Job ID = 4288825 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,487,642 reads read : 38,975,284 reads written : 19,487,642 reads 0-length : 19,487,642 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: 00:17:39 19487642 reads; of these: 19487642 (100.00%) were unpaired; of these: 930926 (4.78%) aligned 0 times 12818890 (65.78%) aligned exactly 1 time 5737826 (29.44%) aligned >1 times 95.22% overall alignment rate Time searching: 00:17:42 Overall time: 00:17:42 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 8 files... [bam_rmdupse_core] 797087 / 18556716 = 0.0430 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.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 @ Tue, 10 Dec 2019 12:38:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:38:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:38:10: 1000000 INFO @ Tue, 10 Dec 2019 12:38:18: 2000000 INFO @ Tue, 10 Dec 2019 12:38:26: 3000000 INFO @ Tue, 10 Dec 2019 12:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.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 @ Tue, 10 Dec 2019 12:38:32: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:38:32: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:38:34: 4000000 INFO @ Tue, 10 Dec 2019 12:38:41: 1000000 INFO @ Tue, 10 Dec 2019 12:38:42: 5000000 INFO @ Tue, 10 Dec 2019 12:38:51: 6000000 INFO @ Tue, 10 Dec 2019 12:38:51: 2000000 INFO @ Tue, 10 Dec 2019 12:38:59: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:39:01: 3000000 INFO @ Tue, 10 Dec 2019 12:39:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.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 @ Tue, 10 Dec 2019 12:39:02: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:39:02: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:39:07: 8000000 INFO @ Tue, 10 Dec 2019 12:39:10: 1000000 INFO @ Tue, 10 Dec 2019 12:39:10: 4000000 INFO @ Tue, 10 Dec 2019 12:39:15: 9000000 INFO @ Tue, 10 Dec 2019 12:39:17: 2000000 INFO @ Tue, 10 Dec 2019 12:39:20: 5000000 INFO @ Tue, 10 Dec 2019 12:39:23: 10000000 INFO @ Tue, 10 Dec 2019 12:39:25: 3000000 INFO @ Tue, 10 Dec 2019 12:39:29: 6000000 INFO @ Tue, 10 Dec 2019 12:39:31: 11000000 INFO @ Tue, 10 Dec 2019 12:39:32: 4000000 INFO @ Tue, 10 Dec 2019 12:39:39: 7000000 INFO @ Tue, 10 Dec 2019 12:39:39: 12000000 INFO @ Tue, 10 Dec 2019 12:39:40: 5000000 INFO @ Tue, 10 Dec 2019 12:39:48: 13000000 INFO @ Tue, 10 Dec 2019 12:39:48: 6000000 INFO @ Tue, 10 Dec 2019 12:39:48: 8000000 INFO @ Tue, 10 Dec 2019 12:39:55: 7000000 INFO @ Tue, 10 Dec 2019 12:39:56: 14000000 INFO @ Tue, 10 Dec 2019 12:39:57: 9000000 INFO @ Tue, 10 Dec 2019 12:40:02: 8000000 INFO @ Tue, 10 Dec 2019 12:40:04: 15000000 INFO @ Tue, 10 Dec 2019 12:40:06: 10000000 INFO @ Tue, 10 Dec 2019 12:40:10: 9000000 INFO @ Tue, 10 Dec 2019 12:40:12: 16000000 INFO @ Tue, 10 Dec 2019 12:40:16: 11000000 INFO @ Tue, 10 Dec 2019 12:40:17: 10000000 INFO @ Tue, 10 Dec 2019 12:40:20: 17000000 INFO @ Tue, 10 Dec 2019 12:40:24: 11000000 INFO @ Tue, 10 Dec 2019 12:40:25: 12000000 INFO @ Tue, 10 Dec 2019 12:40:26: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:40:26: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:40:26: #1 total tags in treatment: 17759629 INFO @ Tue, 10 Dec 2019 12:40:26: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:40:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:40:27: #1 tags after filtering in treatment: 17759489 INFO @ Tue, 10 Dec 2019 12:40:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:40:27: #1 finished! INFO @ Tue, 10 Dec 2019 12:40:27: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:40:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:40:29: #2 number of paired peaks: 6414 INFO @ Tue, 10 Dec 2019 12:40:29: start model_add_line... INFO @ Tue, 10 Dec 2019 12:40:29: start X-correlation... INFO @ Tue, 10 Dec 2019 12:40:29: end of X-cor INFO @ Tue, 10 Dec 2019 12:40:29: #2 finished! INFO @ Tue, 10 Dec 2019 12:40:29: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:40:29: #2 alternative fragment length(s) may be 51,514,560 bps INFO @ Tue, 10 Dec 2019 12:40:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.05_model.r WARNING @ Tue, 10 Dec 2019 12:40:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:40:29: #2 You may need to consider one of the