Job ID = 2590452 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,871,876 reads read : 35,743,752 reads written : 17,871,876 reads 0-length : 17,871,876 spots read : 17,898,947 reads read : 35,797,894 reads written : 17,898,947 reads 0-length : 17,898,947 spots read : 17,773,726 reads read : 35,547,452 reads written : 17,773,726 reads 0-length : 17,773,726 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: 00:14:14 53544549 reads; of these: 53544549 (100.00%) were unpaired; of these: 2302297 (4.30%) aligned 0 times 43362591 (80.98%) aligned exactly 1 time 7879661 (14.72%) aligned >1 times 95.70% overall alignment rate Time searching: 00:14:14 Overall time: 00:14:14 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 24 files... [bam_rmdupse_core] 12706622 / 51242252 = 0.2480 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 22:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.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 22:23:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:23:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.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 22:23:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:23:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.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 22:23:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:23:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:23:56: 1000000 INFO @ Mon, 12 Aug 2019 22:23:56: 1000000 INFO @ Mon, 12 Aug 2019 22:23:58: 1000000 INFO @ Mon, 12 Aug 2019 22:24:03: 2000000 INFO @ Mon, 12 Aug 2019 22:24:04: 2000000 INFO @ Mon, 12 Aug 2019 22:24:06: 2000000 INFO @ Mon, 12 Aug 2019 22:24:11: 3000000 INFO @ Mon, 12 Aug 2019 22:24:14: 3000000 INFO @ Mon, 12 Aug 2019 22:24:14: 3000000 INFO @ Mon, 12 Aug 2019 22:24:19: 4000000 INFO @ Mon, 12 Aug 2019 22:24:23: 4000000 INFO @ Mon, 12 Aug 2019 22:24:24: 4000000 INFO @ Mon, 12 Aug 2019 22:24:26: 5000000 INFO @ Mon, 12 Aug 2019 22:24:31: 5000000 INFO @ Mon, 12 Aug 2019 22:24:33: 6000000 INFO @ Mon, 12 Aug 2019 22:24:33: 5000000 INFO @ Mon, 12 Aug 2019 22:24:39: 6000000 INFO @ Mon, 12 Aug 2019 22:24:40: 7000000 INFO @ Mon, 12 Aug 2019 22:24:43: 6000000 INFO @ Mon, 12 Aug 2019 22:24:47: 7000000 INFO @ Mon, 12 Aug 2019 22:24:48: 8000000 INFO @ Mon, 12 Aug 2019 22:24:52: 7000000 INFO @ Mon, 12 Aug 2019 22:24:55: 9000000 INFO @ Mon, 12 Aug 2019 22:24:55: 8000000 INFO @ Mon, 12 Aug 2019 22:25:02: 8000000 INFO @ Mon, 12 Aug 2019 22:25:02: 10000000 INFO @ Mon, 12 Aug 2019 22:25:04: 9000000 INFO @ Mon, 12 Aug 2019 22:25:10: 11000000 INFO @ Mon, 12 Aug 2019 22:25:12: 10000000 INFO @ Mon, 12 Aug 2019 22:25:12: 9000000 INFO @ Mon, 12 Aug 2019 22:25:17: 12000000 INFO @ Mon, 12 Aug 2019 22:25:20: 11000000 INFO @ Mon, 12 Aug 2019 22:25:21: 10000000 INFO @ Mon, 12 Aug 2019 22:25:24: 13000000 INFO @ Mon, 12 Aug 2019 22:25:28: 12000000 INFO @ Mon, 12 Aug 2019 22:25:31: 11000000 INFO @ Mon, 12 Aug 2019 22:25:31: 14000000 INFO @ Mon, 12 Aug 2019 22:25:36: 13000000 INFO @ Mon, 12 Aug 2019 22:25:39: 15000000 INFO @ Mon, 12 Aug 2019 22:25:40: 12000000 INFO @ Mon, 12 Aug 2019 22:25:44: 14000000 INFO @ Mon, 12 Aug 2019 22:25:46: 16000000 INFO @ Mon, 12 Aug 2019 22:25:50: 13000000 INFO @ Mon, 12 Aug 2019 22:25:52: 15000000 INFO @ Mon, 12 Aug 2019 22:25:53: 17000000 INFO @ Mon, 12 Aug 2019 22:25:59: 14000000 INFO @ Mon, 12 Aug 2019 22:26:00: 16000000 INFO @ Mon, 12 Aug 2019 22:26:00: 18000000 INFO @ Mon, 12 Aug 2019 22:26:08: 19000000 INFO @ Mon, 12 Aug 2019 22:26:08: 17000000 INFO @ Mon, 12 Aug 2019 22:26:08: 15000000 INFO @ Mon, 12 Aug 2019 22:26:15: 20000000 INFO @ Mon, 12 Aug 2019 22:26:16: 18000000 INFO @ Mon, 12 Aug 2019 22:26:18: 16000000 INFO @ Mon, 12 Aug 2019 22:26:22: 21000000 INFO @ Mon, 12 Aug 2019 22:26:24: 19000000 INFO @ Mon, 12 Aug 2019 22:26:27: 17000000 INFO @ Mon, 12 Aug 2019 22:26:30: 22000000 INFO @ Mon, 12 Aug 2019 22:26:32: 20000000 INFO @ Mon, 12 Aug 2019 22:26:37: 18000000 INFO @ Mon, 12 Aug 2019 22:26:37: 23000000 INFO @ Mon, 12 Aug 2019 22:26:40: 21000000 INFO @ Mon, 12 Aug 2019 22:26:44: 24000000 INFO @ Mon, 12 Aug 2019 22:26:47: 19000000 INFO @ Mon, 12 Aug 2019 22:26:49: 22000000 INFO @ Mon, 12 Aug 2019 22:26:52: 25000000 INFO @ Mon, 12 Aug 2019 22:26:56: 20000000 INFO @ Mon, 12 Aug 2019 22:26:57: 23000000 INFO @ Mon, 12 Aug 2019 22:26:59: 26000000 INFO @ Mon, 12 Aug 2019 22:27:05: 24000000 INFO @ Mon, 12 Aug 2019 22:27:06: 27000000 INFO @ Mon, 12 Aug 2019 22:27:06: 21000000 INFO @ Mon, 12 Aug 2019 22:27:13: 25000000 INFO @ Mon, 12 Aug 2019 22:27:13: 28000000 INFO @ Mon, 12 Aug 2019 22:27:16: 22000000 INFO @ Mon, 12 Aug 2019 22:27:21: 29000000 INFO @ Mon, 12 Aug 2019 22:27:21: 26000000 INFO @ Mon, 12 Aug 2019 22:27:26: 23000000 INFO @ Mon, 12 Aug 2019 22:27:28: 30000000 INFO @ Mon, 12 Aug 2019 22:27:29: 27000000 INFO @ Mon, 12 Aug 2019 22:27:35: 31000000 INFO @ Mon, 12 Aug 2019 22:27:36: 24000000 INFO @ Mon, 12 Aug 2019 22:27:37: 28000000 INFO @ Mon, 12 Aug 2019 22:27:43: 32000000 INFO @ Mon, 12 Aug 2019 22:27:46: 29000000 INFO @ Mon, 12 Aug 2019 22:27:46: 25000000 INFO @ Mon, 12 Aug 2019 22:27:50: 33000000 INFO @ Mon, 12 Aug 2019 22:27:54: 30000000 INFO @ Mon, 12 Aug 2019 22:27:56: 26000000 INFO @ Mon, 12 Aug 2019 22:27:57: 34000000 INFO @ Mon, 12 Aug 2019 22:28:02: 31000000 INFO @ Mon, 12 Aug 2019 22:28:04: 35000000 INFO @ Mon, 12 Aug 2019 22:28:05: 27000000 INFO @ Mon, 12 Aug 2019 22:28:10: 32000000 INFO @ Mon, 12 Aug 2019 22:28:11: 36000000 INFO @ Mon, 12 Aug 2019 22:28:15: 28000000 INFO @ Mon, 12 Aug 2019 22:28:18: 37000000 INFO @ Mon, 12 Aug 2019 22:28:18: 33000000 INFO @ Mon, 12 Aug 2019 22:28:25: 29000000 INFO @ Mon, 12 Aug 2019 22:28:25: 38000000 INFO @ Mon, 12 Aug 2019 22:28:27: 34000000 INFO @ Mon, 12 Aug 2019 22:28:30: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:28:30: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:28:30: #1 total tags in treatment: 38535630 INFO @ Mon, 12 Aug 2019 22:28:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:28:30: #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 22:28:30: #1 tags after filtering in treatment: 38535630 INFO @ Mon, 12 Aug 2019 22:28:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:28:30: #1 finished! INFO @ Mon, 12 Aug 2019 22:28:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:28:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:28:34: #2 number of paired peaks: 491 WARNING @ Mon, 12 Aug 2019 22:28:34: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 12 Aug 2019 22:28:34: start model_add_line... INFO @ Mon, 12 Aug 2019 22:28:34: start X-correlation... INFO @ Mon, 12 Aug 2019 22:28:34: end of X-cor INFO @ Mon, 12 Aug 2019 22:28:34: #2 finished! INFO @ Mon, 12 Aug 2019 22:28:34: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 22:28:34: #2 alternative fragment length(s) may be 4,115 bps INFO @ Mon, 12 Aug 2019 22:28:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.10_model.r INFO @ Mon, 12 Aug 2019 22:28:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:28:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:28:34: 35000000 INFO @ Mon, 12 Aug 2019 22:28:36: 30000000 INFO @ Mon, 12 Aug 2019 22:28:42: 36000000 INFO @ Mon, 12 Aug 2019 22:28:46: 31000000 INFO @ Mon, 12 Aug 2019 22:28:50: 37000000 INFO @ Mon, 12 Aug 2019 22:28:56: 32000000 INFO @ Mon, 12 Aug 2019 22:28:58: 38000000 INFO @ Mon, 12 Aug 2019 22:29:03: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:29:03: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:29:03: #1 total tags in treatment: 38535630 INFO @ Mon, 12 Aug 2019 22:29:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:29:03: #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 22:29:03: #1 tags after filtering in treatment: 38535630 INFO @ Mon, 12 Aug 2019 22:29:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:29:03: #1 finished! INFO @ Mon, 12 Aug 2019 22:29:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:29:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:29:05: 33000000 INFO @ Mon, 12 Aug 2019 22:29:07: #2 number of paired peaks: 491 WARNING @ Mon, 12 Aug 2019 22:29:07: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 12 Aug 2019 22:29:07: start model_add_line... INFO @ Mon, 12 Aug 2019 22:29:07: start X-correlation... INFO @ Mon, 12 Aug 2019 22:29:07: end of X-cor INFO @ Mon, 12 Aug 2019 22:29:07: #2 finished! INFO @ Mon, 12 Aug 2019 22:29:07: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 22:29:07: #2 alternative fragment length(s) may be 4,115 bps INFO @ Mon, 12 Aug 2019 22:29:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.20_model.r INFO @ Mon, 12 Aug 2019 22:29:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:29:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:29:15: 34000000 INFO @ Mon, 12 Aug 2019 22:29:23: 35000000 INFO @ Mon, 12 Aug 2019 22:29:33: 36000000 INFO @ Mon, 12 Aug 2019 22:29:42: 37000000 INFO @ Mon, 12 Aug 2019 22:29:51: 38000000 INFO @ Mon, 12 Aug 2019 22:29:56: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:29:56: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:29:56: #1 total tags in treatment: 38535630 INFO @ Mon, 12 Aug 2019 22:29:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:29:56: #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 22:29:56: #1 tags after filtering in treatment: 38535630 INFO @ Mon, 12 Aug 2019 22:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:29:56: #1 finished! INFO @ Mon, 12 Aug 2019 22:29:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:30:00: #2 number of paired peaks: 491 WARNING @ Mon, 12 Aug 2019 22:30:00: Fewer paired peaks (491) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 491 pairs to build model! INFO @ Mon, 12 Aug 2019 22:30:00: start model_add_line... INFO @ Mon, 12 Aug 2019 22:30:00: start X-correlation... INFO @ Mon, 12 Aug 2019 22:30:00: end of X-cor INFO @ Mon, 12 Aug 2019 22:30:00: #2 finished! INFO @ Mon, 12 Aug 2019 22:30:00: #2 predicted fragment length is 115 bps INFO @ Mon, 12 Aug 2019 22:30:00: #2 alternative fragment length(s) may be 4,115 bps INFO @ Mon, 12 Aug 2019 22:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.05_model.r INFO @ Mon, 12 Aug 2019 22:30:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:30:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:30:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:30:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:30:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:30:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.10_summits.bed INFO @ Mon, 12 Aug 2019 22:30:41: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7127 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.20_summits.bed INFO @ Mon, 12 Aug 2019 22:31:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2777 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:31:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:32:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:32:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:32:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981684/SRX3981684.05_summits.bed INFO @ Mon, 12 Aug 2019 22:32:08: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11766 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。