Job ID = 2590453 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,555,512 reads read : 27,111,024 reads written : 13,555,512 reads 0-length : 13,555,512 spots read : 13,557,217 reads read : 27,114,434 reads written : 13,557,217 reads 0-length : 13,557,217 spots read : 13,480,358 reads read : 26,960,716 reads written : 13,480,358 reads 0-length : 13,480,358 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: 00:13:18 40593087 reads; of these: 40593087 (100.00%) were unpaired; of these: 1181668 (2.91%) aligned 0 times 32730804 (80.63%) aligned exactly 1 time 6680615 (16.46%) aligned >1 times 97.09% overall alignment rate Time searching: 00:13:18 Overall time: 00:13:18 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] 7451236 / 39411419 = 0.1891 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 22:17:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.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 22:17:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.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 22:17:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.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 22:17:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:32: 1000000 INFO @ Mon, 12 Aug 2019 22:17:34: 1000000 INFO @ Mon, 12 Aug 2019 22:17:36: 1000000 INFO @ Mon, 12 Aug 2019 22:17:40: 2000000 INFO @ Mon, 12 Aug 2019 22:17:45: 2000000 INFO @ Mon, 12 Aug 2019 22:17:46: 2000000 INFO @ Mon, 12 Aug 2019 22:17:47: 3000000 INFO @ Mon, 12 Aug 2019 22:17:54: 4000000 INFO @ Mon, 12 Aug 2019 22:17:55: 3000000 INFO @ Mon, 12 Aug 2019 22:17:57: 3000000 INFO @ Mon, 12 Aug 2019 22:18:02: 5000000 INFO @ Mon, 12 Aug 2019 22:18:05: 4000000 INFO @ Mon, 12 Aug 2019 22:18:07: 4000000 INFO @ Mon, 12 Aug 2019 22:18:09: 6000000 INFO @ Mon, 12 Aug 2019 22:18:16: 5000000 INFO @ Mon, 12 Aug 2019 22:18:16: 7000000 INFO @ Mon, 12 Aug 2019 22:18:17: 5000000 INFO @ Mon, 12 Aug 2019 22:18:23: 8000000 INFO @ Mon, 12 Aug 2019 22:18:26: 6000000 INFO @ Mon, 12 Aug 2019 22:18:28: 6000000 INFO @ Mon, 12 Aug 2019 22:18:31: 9000000 INFO @ Mon, 12 Aug 2019 22:18:37: 7000000 INFO @ Mon, 12 Aug 2019 22:18:39: 7000000 INFO @ Mon, 12 Aug 2019 22:18:40: 10000000 INFO @ Mon, 12 Aug 2019 22:18:49: 8000000 INFO @ Mon, 12 Aug 2019 22:18:51: 8000000 INFO @ Mon, 12 Aug 2019 22:18:53: 11000000 INFO @ Mon, 12 Aug 2019 22:19:01: 9000000 INFO @ Mon, 12 Aug 2019 22:19:03: 9000000 INFO @ Mon, 12 Aug 2019 22:19:06: 12000000 INFO @ Mon, 12 Aug 2019 22:19:14: 10000000 INFO @ Mon, 12 Aug 2019 22:19:16: 10000000 INFO @ Mon, 12 Aug 2019 22:19:19: 13000000 INFO @ Mon, 12 Aug 2019 22:19:26: 11000000 INFO @ Mon, 12 Aug 2019 22:19:28: 11000000 INFO @ Mon, 12 Aug 2019 22:19:31: 14000000 INFO @ Mon, 12 Aug 2019 22:19:38: 12000000 INFO @ Mon, 12 Aug 2019 22:19:40: 12000000 INFO @ Mon, 12 Aug 2019 22:19:44: 15000000 INFO @ Mon, 12 Aug 2019 22:19:51: 13000000 INFO @ Mon, 12 Aug 2019 22:19:52: 13000000 INFO @ Mon, 12 Aug 2019 22:19:57: 16000000 INFO @ Mon, 12 Aug 2019 22:20:02: 14000000 INFO @ Mon, 12 Aug 2019 22:20:04: 14000000 INFO @ Mon, 12 Aug 2019 22:20:04: 17000000 INFO @ Mon, 12 Aug 2019 22:20:12: 18000000 INFO @ Mon, 12 Aug 2019 22:20:12: 15000000 INFO @ Mon, 12 Aug 2019 22:20:14: 15000000 INFO @ Mon, 12 Aug 2019 22:20:19: 19000000 INFO @ Mon, 12 Aug 2019 22:20:23: 16000000 INFO @ Mon, 12 Aug 2019 22:20:24: 16000000 INFO @ Mon, 12 Aug 2019 22:20:26: 20000000 INFO @ Mon, 12 Aug 2019 22:20:33: 17000000 INFO @ Mon, 12 Aug 2019 22:20:33: 21000000 INFO @ Mon, 12 Aug 2019 22:20:35: 17000000 INFO @ Mon, 12 Aug 2019 22:20:41: 22000000 INFO @ Mon, 12 Aug 2019 22:20:43: 18000000 INFO @ Mon, 12 Aug 2019 22:20:45: 18000000 INFO @ Mon, 12 Aug 2019 22:20:48: 23000000 INFO @ Mon, 12 Aug 2019 22:20:54: 19000000 INFO @ Mon, 12 Aug 2019 22:20:55: 24000000 INFO @ Mon, 12 Aug 2019 22:20:55: 19000000 INFO @ Mon, 12 Aug 2019 22:21:03: 25000000 INFO @ Mon, 12 Aug 2019 22:21:04: 20000000 INFO @ Mon, 12 Aug 2019 22:21:06: 20000000 INFO @ Mon, 12 Aug 2019 22:21:10: 26000000 INFO @ Mon, 12 Aug 2019 22:21:14: 21000000 INFO @ Mon, 12 Aug 2019 22:21:16: 21000000 INFO @ Mon, 12 Aug 2019 22:21:17: 27000000 INFO @ Mon, 12 Aug 2019 22:21:25: 22000000 INFO @ Mon, 12 Aug 2019 22:21:26: 28000000 INFO @ Mon, 12 Aug 2019 22:21:26: 22000000 INFO @ Mon, 12 Aug 2019 22:21:35: 29000000 INFO @ Mon, 12 Aug 2019 22:21:36: 23000000 INFO @ Mon, 12 Aug 2019 22:21:37: 23000000 INFO @ Mon, 12 Aug 2019 22:21:44: 30000000 INFO @ Mon, 12 Aug 2019 22:21:46: 24000000 INFO @ Mon, 12 Aug 2019 22:21:48: 24000000 INFO @ Mon, 12 Aug 2019 22:21:53: 31000000 INFO @ Mon, 12 Aug 2019 22:21:58: 25000000 INFO @ Mon, 12 Aug 2019 22:22:00: 25000000 INFO @ Mon, 12 Aug 2019 22:22:03: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:22:03: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:22:03: #1 total tags in treatment: 31960183 INFO @ Mon, 12 Aug 2019 