other alternative d(s): 51,514,560 WARNING @ Tue, 10 Dec 2019 12:40:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:40:29: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:40:32: 12000000 INFO @ Tue, 10 Dec 2019 12:40:35: 13000000 INFO @ Tue, 10 Dec 2019 12:40:40: 13000000 INFO @ Tue, 10 Dec 2019 12:40:44: 14000000 INFO @ Tue, 10 Dec 2019 12:40:47: 14000000 INFO @ Tue, 10 Dec 2019 12:40:53: 15000000 INFO @ Tue, 10 Dec 2019 12:40:55: 15000000 INFO @ Tue, 10 Dec 2019 12:41:02: 16000000 INFO @ Tue, 10 Dec 2019 12:41:02: 16000000 INFO @ Tue, 10 Dec 2019 12:41:10: 17000000 INFO @ Tue, 10 Dec 2019 12:41:12: 17000000 INFO @ Tue, 10 Dec 2019 12:41:16: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:41:16: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:41:16: #1 total tags in treatment: 17759629 INFO @ Tue, 10 Dec 2019 12:41:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:41:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:41:16: #1 tags after filtering in treatment: 17759489 INFO @ Tue, 10 Dec 2019 12:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:41:16: #1 finished! INFO @ Tue, 10 Dec 2019 12:41:16: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:41:18: #2 number of paired peaks: 6414 INFO @ Tue, 10 Dec 2019 12:41:18: start model_add_line... INFO @ Tue, 10 Dec 2019 12:41:19: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:41:19: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:41:19: #1 total tags in treatment: 17759629 INFO @ Tue, 10 Dec 2019 12:41:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:41:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 12:41:19: start X-correlation... INFO @ Tue, 10 Dec 2019 12:41:19: end of X-cor INFO @ Tue, 10 Dec 2019 12:41:19: #2 finished! INFO @ Tue, 10 Dec 2019 12:41:19: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:41:19: #2 alternative fragment length(s) may be 51,514,560 bps INFO @ Tue, 10 Dec 2019 12:41:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.20_model.r WARNING @ Tue, 10 Dec 2019 12:41:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:41:19: #2 You may need to consider one of the other alternative d(s): 51,514,560 WARNING @ Tue, 10 Dec 2019 12:41:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:41:19: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:41:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:41:19: #1 tags after filtering in treatment: 17759489 INFO @ Tue, 10 Dec 2019 12:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:41:19: #1 finished! INFO @ Tue, 10 Dec 2019 12:41:19: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:41:21: #2 number of paired peaks: 6414 INFO @ Tue, 10 Dec 2019 12:41:21: start model_add_line... INFO @ Tue, 10 Dec 2019 12:41:21: start X-correlation... INFO @ Tue, 10 Dec 2019 12:41:21: end of X-cor INFO @ Tue, 10 Dec 2019 12:41:21: #2 finished! INFO @ Tue, 10 Dec 2019 12:41:21: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:41:21: #2 alternative fragment length(s) may be 51,514,560 bps INFO @ Tue, 10 Dec 2019 12:41:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.10_model.r WARNING @ Tue, 10 Dec 2019 12:41:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:41:22: #2 You may need to consider one of the other alternative d(s): 51,514,560 WARNING @ Tue, 10 Dec 2019 12:41:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 12:41:22: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:41:26: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:41:53: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:41:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:41:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.05_summits.bed INFO @ Tue, 10 Dec 2019 12:41:53: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (1828 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:42:15: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:42:18: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.20_summits.bed INFO @ Tue, 10 Dec 2019 12:42:42: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (396 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654072/SRX4654072.10_summits.bed INFO @ Tue, 10 Dec 2019 12:42:45: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (934 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。