Job ID = 2003702 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 74,610,975 reads read : 149,221,950 reads written : 74,610,975 reads 0-length : 74,610,975 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:23:15 74610975 reads; of these: 74610975 (100.00%) were unpaired; of these: 3047368 (4.08%) aligned 0 times 51785018 (69.41%) aligned exactly 1 time 19778589 (26.51%) aligned >1 times 95.92% overall alignment rate Time searching: 01:23:18 Overall time: 01:23:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 32 files... [bam_rmdupse_core] 38413576 / 71563607 = 0.5368 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 @ Fri, 05 Jul 2019 16:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 16:24:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:24:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 16:24:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:24:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:24:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 05 Jul 2019 16:24:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 16:24:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 16:24:57: 1000000 INFO @ Fri, 05 Jul 2019 16:24:57: 1000000 INFO @ Fri, 05 Jul 2019 16:24:58: 1000000 INFO @ Fri, 05 Jul 2019 16:25:07: 2000000 INFO @ Fri, 05 Jul 2019 16:25:07: 2000000 INFO @ Fri, 05 Jul 2019 16:25:08: 2000000 INFO @ Fri, 05 Jul 2019 16:25:17: 3000000 INFO @ Fri, 05 Jul 2019 16:25:17: 3000000 INFO @ Fri, 05 Jul 2019 16:25:18: 3000000 INFO @ Fri, 05 Jul 2019 16:25:26: 4000000 INFO @ Fri, 05 Jul 2019 16:25:27: 4000000 INFO @ Fri, 05 Jul 2019 16:25:28: 4000000 INFO @ Fri, 05 Jul 2019 16:25:36: 5000000 INFO @ Fri, 05 Jul 2019 16:25:37: 5000000 INFO @ Fri, 05 Jul 2019 16:25:37: 5000000 INFO @ Fri, 05 Jul 2019 16:25:45: 6000000 INFO @ Fri, 05 Jul 2019 16:25:47: 6000000 INFO @ Fri, 05 Jul 2019 16:25:47: 6000000 INFO @ Fri, 05 Jul 2019 16:25:54: 7000000 INFO @ Fri, 05 Jul 2019 16:25:56: 7000000 INFO @ Fri, 05 Jul 2019 16:25:56: 7000000 INFO @ Fri, 05 Jul 2019 16:26:03: 8000000 INFO @ Fri, 05 Jul 2019 16:26:05: 8000000 INFO @ Fri, 05 Jul 2019 16:26:06: 8000000 INFO @ Fri, 05 Jul 2019 16:26:13: 9000000 INFO @ Fri, 05 Jul 2019 16:26:15: 9000000 INFO @ Fri, 05 Jul 2019 16:26:15: 9000000 INFO @ Fri, 05 Jul 2019 16:26:22: 10000000 INFO @ Fri, 05 Jul 2019 16:26:25: 10000000 INFO @ Fri, 05 Jul 2019 16:26:25: 10000000 INFO @ Fri, 05 Jul 2019 16:26:31: 11000000 INFO @ Fri, 05 Jul 2019 16:26:34: 11000000 INFO @ Fri, 05 Jul 2019 16:26:34: 11000000 INFO @ Fri, 05 Jul 2019 16:26:40: 12000000 INFO @ Fri, 05 Jul 2019 16:26:44: 12000000 INFO @ Fri, 05 Jul 2019 16:26:44: 12000000 INFO @ Fri, 05 Jul 2019 16:26:49: 13000000 INFO @ Fri, 05 Jul 2019 16:26:53: 13000000 INFO @ Fri, 05 Jul 2019 16:26:53: 13000000 INFO @ Fri, 05 Jul 2019 16:26:58: 14000000 INFO @ Fri, 05 Jul 2019 16:27:02: 14000000 INFO @ Fri, 05 Jul 2019 16:27:02: 14000000 INFO @ Fri, 05 Jul 2019 16:27:07: 15000000 INFO @ Fri, 05 Jul 2019 16:27:12: 15000000 INFO @ Fri, 05 Jul 2019 16:27:12: 15000000 INFO @ Fri, 05 Jul 2019 16:27:16: 16000000 INFO @ Fri, 05 Jul 2019 16:27:21: 16000000 INFO @ Fri, 05 Jul 2019 16:27:21: 16000000 INFO @ Fri, 05 Jul 2019 16:27:25: 17000000 INFO @ Fri, 05 Jul 2019 16:27:30: 17000000 INFO @ Fri, 05 Jul 2019 16:27:30: 17000000 INFO @ Fri, 05 Jul 2019 16:27:34: 18000000 INFO @ Fri, 05 Jul 2019 16:27:40: 18000000 INFO @ Fri, 05 Jul 2019 16:27:40: 18000000 INFO @ Fri, 05 Jul 2019 16:27:43: 19000000 INFO @ Fri, 05 Jul 2019 16:27:49: 19000000 INFO @ Fri, 05 Jul 2019 16:27:50: 19000000 INFO @ Fri, 05 Jul 2019 16:27:53: 20000000 INFO @ Fri, 05 Jul 2019 16:27:59: 