Job ID = 2590489 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,498,121 reads read : 12,996,242 reads written : 6,498,121 reads 0-length : 6,498,121 spots read : 6,487,981 reads read : 12,975,962 reads written : 6,487,981 reads 0-length : 6,487,981 spots read : 6,523,488 reads read : 13,046,976 reads written : 6,523,488 reads 0-length : 6,523,488 spots read : 6,557,689 reads read : 13,115,378 reads written : 6,557,689 reads 0-length : 6,557,689 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: 00:08:05 26067279 reads; of these: 26067279 (100.00%) were unpaired; of these: 911306 (3.50%) aligned 0 times 20214236 (77.55%) aligned exactly 1 time 4941737 (18.96%) aligned >1 times 96.50% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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 12 files... [bam_rmdupse_core] 3825357 / 25155973 = 0.1521 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 22:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.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 22:17:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.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 22:17:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.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 22:17:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:17:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:17:53: 1000000 INFO @ Mon, 12 Aug 2019 22:17:57: 1000000 INFO @ Mon, 12 Aug 2019 22:17:58: 1000000 INFO @ Mon, 12 Aug 2019 22:18:00: 2000000 INFO @ Mon, 12 Aug 2019 22:18:06: 2000000 INFO @ Mon, 12 Aug 2019 22:18:06: 3000000 INFO @ Mon, 12 Aug 2019 22:18:07: 2000000 INFO @ Mon, 12 Aug 2019 22:18:13: 4000000 INFO @ Mon, 12 Aug 2019 22:18:15: 3000000 INFO @ Mon, 12 Aug 2019 22:18:16: 3000000 INFO @ Mon, 12 Aug 2019 22:18:19: 5000000 INFO @ Mon, 12 Aug 2019 22:18:24: 4000000 INFO @ Mon, 12 Aug 2019 22:18:25: 4000000 INFO @ Mon, 12 Aug 2019 22:18:26: 6000000 INFO @ Mon, 12 Aug 2019 22:18:32: 7000000 INFO @ Mon, 12 Aug 2019 22:18:33: 5000000 INFO @ Mon, 12 Aug 2019 22:18:34: 5000000 INFO @ Mon, 12 Aug 2019 22:18:39: 8000000 INFO @ Mon, 12 Aug 2019 22:18:41: 6000000 INFO @ Mon, 12 Aug 2019 22:18:42: 6000000 INFO @ Mon, 12 Aug 2019 22:18:45: 9000000 INFO @ Mon, 12 Aug 2019 22:18:50: 7000000 INFO @ Mon, 12 Aug 2019 22:18:50: 7000000 INFO @ Mon, 12 Aug 2019 22:18:52: 10000000 INFO @ Mon, 12 Aug 2019 22:18:58: 8000000 INFO @ Mon, 12 Aug 2019 22:18:58: 11000000 INFO @ Mon, 12 Aug 2019 22:18:59: 8000000 INFO @ Mon, 12 Aug 2019 22:19:05: 12000000 INFO @ Mon, 12 Aug 2019 22:19:06: 9000000 INFO @ Mon, 12 Aug 2019 22:19:07: 9000000 INFO @ Mon, 12 Aug 2019 22:19:11: 13000000 INFO @ Mon, 12 Aug 2019 22:19:14: 10000000 INFO @ Mon, 12 Aug 2019 22:19:15: 10000000 INFO @ Mon, 12 Aug 2019 22:19:18: 14000000 INFO @ Mon, 12 Aug 2019 22:19:23: 11000000 INFO @ Mon, 12 Aug 2019 22:19:24: 11000000 INFO @ Mon, 12 Aug 2019 22:19:24: 15000000 INFO @ Mon, 12 Aug 2019 22:19:31: 16000000 INFO @ Mon, 12 Aug 2019 22:19:31: 12000000 INFO @ Mon, 12 Aug 2019 22:19:32: 12000000 INFO @ Mon, 12 Aug 2019 22:19:37: 17000000 INFO @ Mon, 12 Aug 2019 22:19:39: 13000000 INFO @ Mon, 12 Aug 2019 22:19:40: 13000000 INFO @ Mon, 12 Aug 2019 22:19:44: 18000000 INFO @ Mon, 12 Aug 2019 22:19:48: 14000000 INFO @ Mon, 12 Aug 2019 22:19:49: 14000000 INFO @ Mon, 12 Aug 2019 22:19:51: 19000000 INFO @ Mon, 12 Aug 2019 22:19:56: 15000000 INFO @ Mon, 12 Aug 2019 22:19:57: 15000000 INFO @ Mon, 12 Aug 2019 22:19:57: 20000000 INFO @ Mon, 12 Aug 2019 22:20:04: 21000000 INFO @ Mon, 12 Aug 2019 22:20:05: 16000000 INFO @ Mon, 12 Aug 2019 22:20:05: 16000000 INFO @ Mon, 12 Aug 2019 22:20:06: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:20:06: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:20:06: #1 total tags in treatment: 21330616 INFO @ Mon, 12 Aug 2019 22:20:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:20:06: #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 22:20:06: #1 tags after filtering in treatment: 21330616 INFO @ Mon, 12 Aug 2019 22:20:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:20:06: #1 finished! INFO @ Mon, 12 Aug 2019 22:20:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:20:08: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 22:20:08: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 22:20:08: start model_add_line... INFO @ Mon, 12 Aug 2019 22:20:08: start X-correlation... INFO @ Mon, 12 Aug 2019 22:20:08: end of X-cor INFO @ Mon, 12 Aug 2019 22:20:08: #2 finished! INFO @ Mon, 12 Aug 2019 22:20:08: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 22:20:08: #2 alternative fragment length(s) may be 4,55,71 