22:22:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:22:03: #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 22:22:04: #1 tags after filtering in treatment: 31960183 INFO @ Mon, 12 Aug 2019 22:22:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:22:04: #1 finished! INFO @ Mon, 12 Aug 2019 22:22:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:22:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:22:07: #2 number of paired peaks: 627 WARNING @ Mon, 12 Aug 2019 22:22:07: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Mon, 12 Aug 2019 22:22:07: start model_add_line... INFO @ Mon, 12 Aug 2019 22:22:07: start X-correlation... INFO @ Mon, 12 Aug 2019 22:22:07: end of X-cor INFO @ Mon, 12 Aug 2019 22:22:07: #2 finished! INFO @ Mon, 12 Aug 2019 22:22:07: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 22:22:07: #2 alternative fragment length(s) may be 4,127 bps INFO @ Mon, 12 Aug 2019 22:22:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.10_model.r INFO @ Mon, 12 Aug 2019 22:22:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:22:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:22:09: 26000000 INFO @ Mon, 12 Aug 2019 22:22:10: 26000000 INFO @ Mon, 12 Aug 2019 22:22:19: 27000000 INFO @ Mon, 12 Aug 2019 22:22:20: 27000000 INFO @ Mon, 12 Aug 2019 22:22:29: 28000000 INFO @ Mon, 12 Aug 2019 22:22:31: 28000000 INFO @ Mon, 12 Aug 2019 22:22:39: 29000000 INFO @ Mon, 12 Aug 2019 22:22:41: 29000000 INFO @ Mon, 12 Aug 2019 22:22:49: 30000000 INFO @ Mon, 12 Aug 2019 22:22:51: 30000000 INFO @ Mon, 12 Aug 2019 22:22:59: 31000000 INFO @ Mon, 12 Aug 2019 22:23:01: 31000000 INFO @ Mon, 12 Aug 2019 22:23:09: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:09: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:09: #1 total tags in treatment: 31960183 INFO @ Mon, 12 Aug 2019 22:23:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:09: #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 22:23:10: #1 tags after filtering in treatment: 31960183 INFO @ Mon, 12 Aug 2019 22:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:10: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:10: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:23:10: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:23:10: #1 total tags in treatment: 31960183 INFO @ Mon, 12 Aug 2019 22:23:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:23:10: #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 22:23:11: #1 tags after filtering in treatment: 31960183 INFO @ Mon, 12 Aug 2019 22:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:23:11: #1 finished! INFO @ Mon, 12 Aug 2019 22:23:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:23:13: #2 number of paired peaks: 627 WARNING @ Mon, 12 Aug 2019 22:23:13: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:13: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:13: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:13: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:13: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:13: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 22:23:13: #2 alternative fragment length(s) may be 4,127 bps INFO @ Mon, 12 Aug 2019 22:23:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.05_model.r INFO @ Mon, 12 Aug 2019 22:23:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:23:14: #2 number of paired peaks: 627 WARNING @ Mon, 12 Aug 2019 22:23:14: Fewer paired peaks (627) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 627 pairs to build model! INFO @ Mon, 12 Aug 2019 22:23:14: start model_add_line... INFO @ Mon, 12 Aug 2019 22:23:14: start X-correlation... INFO @ Mon, 12 Aug 2019 22:23:14: end of X-cor INFO @ Mon, 12 Aug 2019 22:23:14: #2 finished! INFO @ Mon, 12 Aug 2019 22:23:14: #2 predicted fragment length is 127 bps INFO @ Mon, 12 Aug 2019 22:23:14: #2 alternative fragment length(s) may be 4,127 bps INFO @ Mon, 12 Aug 2019 22:23:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.20_model.r INFO @ Mon, 12 Aug 2019 22:23:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:23:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:24:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:24:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.10_summits.bed INFO @ Mon, 12 Aug 2019 22:24:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6299 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:24:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:24:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:25:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.05_summits.bed INFO @ Mon, 12 Aug 2019 22:25:08: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (9405 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981685/SRX3981685.20_summits.bed INFO @ Mon, 12 Aug 2019 22:25:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2742 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。