20000000 INFO @ Fri, 05 Jul 2019 16:27:59: 20000000 INFO @ Fri, 05 Jul 2019 16:28:02: 21000000 INFO @ Fri, 05 Jul 2019 16:28:09: 21000000 INFO @ Fri, 05 Jul 2019 16:28:09: 21000000 INFO @ Fri, 05 Jul 2019 16:28:11: 22000000 INFO @ Fri, 05 Jul 2019 16:28:19: 22000000 INFO @ Fri, 05 Jul 2019 16:28:19: 22000000 INFO @ Fri, 05 Jul 2019 16:28:21: 23000000 INFO @ Fri, 05 Jul 2019 16:28:28: 23000000 INFO @ Fri, 05 Jul 2019 16:28:29: 23000000 INFO @ Fri, 05 Jul 2019 16:28:30: 24000000 INFO @ Fri, 05 Jul 2019 16:28:38: 24000000 INFO @ Fri, 05 Jul 2019 16:28:38: 24000000 INFO @ Fri, 05 Jul 2019 16:28:39: 25000000 INFO @ Fri, 05 Jul 2019 16:28:48: 25000000 INFO @ Fri, 05 Jul 2019 16:28:48: 25000000 INFO @ Fri, 05 Jul 2019 16:28:48: 26000000 INFO @ Fri, 05 Jul 2019 16:28:57: 26000000 INFO @ Fri, 05 Jul 2019 16:28:57: 26000000 INFO @ Fri, 05 Jul 2019 16:28:58: 27000000 INFO @ Fri, 05 Jul 2019 16:29:07: 27000000 INFO @ Fri, 05 Jul 2019 16:29:07: 28000000 INFO @ Fri, 05 Jul 2019 16:29:07: 27000000 INFO @ Fri, 05 Jul 2019 16:29:16: 29000000 INFO @ Fri, 05 Jul 2019 16:29:17: 28000000 INFO @ Fri, 05 Jul 2019 16:29:17: 28000000 INFO @ Fri, 05 Jul 2019 16:29:25: 30000000 INFO @ Fri, 05 Jul 2019 16:29:26: 29000000 INFO @ Fri, 05 Jul 2019 16:29:26: 29000000 INFO @ Fri, 05 Jul 2019 16:29:34: 31000000 INFO @ Fri, 05 Jul 2019 16:29:36: 30000000 INFO @ Fri, 05 Jul 2019 16:29:36: 30000000 INFO @ Fri, 05 Jul 2019 16:29:44: 32000000 INFO @ Fri, 05 Jul 2019 16:29:45: 31000000 INFO @ Fri, 05 Jul 2019 16:29:46: 31000000 INFO @ Fri, 05 Jul 2019 16:29:53: 33000000 INFO @ Fri, 05 Jul 2019 16:29:55: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:29:55: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:29:55: #1 total tags in treatment: 33150031 INFO @ Fri, 05 Jul 2019 16:29:55: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:29:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:29:55: 32000000 INFO @ Fri, 05 Jul 2019 16:29:55: #1 tags after filtering in treatment: 33149957 INFO @ Fri, 05 Jul 2019 16:29:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:29:55: #1 finished! INFO @ Fri, 05 Jul 2019 16:29:55: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:29:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:29:56: 32000000 INFO @ Fri, 05 Jul 2019 16:30:00: #2 number of paired peaks: 18243 INFO @ Fri, 05 Jul 2019 16:30:00: start model_add_line... INFO @ Fri, 05 Jul 2019 16:30:00: start X-correlation... INFO @ Fri, 05 Jul 2019 16:30:00: end of X-cor INFO @ Fri, 05 Jul 2019 16:30:00: #2 finished! INFO @ Fri, 05 Jul 2019 16:30:00: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 16:30:00: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 05 Jul 2019 16:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.10_model.r WARNING @ Fri, 05 Jul 2019 16:30:00: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:30:00: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Fri, 05 Jul 2019 16:30:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:30:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:30:05: 33000000 INFO @ Fri, 05 Jul 2019 16:30:05: 33000000 INFO @ Fri, 05 Jul 2019 16:30:07: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:30:07: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:30:07: #1 total tags in treatment: 33150031 INFO @ Fri, 05 Jul 2019 16:30:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:30:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:30:07: #1 tag size is determined as 75 bps INFO @ Fri, 05 Jul 2019 16:30:07: #1 tag size = 75 INFO @ Fri, 05 Jul 2019 16:30:07: #1 total tags in treatment: 33150031 INFO @ Fri, 