Job ID = 2590354 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,060,408 reads read : 28,120,816 reads written : 14,060,408 reads 0-length : 14,060,408 spots read : 13,860,439 reads read : 27,720,878 reads written : 13,860,439 reads 0-length : 13,860,439 spots read : 14,040,987 reads read : 28,081,974 reads written : 14,040,987 reads 0-length : 14,040,987 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: 00:13:37 41961834 reads; of these: 41961834 (100.00%) were unpaired; of these: 1852957 (4.42%) aligned 0 times 32127321 (76.56%) aligned exactly 1 time 7981556 (19.02%) aligned >1 times 95.58% overall alignment rate Time searching: 00:13:37 Overall time: 00:13:37 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] 6793261 / 40108877 = 0.1694 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 21:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.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 21:33:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:33:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.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 21:33:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:33:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:33:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.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 21:33:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:33:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:33:46: 1000000 INFO @ Mon, 12 Aug 2019 21:33:47: 1000000 INFO @ Mon, 12 Aug 2019 21:33:47: 1000000 INFO @ Mon, 12 Aug 2019 21:33:55: 2000000 INFO @ Mon, 12 Aug 2019 21:33:56: 2000000 INFO @ Mon, 12 Aug 2019 21:33:57: 2000000 INFO @ Mon, 12 Aug 2019 21:34:05: 3000000 INFO @ Mon, 12 Aug 2019 21:34:05: 3000000 INFO @ Mon, 12 Aug 2019 21:34:07: 3000000 INFO @ Mon, 12 Aug 2019 21:34:13: 4000000 INFO @ Mon, 12 Aug 2019 21:34:14: 4000000 INFO @ Mon, 12 Aug 2019 21:34:16: 4000000 INFO @ Mon, 12 Aug 2019 21:34:22: 5000000 INFO @ Mon, 12 Aug 2019 21:34:24: 5000000 INFO @ Mon, 12 Aug 2019 21:34:26: 5000000 INFO @ Mon, 12 Aug 2019 21:34:31: 6000000 INFO @ Mon, 12 Aug 2019 21:34:33: 6000000 INFO @ Mon, 12 Aug 2019 21:34:35: 6000000 INFO @ Mon, 12 Aug 2019 21:34:39: 7000000 INFO @ Mon, 12 Aug 2019 21:34:43: 7000000 INFO @ Mon, 12 Aug 2019 21:34:45: 7000000 INFO @ Mon, 12 Aug 2019 21:34:48: 8000000 INFO @ Mon, 12 Aug 2019 21:34:52: 8000000 INFO @ Mon, 12 Aug 2019 21:34:54: 8000000 INFO @ Mon, 12 Aug 2019 21:34:56: 9000000 INFO @ Mon, 12 Aug 2019 21:35:01: 9000000 INFO @ Mon, 12 Aug 2019 21:35:04: 9000000 INFO @ Mon, 12 Aug 2019 21:35:04: 10000000 INFO @ Mon, 12 Aug 2019 21:35:11: 10000000 INFO @ Mon, 12 Aug 2019 21:35:13: 11000000 INFO @ Mon, 12 Aug 2019 21:35:14: 10000000 INFO @ Mon, 12 Aug 2019 21:35:20: 11000000 INFO @ Mon, 12 Aug 2019 21:35:21: 12000000 INFO @ Mon, 12 Aug 2019 21:35:23: 11000000 INFO @ Mon, 12 Aug 2019 21:35:29: 12000000 INFO @ Mon, 12 Aug 2019 21:35:29: 13000000 INFO @ Mon, 12 Aug 2019 21:35:33: 12000000 INFO @ Mon, 12 Aug 2019 21:35:38: 14000000 INFO @ Mon, 12 Aug 2019 21:35:38: 13000000 INFO @ Mon, 12 Aug 2019 21:35:42: 13000000 INFO @ Mon, 12 Aug 2019 21:35:47: 15000000 INFO @ Mon, 12 Aug 2019 21:35:48: 14000000 INFO @ Mon, 12 Aug 2019 21:35:52: 14000000 INFO @ Mon, 12 Aug 2019 21:35:55: 16000000 INFO @ Mon, 12 Aug 2019 21:35:57: 15000000 INFO @ Mon, 12 Aug 2019 21:36:02: 15000000 INFO @ Mon, 12 Aug 2019 21:36:04: 17000000 INFO @ Mon, 12 Aug 2019 21:36:07: 16000000 INFO @ Mon, 12 Aug 2019 21:36:12: 16000000 INFO @ Mon, 12 Aug 2019 21:36:13: 18000000 INFO @ Mon, 12 Aug 2019 