bps INFO @ Mon, 12 Aug 2019 22:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.05_model.r WARNING @ Mon, 12 Aug 2019 22:20:08: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:20:08: #2 You may need to consider one of the other alternative d(s): 4,55,71 WARNING @ Mon, 12 Aug 2019 22:20:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:20:08: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:20:13: 17000000 INFO @ Mon, 12 Aug 2019 22:20:14: 17000000 INFO @ Mon, 12 Aug 2019 22:20:21: 18000000 INFO @ Mon, 12 Aug 2019 22:20:22: 18000000 INFO @ Mon, 12 Aug 2019 22:20:29: 19000000 INFO @ Mon, 12 Aug 2019 22:20:30: 19000000 INFO @ Mon, 12 Aug 2019 22:20:38: 20000000 INFO @ Mon, 12 Aug 2019 22:20:38: 20000000 INFO @ Mon, 12 Aug 2019 22:20:46: 21000000 INFO @ Mon, 12 Aug 2019 22:20:46: 21000000 INFO @ Mon, 12 Aug 2019 22:20:49: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:20:49: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:20:49: #1 total tags in treatment: 21330616 INFO @ Mon, 12 Aug 2019 22:20:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:20:49: #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 22:20:49: #1 tags after filtering in treatment: 21330616 INFO @ Mon, 12 Aug 2019 22:20:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:20:49: #1 finished! INFO @ Mon, 12 Aug 2019 22:20:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:20:49: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:20:49: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:20:49: #1 total tags in treatment: 21330616 INFO @ Mon, 12 Aug 2019 22:20:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:20:49: #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 22:20:50: #1 tags after filtering in treatment: 21330616 INFO @ Mon, 12 Aug 2019 22:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:20:50: #1 finished! INFO @ Mon, 12 Aug 2019 22:20:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:20:51: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 22:20:51: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 22:20:51: start model_add_line... INFO @ Mon, 12 Aug 2019 22:20:51: start X-correlation... INFO @ Mon, 12 Aug 2019 22:20:51: end of X-cor INFO @ Mon, 12 Aug 2019 22:20:51: #2 finished! INFO @ Mon, 12 Aug 2019 22:20:51: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 22:20:51: #2 alternative fragment length(s) may be 4,55,71 bps INFO @ Mon, 12 Aug 2019 22:20:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.10_model.r WARNING @ Mon, 12 Aug 2019 22:20:51: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:20:51: #2 You may need to consider one of the other alternative d(s): 4,55,71 WARNING @ Mon, 12 Aug 2019 22:20:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:20:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:20:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:20:52: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 22:20:52: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 22:20:52: start model_add_line... INFO @ Mon, 12 Aug 2019 22:20:52: start X-correlation... INFO @ Mon, 12 Aug 2019 22:20:52: end of X-cor INFO @ Mon, 12 Aug 2019 22:20:52: #2 finished! INFO @ Mon, 12 Aug 2019 22:20:52: #2 predicted fragment length is 55 bps INFO @ Mon, 12 Aug 2019 22:20:52: #2 alternative fragment length(s) may be 4,55,71 bps INFO @ Mon, 12 Aug 2019 22:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.20_model.r WARNING @ Mon, 12 Aug 2019 22:20:52: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:20:52: #2 You may need to consider one of the other alternative d(s): 4,55,71 WARNING @ Mon, 12 Aug 2019 22:20:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:20:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:21:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:21:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:21:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:21:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.05_summits.bed INFO @ Mon, 12 Aug 2019 22:21:27: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5081 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:21:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:21:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:22:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.10_summits.bed INFO @ Mon, 12 Aug 2019 22:22:09: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1853 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981716/SRX3981716.20_summits.bed INFO @ Mon, 12 Aug 2019 22:22:11: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (645 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。