05 Jul 2019 16:30:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 16:30:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 16:30:08: #1 tags after filtering in treatment: 33149957 INFO @ Fri, 05 Jul 2019 16:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:30:08: #1 finished! INFO @ Fri, 05 Jul 2019 16:30:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:30:08: #1 tags after filtering in treatment: 33149957 INFO @ Fri, 05 Jul 2019 16:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 16:30:08: #1 finished! INFO @ Fri, 05 Jul 2019 16:30:08: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 16:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 16:30:12: #2 number of paired peaks: 18243 INFO @ Fri, 05 Jul 2019 16:30:12: start model_add_line... INFO @ Fri, 05 Jul 2019 16:30:12: #2 number of paired peaks: 18243 INFO @ Fri, 05 Jul 2019 16:30:12: start model_add_line... INFO @ Fri, 05 Jul 2019 16:30:13: start X-correlation... INFO @ Fri, 05 Jul 2019 16:30:13: end of X-cor INFO @ Fri, 05 Jul 2019 16:30:13: #2 finished! INFO @ Fri, 05 Jul 2019 16:30:13: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 16:30:13: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 05 Jul 2019 16:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.20_model.r WARNING @ Fri, 05 Jul 2019 16:30:13: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:30:13: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Fri, 05 Jul 2019 16:30:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:30:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:30:13: start X-correlation... INFO @ Fri, 05 Jul 2019 16:30:13: end of X-cor INFO @ Fri, 05 Jul 2019 16:30:13: #2 finished! INFO @ Fri, 05 Jul 2019 16:30:13: #2 predicted fragment length is 80 bps INFO @ Fri, 05 Jul 2019 16:30:13: #2 alternative fragment length(s) may be 80 bps INFO @ Fri, 05 Jul 2019 16:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.05_model.r WARNING @ Fri, 05 Jul 2019 16:30:13: #2 Since the d (80) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 16:30:13: #2 You may need to consider one of the other alternative d(s): 80 WARNING @ Fri, 05 Jul 2019 16:30:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 16:30:13: #3 Call peaks... INFO @ Fri, 05 Jul 2019 16:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 16:31:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:31:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:31:57: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 16:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.10_peaks.xls INFO @ Fri, 05 Jul 2019 16:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.10_summits.bed INFO @ Fri, 05 Jul 2019 16:32:37: Done! pass1 - making usageList (59 chroms): 2 millis pass2 - checking and writing primary data (1766 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 16:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.20_peaks.xls INFO @ Fri, 05 Jul 2019 16:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.20_summits.bed INFO @ Fri, 05 Jul 2019 16:32:51: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (707 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 16:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.05_peaks.xls INFO @ Fri, 05 Jul 2019 16:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 16:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4370841/SRX4370841.05_summits.bed INFO @ Fri, 05 Jul 2019 16:32:51: Done! pass1 - making usageList (92 chroms): 2 millis pass2 - checking and writing primary data (6187 records, 4 fields): 15 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。