21:36:16: 17000000 INFO @ Mon, 12 Aug 2019 21:36:22: 19000000 INFO @ Mon, 12 Aug 2019 21:36:22: 17000000 INFO @ Mon, 12 Aug 2019 21:36:26: 18000000 INFO @ Mon, 12 Aug 2019 21:36:31: 20000000 INFO @ Mon, 12 Aug 2019 21:36:32: 18000000 INFO @ Mon, 12 Aug 2019 21:36:36: 19000000 INFO @ Mon, 12 Aug 2019 21:36:39: 21000000 INFO @ Mon, 12 Aug 2019 21:36:43: 19000000 INFO @ Mon, 12 Aug 2019 21:36:45: 20000000 INFO @ Mon, 12 Aug 2019 21:36:48: 22000000 INFO @ Mon, 12 Aug 2019 21:36:53: 20000000 INFO @ Mon, 12 Aug 2019 21:36:55: 21000000 INFO @ Mon, 12 Aug 2019 21:36:57: 23000000 INFO @ Mon, 12 Aug 2019 21:37:02: 21000000 INFO @ Mon, 12 Aug 2019 21:37:04: 22000000 INFO @ Mon, 12 Aug 2019 21:37:05: 24000000 INFO @ Mon, 12 Aug 2019 21:37:12: 22000000 INFO @ Mon, 12 Aug 2019 21:37:13: 23000000 INFO @ Mon, 12 Aug 2019 21:37:14: 25000000 INFO @ Mon, 12 Aug 2019 21:37:21: 23000000 INFO @ Mon, 12 Aug 2019 21:37:22: 26000000 INFO @ Mon, 12 Aug 2019 21:37:23: 24000000 INFO @ Mon, 12 Aug 2019 21:37:31: 27000000 INFO @ Mon, 12 Aug 2019 21:37:31: 24000000 INFO @ Mon, 12 Aug 2019 21:37:32: 25000000 INFO @ Mon, 12 Aug 2019 21:37:39: 28000000 INFO @ Mon, 12 Aug 2019 21:37:41: 25000000 INFO @ Mon, 12 Aug 2019 21:37:42: 26000000 INFO @ Mon, 12 Aug 2019 21:37:48: 29000000 INFO @ Mon, 12 Aug 2019 21:37:50: 26000000 INFO @ Mon, 12 Aug 2019 21:37:51: 27000000 INFO @ Mon, 12 Aug 2019 21:37:57: 30000000 INFO @ Mon, 12 Aug 2019 21:38:00: 27000000 INFO @ Mon, 12 Aug 2019 21:38:01: 28000000 INFO @ Mon, 12 Aug 2019 21:38:06: 31000000 INFO @ Mon, 12 Aug 2019 21:38:10: 28000000 INFO @ Mon, 12 Aug 2019 21:38:10: 29000000 INFO @ Mon, 12 Aug 2019 21:38:14: 32000000 INFO @ Mon, 12 Aug 2019 21:38:19: 29000000 INFO @ Mon, 12 Aug 2019 21:38:20: 30000000 INFO @ Mon, 12 Aug 2019 21:38:23: 33000000 INFO @ Mon, 12 Aug 2019 21:38:26: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:38:26: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:38:26: #1 total tags in treatment: 33315616 INFO @ Mon, 12 Aug 2019 21:38:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:38:26: #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 21:38:27: #1 tags after filtering in treatment: 33315616 INFO @ Mon, 12 Aug 2019 21:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:38:27: #1 finished! INFO @ Mon, 12 Aug 2019 21:38:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:38:29: 31000000 INFO @ Mon, 12 Aug 2019 21:38:29: 30000000 INFO @ Mon, 12 Aug 2019 21:38:30: #2 number of paired peaks: 272 WARNING @ Mon, 12 Aug 2019 21:38:30: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Mon, 12 Aug 2019 21:38:30: start model_add_line... INFO @ Mon, 12 Aug 2019 21:38:30: start X-correlation... INFO @ Mon, 12 Aug 2019 21:38:30: end of X-cor INFO @ Mon, 12 Aug 2019 21:38:30: #2 finished! INFO @ Mon, 12 Aug 2019 21:38:30: #2 predicted fragment length is 105 bps INFO @ Mon, 12 Aug 2019 21:38:30: #2 alternative fragment length(s) may be 3,105,131 bps INFO @ Mon, 12 Aug 2019 21:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.20_model.r INFO @ Mon, 12 Aug 2019 21:38:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:38:39: 31000000 INFO @ Mon, 12 Aug 2019 21:38:39: 32000000 INFO @ Mon, 12 Aug 2019 21:38:49: 33000000 INFO @ Mon, 12 Aug 2019 21:38:49: 32000000 INFO @ Mon, 12 Aug 2019 21:38:53: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:38:53: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:38:53: #1 total tags in treatment: 33315616 INFO @ Mon, 12 Aug 2019 21:38:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:38:53: #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 21:38:53: #1 tags after filtering in treatment: 33315616 INFO @ Mon, 12 Aug 2019 21:38:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:38:53: #1 finished! INFO @ Mon, 12 Aug 2019 21:38:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:38:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:38:56: #2 number of paired peaks: 272 WARNING @ Mon, 12 Aug 2019 21:38:56: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Mon, 12 Aug 2019 21:38:56: start model_add_line... INFO @ Mon, 12 Aug 2019 21:38:56: start X-correlation... INFO @ Mon, 12 Aug 2019 21:38:56: end of X-cor INFO @ Mon, 12 Aug 2019 21:38:56: #2 finished! INFO @ Mon, 12 Aug 2019 21:38:56: #2 predicted fragment length is 105 bps INFO @ Mon, 12 Aug 2019 21:38:56: #2 alternative fragment length(s) may be 3,105,131 bps INFO @ Mon, 12 Aug 2019 21:38:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.05_model.r INFO @ Mon, 12 Aug 2019 21:38:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:38:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:38:59: 33000000 INFO @ Mon, 12 Aug 2019 21:39:02: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 21:39:02: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 21:39:02: #1 total tags in treatment: 33315616 INFO @ Mon, 12 Aug 2019 21:39:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:39:02: #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 21:39:02: #1 tags after filtering in treatment: 33315616 INFO @ Mon, 12 Aug 2019 21:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:39:02: #1 finished! INFO @ Mon, 12 Aug 2019 21:39:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:39:05: #2 number of paired peaks: 272 WARNING @ Mon, 12 Aug 2019 21:39:05: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Mon, 12 Aug 2019 21:39:05: start model_add_line... INFO @ Mon, 12 Aug 2019 21:39:06: start X-correlation... INFO @ Mon, 12 Aug 2019 21:39:06: end of X-cor INFO @ Mon, 12 Aug 2019 21:39:06: #2 finished! INFO @ Mon, 12 Aug 2019 21:39:06: #2 predicted fragment length is 105 bps INFO @ Mon, 12 Aug 2019 21:39:06: #2 alternative fragment length(s) may be 3,105,131 bps INFO @ Mon, 12 Aug 2019 21:39:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.10_model.r INFO @ Mon, 12 Aug 2019 21:39:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:39:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:39:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:40:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:40:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:40:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:40:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:40:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.20_summits.bed INFO @ Mon, 12 Aug 2019 21:40:28: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1629 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:41:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:41:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:41:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.05_summits.bed INFO @ Mon, 12 Aug 2019 21:41:00: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10639 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:41:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:41:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:41:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981627/SRX3981627.10_summits.bed INFO @ Mon, 12 Aug 2019 21:41:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5678 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。