Job ID = 4288963 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,499,306 reads read : 46,998,612 reads written : 23,499,306 reads 0-length : 23,499,306 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: 00:00:01 Multiseed full-index search: 00:30:01 23499306 reads; of these: 23499306 (100.00%) were unpaired; of these: 2603812 (11.08%) aligned 0 times 17235465 (73.34%) aligned exactly 1 time 3660029 (15.58%) aligned >1 times 88.92% overall alignment rate Time searching: 00:30:03 Overall time: 00:30:03 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 12 files... [bam_rmdupse_core] 2886061 / 20895494 = 0.1381 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:43:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.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 13:43:41: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:43:41: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:43:52: 1000000 INFO @ Tue, 10 Dec 2019 13:44:03: 2000000 INFO @ Tue, 10 Dec 2019 13:44:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.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 13:44:10: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:44:10: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:44:14: 3000000 INFO @ Tue, 10 Dec 2019 13:44:20: 1000000 INFO @ Tue, 10 Dec 2019 13:44:25: 4000000 INFO @ Tue, 10 Dec 2019 13:44:30: 2000000 INFO @ Tue, 10 Dec 2019 13:44:37: 5000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:44:40: 3000000 INFO @ Tue, 10 Dec 2019 13:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.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 13:44:41: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:44:41: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:44:49: 6000000 INFO @ Tue, 10 Dec 2019 13:44:50: 4000000 INFO @ Tue, 10 Dec 2019 13:44:55: 1000000 INFO @ Tue, 10 Dec 2019 13:45:00: 5000000 INFO @ Tue, 10 Dec 2019 13:45:01: 7000000 INFO @ Tue, 10 Dec 2019 13:45:08: 2000000 INFO @ Tue, 10 Dec 2019 13:45:10: 6000000 INFO @ Tue, 10 Dec 2019 13:45:13: 8000000 INFO @ Tue, 10 Dec 2019 13:45:21: 7000000 INFO @ Tue, 10 Dec 2019 13:45:22: 3000000 INFO @ Tue, 10 Dec 2019 13:45:25: 9000000 INFO @ Tue, 10 Dec 2019 13:45:31: 8000000 INFO @ Tue, 10 Dec 2019 13:45:37: 4000000 INFO @ Tue, 10 Dec 2019 13:45:37: 10000000 INFO @ Tue, 10 Dec 2019 13:45:41: 9000000 INFO @ Tue, 10 Dec 2019 13:45:49: 11000000 INFO @ Tue, 10 Dec 2019 13:45:50: 5000000 INFO @ Tue, 10 Dec 2019 13:45:51: 10000000 INFO @ Tue, 10 Dec 2019 13:46:00: 12000000 INFO @ Tue, 10 Dec 2019 13:46:01: 11000000 INFO @ Tue, 10 Dec 2019 13:46:04: 6000000 INFO @ Tue, 10 Dec 2019 13:46:11: 12000000 INFO @ Tue, 10 Dec 2019 13:46:12: 13000000 INFO @ Tue, 10 Dec 2019 13:46:17: 7000000 INFO @ Tue, 10 Dec 2019 13:46:20: 13000000 INFO @ Tue, 10 Dec 2019 13:46:23: 14000000 INFO @ Tue, 10 Dec 2019 13:46:30: 14000000 INFO @ Tue, 10 Dec 2019 13:46:31: 8000000 INFO @ Tue, 10 Dec 2019 13:46:35: 15000000 INFO @ Tue, 10 Dec 2019 13:46:40: 15000000 INFO @ Tue, 10 Dec 2019 13:46:44: 9000000 INFO @ Tue, 10 Dec 2019 13:46:47: 16000000 INFO @ Tue, 10 Dec 2019 13:46:50: 16000000 INFO @ Tue, 10 Dec 2019 13:46:57: 10000000 INFO @ Tue, 10 Dec 2019 13:46:58: 17000000 INFO @ Tue, 10 Dec 2019 13:47:00: 17000000 INFO @ Tue, 10 Dec 2019 13:47:10: 18000000 INFO @ Tue, 10 Dec 2019 13:47:10: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:47:10: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:47:10: #1 total tags in treatment: 18009433 INFO @ Tue, 10 Dec 2019 13:47:10: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:47:10: #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 13:47:10: 18000000 INFO @ Tue, 10 Dec 2019 13:47:10: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:47:10: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:47:10: #1 total tags in treatment: 18009433 INFO @ Tue, 10 Dec 2019 13:47:10: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:47:10: #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 