Job ID = 4178646 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 55,682,788 reads read : 111,365,576 reads written : 55,682,788 reads 0-length : 55,682,788 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:31:20 55682788 reads; of these: 55682788 (100.00%) were unpaired; of these: 4387750 (7.88%) aligned 0 times 16369004 (29.40%) aligned exactly 1 time 34926034 (62.72%) aligned >1 times 92.12% overall alignment rate Time searching: 01:31:21 Overall time: 01:31:21 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] 27159023 / 51295038 = 0.5295 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 15:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.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 @ Thu, 05 Dec 2019 15:38:06: #1 read tag files... INFO @ Thu, 05 Dec 2019 15:38:06: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 15:38:15: 1000000 INFO @ Thu, 05 Dec 2019 15:38:25: 2000000 INFO @ Thu, 05 Dec 2019 15:38:34: 3000000 INFO @ Thu, 05 Dec 2019 15:38:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.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 @ Thu, 05 Dec 2019 15:38:35: #1 read tag files... INFO @ Thu, 05 Dec 2019 15:38:35: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 15:38:44: 4000000 INFO @ Thu, 05 Dec 2019 15:38:45: 1000000 INFO @ Thu, 05 Dec 2019 15:38:55: 5000000 INFO @ Thu, 05 Dec 2019 15:38:56: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 15:39:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.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 @ Thu, 05 Dec 2019 15:39:05: #1 read tag files... INFO @ Thu, 05 Dec 2019 15:39:05: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 15:39:06: 6000000 INFO @ Thu, 05 Dec 2019 15:39:07: 3000000 INFO @ Thu, 05 Dec 2019 15:39:16: 1000000 INFO @ Thu, 05 Dec 2019 15:39:18: 7000000 INFO @ Thu, 05 Dec 2019 15:39:18: 4000000 INFO @ Thu, 05 Dec 2019 15:39:29: 2000000 INFO @ Thu, 05 Dec 2019 15:39:30: 5000000 INFO @ Thu, 05 Dec 2019 15:39:30: 8000000 INFO @ Thu, 05 Dec 2019 15:39:42: 3000000 INFO @ Thu, 05 Dec 2019 15:39:43: 9000000 INFO @ Thu, 05 Dec 2019 15:39:44: 6000000 INFO @ Thu, 05 Dec 2019 15:39:55: 4000000 INFO @ Thu, 05 Dec 2019 15:39:56: 10000000 INFO @ Thu, 05 Dec 2019 15:39:56: 7000000 INFO @ Thu, 05 Dec 2019 15:40:08: 5000000 INFO @ Thu, 05 Dec 2019 15:40:08: 11000000 INFO @ Thu, 05 Dec 2019 15:40:08: 8000000 INFO @ Thu, 05 Dec 2019 15:40:20: 12000000 INFO @ Thu, 05 Dec 2019 15:40:20: 9000000 INFO @ Thu, 05 Dec 2019 15:40:21: 6000000 INFO @ Thu, 05 Dec 2019 15:40:33: 10000000 INFO @ Thu, 05 Dec 2019 15:40:33: 13000000 INFO @ Thu, 05 Dec 2019 15:40:35: 7000000 INFO @ Thu, 05 Dec 2019 15:40:46: 14000000 INFO @ Thu, 05 Dec 2019 15:40:46: 11000000 INFO @ Thu, 05 Dec 2019 15:40:49: 8000000 INFO @ Thu, 05 Dec 2019 15:40:58: 15000000 INFO @ Thu, 05 Dec 2019 15:40:59: 12000000 INFO @ Thu, 05 Dec 2019 15:41:02: 9000000 INFO @ Thu, 05 Dec 2019 15:41:11: 16000000 INFO @ Thu, 05 Dec 2019 15:41:11: 13000000 INFO @ Thu, 05 Dec 2019 15:41:16: 10000000 INFO @ Thu, 05 Dec 2019 15:41:23: 17000000 INFO @ Thu, 05 Dec 2019 15:41:23: 14000000 INFO @ Thu, 05 Dec 2019 15:41:31: 11000000 INFO @ Thu, 05 Dec 2019 15:41:35: 18000000 INFO @ Thu, 05 Dec 2019 15:41:36: 15000000 INFO @ Thu, 05 Dec 2019 15:41:45: 12000000 INFO @ Thu, 05 Dec 2019 15:41:48: 19000000 INFO @ Thu, 05 Dec 2019 15:41:48: 16000000 INFO @ Thu, 05 Dec 2019 15:41:59: 13000000 INFO @ Thu, 05 Dec 2019 15:42:00: 17000000 INFO @ Thu, 05 Dec 2019 15:42:00: 20000000 INFO @ Thu, 05 Dec 2019 15:42:13: 18000000 INFO @ Thu, 05 Dec 2019 15:42:13: 14000000 INFO @ Thu, 05 Dec 2019 15:42:13: 21000000 INFO @ Thu, 05 Dec 2019 15:42:25: 19000000 INFO @ Thu, 05 Dec 2019 15:42:25: 22000000 INFO @ Thu, 05 Dec 2019 15:42:26: 15000000 INFO @ Thu, 05 Dec 2019 15:42:38: 23000000 INFO @ Thu, 05 Dec 2019 15:42:38: 20000000 INFO @ Thu, 05 Dec 2019 15:42:40: 16000000 INFO @ Thu, 05 Dec 2019 15:42:50: 24000000 INFO @ Thu, 05 Dec 2019 15:42:51: 21000000 INFO @ Thu, 05 Dec 2019 15:42:52: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 15:42:52: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 15:42:52: #1 total tags in treatment: 24136015 INFO @ Thu, 05 Dec 2019 15:42:52: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 15:42:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 15:42:52: #1 tags after filtering in treatment: 24136015 INFO @ Thu, 05 Dec 2019 15:42:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 15:42:52: #1 finished! INFO @ Thu, 05 Dec 2019 15:42:52: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 15:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 15:42:53: 17000000 INFO @ Thu, 05 Dec 2019 15:42:55: #2 number of paired peaks: 5158 INFO @ Thu, 05 Dec 2019 15:42:55: start model_add_line... INFO @ Thu, 05 Dec 2019 15:42:56: start X-correlation... INFO @ Thu, 05 Dec 2019 15:42:56: end of X-cor INFO @ Thu, 05 Dec 2019 15:42:56: #2 finished! INFO @ Thu, 05 Dec 2019 15:42:56: #2 predicted fragment length is 111 bps INFO @ Thu, 05 Dec 2019 15:42:56: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 05 Dec 2019 15:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.05_model.r INFO @ Thu, 05 Dec 2019 15:43:01: 22000000 WARNING @ Thu, 05 Dec 2019 15:43:03: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 15:43:03: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Thu, 05 Dec 2019 15:43:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 15:43:03: #3 Call peaks... INFO @ Thu, 05 Dec 2019 15:43:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 15:43:07: 18000000 INFO @ Thu, 05 Dec 2019 15:43:12: 23000000 INFO @ Thu, 05 Dec 2019 15:43:20: 19000000 INFO @ Thu, 05 Dec 2019 15:43:23: 24000000 INFO @ Thu, 05 Dec 2019 15:43:25: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 15:43:25: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 15:43:25: #1 total tags in treatment: 24136015 INFO @ Thu, 05 Dec 2019 15:43:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 15:43:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 15:43:25: #1 tags after filtering in treatment: 24136015 INFO @ Thu, 05 Dec 2019 15:43:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 15:43:25: #1 finished! INFO @ Thu, 05 Dec 2019 15:43:25: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 15:43:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 15:43:28: #2 number of paired peaks: 5158 INFO @ Thu, 05 Dec 2019 15:43:28: start model_add_line... INFO @ Thu, 05 Dec 2019 15:43:29: start X-correlation... INFO @ Thu, 05 Dec 2019 15:43:29: end of X-cor INFO @ Thu, 05 Dec 2019 15:43:29: #2 finished! INFO @ Thu, 05 Dec 2019 15:43:29: #2 predicted fragment length is 111 bps INFO @ Thu, 05 Dec 2019 15:43:29: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 05 Dec 2019 15:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.10_model.r WARNING @ Thu, 05 Dec 2019 15:43:29: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 15:43:29: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Thu, 05 Dec 2019 15:43:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 15:43:29: #3 Call peaks... INFO @ Thu, 05 Dec 2019 15:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 15:43:32: 20000000 INFO @ Thu, 05 Dec 2019 15:43:45: 21000000 INFO @ Thu, 05 Dec 2019 15:43:57: 22000000 INFO @ Thu, 05 Dec 2019 15:44:10: 23000000 INFO @ Thu, 05 Dec 2019 15:44:12: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 15:44:24: 24000000 INFO @ Thu, 05 Dec 2019 15:44:26: #1 tag size is determined as 75 bps INFO @ Thu, 05 Dec 2019 15:44:26: #1 tag size = 75 INFO @ Thu, 05 Dec 2019 15:44:26: #1 total tags in treatment: 24136015 INFO @ Thu, 05 Dec 2019 15:44:26: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 15:44:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 15:44:26: #1 tags after filtering in treatment: 24136015 INFO @ Thu, 05 Dec 2019 15:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 15:44:26: #1 finished! INFO @ Thu, 05 Dec 2019 15:44:26: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 15:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 15:44:29: #2 number of paired peaks: 5158 INFO @ Thu, 05 Dec 2019 15:44:29: start model_add_line... INFO @ Thu, 05 Dec 2019 15:44:29: start X-correlation... INFO @ Thu, 05 Dec 2019 15:44:30: end of X-cor INFO @ Thu, 05 Dec 2019 15:44:30: #2 finished! INFO @ Thu, 05 Dec 2019 15:44:30: #2 predicted fragment length is 111 bps INFO @ Thu, 05 Dec 2019 15:44:30: #2 alternative fragment length(s) may be 111 bps INFO @ Thu, 05 Dec 2019 15:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.20_model.r WARNING @ Thu, 05 Dec 2019 15:44:30: #2 Since the d (111) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 15:44:30: #2 You may need to consider one of the other alternative d(s): 111 WARNING @ Thu, 05 Dec 2019 15:44:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 15:44:30: #3 Call peaks... INFO @ Thu, 05 Dec 2019 15:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 15:44:40: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 15:44:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.05_peaks.xls INFO @ Thu, 05 Dec 2019 15:44:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 15:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.05_summits.bed INFO @ Thu, 05 Dec 2019 15:44:47: Done! pass1 - making usageList (14 chroms): 9 millis pass2 - checking and writing primary data (32568 records, 4 fields): 50 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 05 Dec 2019 15:45:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.10_peaks.xls INFO @ Thu, 05 Dec 2019 15:45:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 15:45:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.10_summits.bed INFO @ Thu, 05 Dec 2019 15:45:15: Done! pass1 - making usageList (14 chroms): 9 millis pass2 - checking and writing primary data (26363 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 15:45:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 05 Dec 2019 15:46:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.20_peaks.xls INFO @ Thu, 05 Dec 2019 15:46:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 15:46:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7158303/SRX7158303.20_summits.bed INFO @ Thu, 05 Dec 2019 15:46:05: Done! pass1 - making usageList (14 chroms): 9 millis pass2 - checking and writing primary data (18467 records, 4 fields): 31 millis CompletedMACS2peakCalling