34 72131533 reads; of these: 72131533 (100.00%) were unpaired; of these: 8258738 (11.45%) aligned 0 times 51549065 (71.47%) aligned exactly 1 time 12323730 (17.09%) aligned >1 times 88.55% overall alignment rate Time searching: 00:22:34 Overall time: 00:22:34 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 28 files... [bam_rmdupse_core] 33513105 / 63872795 = 0.5247 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 @ Tue, 13 Aug 2019 00:01:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.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 @ Tue, 13 Aug 2019 00:01:41: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:01:41: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.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 @ Tue, 13 Aug 2019 00:01:42: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:01:42: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.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 @ Tue, 13 Aug 2019 00:01:43: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:01:43: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:01:50: 1000000 INFO @ Tue, 13 Aug 2019 00:01:50: 1000000 INFO @ Tue, 13 Aug 2019 00:01:51: 1000000 INFO @ Tue, 13 Aug 2019 00:01:57: 2000000 INFO @ Tue, 13 Aug 2019 00:01:59: 2000000 INFO @ Tue, 13 Aug 2019 00:01:59: 2000000 INFO @ Tue, 13 Aug 2019 00:02:04: 3000000 INFO @ Tue, 13 Aug 2019 00:02:07: 3000000 INFO @ Tue, 13 Aug 2019 00:02:07: 3000000 INFO @ Tue, 13 Aug 2019 00:02:10: 4000000 INFO @ Tue, 13 Aug 2019 00:02:14: 4000000 INFO @ Tue, 13 Aug 2019 00:02:15: 4000000 INFO @ Tue, 13 Aug 2019 00:02:17: 5000000 INFO @ Tue, 13 Aug 2019 00:02:22: 5000000 INFO @ Tue, 13 Aug 2019 00:02:23: 5000000 INFO @ Tue, 13 Aug 2019 00:02:25: 6000000 INFO @ Tue, 13 Aug 2019 00:02:29: 6000000 INFO @ Tue, 13 Aug 2019 00:02:30: 6000000 INFO @ Tue, 13 Aug 2019 00:02:31: 7000000 INFO @ Tue, 13 Aug 2019 00:02:37: 7000000 INFO @ Tue, 13 Aug 2019 00:02:37: 7000000 INFO @ Tue, 13 Aug 2019 00:02:38: 8000000 INFO @ Tue, 13 Aug 2019 00:02:44: 8000000 INFO @ Tue, 13 Aug 2019 00:02:45: 9000000 INFO @ Tue, 13 Aug 2019 00:02:45: 8000000 INFO @ Tue, 13 Aug 2019 00:02:52: 10000000 INFO @ Tue, 13 Aug 2019 00:02:52: 9000000 INFO @ Tue, 13 Aug 2019 00:02:53: 9000000 INFO @ Tue, 13 Aug 2019 00:02:58: 11000000 INFO @ Tue, 13 Aug 2019 00:02:59: 10000000 INFO @ Tue, 13 Aug 2019 00:03:00: 10000000 INFO @ Tue, 13 Aug 2019 00:03:05: 12000000 INFO @ Tue, 13 Aug 2019 00:03:07: 11000000 INFO @ Tue, 13 Aug 2019 00:03:08: 11000000 INFO @ Tue, 13 Aug 2019 00:03:11: 13000000 INFO @ Tue, 13 Aug 2019 00:03:14: 12000000 INFO @ Tue, 13 Aug 2019 00:03:16: 12000000 INFO @ Tue, 13 Aug 2019 00:03:18: 14000000 INFO @ Tue, 13 Aug 2019 00:03:22: 13000000 INFO @ Tue, 13 Aug 2019 00:03:24: 13000000 INFO @ Tue, 13 Aug 2019 00:03:25: 15000000 INFO @ Tue, 13 Aug 2019 00:03:29: 14000000 INFO @ Tue, 13 Aug 2019 00:03:31: 14000000 INFO @ Tue, 13 Aug 2019 00:03:31: 16000000 INFO @ Tue, 13 Aug 2019 00:03:37: 15000000 INFO @ Tue, 13 Aug 2019 00:03:38: 17000000 INFO @ Tue, 13 Aug 2019 00:03:39: 15000000 INFO @ Tue, 13 Aug 2019 00:03:45: 18000000 INFO @ Tue, 13 Aug 2019 00:03:45: 16000000 INFO @ Tue, 13 Aug 2019 00:03:47: 16000000 INFO @ Tue, 13 Aug 2019 00:03:51: 19000000 INFO @ Tue, 13 Aug 2019 00:03:53: 17000000 INFO @ Tue, 13 Aug 2019 00:03:54: 17000000 INFO @ Tue, 13 Aug 2019 00:03:58: 20000000 INFO @ Tue, 13 Aug 2019 00:04:00: 18000000 INFO @ Tue, 13 Aug 2019 00:04:01: 18000000 INFO @ Tue, 13 Aug 2019 00:04:05: 21000000 INFO @ Tue, 13 Aug 2019 00:04:08: 19000000 INFO @ Tue, 13 Aug 2019 00:04:09: 19000000 INFO @ Tue, 13 Aug 2019 00:04:11: 22000000 INFO @ Tue, 13 Aug 2019 00:04:16: 20000000 INFO @ Tue, 13 Aug 2019 00:04:16: 20000000 INFO @ Tue, 13 Aug 2019 00:04:18: 23000000 INFO @ Tue, 13 Aug 2019 00:04:24: 21000000 INFO @ Tue, 13 Aug 2019 00:04:24: 21000000 INFO @ Tue, 13 Aug 2019 00:04:25: 24000000 INFO @ Tue, 13 Aug 2019 00:04:31: 25000000 INFO @ Tue, 13 Aug 2019 00:04:31: 22000000 INFO @ Tue, 13 Aug 2019 00:04:31: 22000000 INFO @ Tue, 13 Aug 2019 00:04:38: 26000000 INFO @ Tue, 13 Aug 2019 00:04:39: 23000000 INFO @ Tue, 13 Aug 2019 00:04:39: 23000000 INFO @ Tue, 13 Aug 2019 00:04:45: 27000000 INFO @ Tue, 13 Aug 2019 00:04:47: 24000000 INFO @ Tue, 13 Aug 2019 00:04:47: 24000000 INFO @ Tue, 13 Aug 2019 00:04:51: 28000000 INFO @ Tue, 13 Aug 2019 00:04:54: 25000000 INFO @ Tue, 13 Aug 2019 00:04:55: 25000000 INFO @ Tue, 13 Aug 2019 00:04:58: 29000000 INFO @ Tue, 13 Aug 2019 00:05:02: 26000000 INFO @ Tue, 13 Aug 2019 00:05:03: 26000000 INFO @ Tue, 13 Aug 2019 00:05:05: 30000000 INFO @ Tue, 13 Aug 2019 00:05:07: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:05:07: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:05:07: #1 total tags in treatment: 30359690 INFO @ Tue, 13 Aug 2019 00:05:07: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:05:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:05:08: #1 tags after filtering in treatment: 30359690 INFO @ Tue, 13 Aug 2019 00:05:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:05:08: #1 finished! INFO @ Tue, 13 Aug 2019 00:05:08: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:05:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:05:10: 27000000 INFO @ Tue, 13 Aug 2019 00:05:10: 27000000 INFO @ Tue, 13 Aug 2019 00:05:11: #2 number of paired peaks: 2085 INFO @ Tue, 13 Aug 2019 00:05:11: start model_add_line... INFO @ Tue, 13 Aug 2019 00:05:11: start X-correlation... INFO @ Tue, 13 Aug 2019 00:05:11: end of X-cor INFO @ Tue, 13 Aug 2019 00:05:11: #2 finished! INFO @ Tue, 13 Aug 2019 00:05:11: #2 predicted fragment length is 207 bps INFO @ Tue, 13 Aug 2019 00:05:11: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 13 Aug 2019 00:05:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.20_model.r INFO @ Tue, 13 Aug 2019 00:05:11: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:05:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:05:17: 28000000 INFO @ Tue, 13 Aug 2019 00:05:18: 28000000 INFO @ Tue, 13 Aug 2019 00:05:25: 29000000 INFO @ Tue, 13 Aug 2019 00:05:26: 29000000 INFO @ Tue, 13 Aug 2019 00:05:33: 30000000 INFO @ Tue, 13 Aug 2019 00:05:33: 30000000 INFO @ Tue, 13 Aug 2019 00:05:36: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:05:36: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:05:36: #1 total tags in treatment: 30359690 INFO @ Tue, 13 Aug 2019 00:05:36: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:05:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:05:36: #1 tags after filtering in treatment: 30359690 INFO @ Tue, 13 Aug 2019 00:05:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:05:36: #1 finished! INFO @ Tue, 13 Aug 2019 00:05:36: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:05:36: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:05:36: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:05:36: #1 total tags in treatment: 30359690 INFO @ Tue, 13 Aug 2019 00:05:36: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:05:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:05:37: #1 tags after filtering in treatment: 30359690 INFO @ Tue, 13 Aug 2019 00:05:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:05:37: #1 finished! INFO @ Tue, 13 Aug 2019 00:05:37: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:05:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:05:39: #2 number of paired peaks: 2085 INFO @ Tue, 13 Aug 2019 00:05:39: start model_add_line... INFO @ Tue, 13 Aug 2019 00:05:39: start X-correlation... INFO @ Tue, 13 Aug 2019 00:05:39: end of X-cor INFO @ Tue, 13 Aug 2019 00:05:39: #2 finished! INFO @ Tue, 13 Aug 2019 00:05:39: #2 predicted fragment length is 207 bps INFO @ Tue, 13 Aug 2019 00:05:39: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 13 Aug 2019 00:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.10_model.r INFO @ Tue, 13 Aug 2019 00:05:40: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:05:40: #2 number of paired peaks: 2085 INFO @ Tue, 13 Aug 2019 00:05:40: start model_add_line... INFO @ Tue, 13 Aug 2019 00:05:40: start X-correlation... INFO @ Tue, 13 Aug 2019 00:05:40: end of X-cor INFO @ Tue, 13 Aug 2019 00:05:40: #2 finished! INFO @ Tue, 13 Aug 2019 00:05:40: #2 predicted fragment length is 207 bps INFO @ Tue, 13 Aug 2019 00:05:40: #2 alternative fragment length(s) may be 207 bps INFO @ Tue, 13 Aug 2019 00:05:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.05_model.r INFO @ Tue, 13 Aug 2019 00:05:40: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:05:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:06:45: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:07:12: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:07:14: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:07:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:07:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:07:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.20_summits.bed INFO @ Tue, 13 Aug 2019 00:07:27: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10304 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.10_summits.bed INFO @ Tue, 13 Aug 2019 00:07:51: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (14366 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:07:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:07:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011034/SRX5011034.05_summits.bed INFO @ Tue, 13 Aug 2019 00:07:53: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (17488 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。