13:47:10: #1 tags after filtering in treatment: 18009252 INFO @ Tue, 10 Dec 2019 13:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:47:10: #1 finished! INFO @ Tue, 10 Dec 2019 13:47:10: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:47:11: 11000000 INFO @ Tue, 10 Dec 2019 13:47:11: #1 tags after filtering in treatment: 18009252 INFO @ Tue, 10 Dec 2019 13:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:47:11: #1 finished! INFO @ Tue, 10 Dec 2019 13:47:11: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:47:14: #2 number of paired peaks: 46030 INFO @ Tue, 10 Dec 2019 13:47:14: start model_add_line... INFO @ Tue, 10 Dec 2019 13:47:14: start X-correlation... INFO @ Tue, 10 Dec 2019 13:47:14: end of X-cor INFO @ Tue, 10 Dec 2019 13:47:14: #2 finished! INFO @ Tue, 10 Dec 2019 13:47:14: #2 predicted fragment length is 136 bps INFO @ Tue, 10 Dec 2019 13:47:14: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 10 Dec 2019 13:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.05_model.r WARNING @ Tue, 10 Dec 2019 13:47:14: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:47:14: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 10 Dec 2019 13:47:14: #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 13:47:14: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:47:14: #2 number of paired peaks: 46030 INFO @ Tue, 10 Dec 2019 13:47:14: start model_add_line... INFO @ Tue, 10 Dec 2019 13:47:15: start X-correlation... INFO @ Tue, 10 Dec 2019 13:47:15: end of X-cor INFO @ Tue, 10 Dec 2019 13:47:15: #2 finished! INFO @ Tue, 10 Dec 2019 13:47:15: #2 predicted fragment length is 136 bps INFO @ Tue, 10 Dec 2019 13:47:15: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 10 Dec 2019 13:47:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.10_model.r WARNING @ Tue, 10 Dec 2019 13:47:15: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:47:15: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 10 Dec 2019 13:47:15: #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 13:47:15: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:47:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:47:23: 12000000 INFO @ Tue, 10 Dec 2019 13:47:36: 13000000 INFO @ Tue, 10 Dec 2019 13:47:48: 14000000 INFO @ Tue, 10 Dec 2019 13:48:01: 15000000 INFO @ Tue, 10 Dec 2019 13:48:12: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:48:12: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:48:13: 16000000 INFO @ Tue, 10 Dec 2019 13:48:26: 17000000 INFO @ Tue, 10 Dec 2019 13:48:39: 18000000 INFO @ Tue, 10 Dec 2019 13:48:39: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:48:39: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:48:39: #1 total tags in treatment: 18009433 INFO @ Tue, 10 Dec 2019 13:48:39: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:48:39: #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 13:48:40: #1 tags after filtering in treatment: 18009252 INFO @ Tue, 10 Dec 2019 13:48:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:48:40: #1 finished! INFO @ Tue, 10 Dec 2019 13:48:40: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.10_summits.bed INFO @ Tue, 10 Dec 2019 13:48:41: Done! INFO @ Tue, 10 Dec 2019 13:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.05_peaks.xls pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (6919 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.05_summits.bed INFO @ Tue, 10 Dec 2019 13:48:41: Done! pass1 - making usageList (78 chroms): 2 millis pass2 - checking and writing primary data (11423 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:48:44: #2 number of paired peaks: 46030 INFO @ Tue, 10 Dec 2019 13:48:44: start model_add_line... INFO @ Tue, 10 Dec 2019 13:48:44: start X-correlation... INFO @ Tue, 10 Dec 2019 13:48:44: end of X-cor INFO @ Tue, 10 Dec 2019 13:48:44: #2 finished! INFO @ Tue, 10 Dec 2019 13:48:44: #2 predicted fragment length is 136 bps INFO @ Tue, 10 Dec 2019 13:48:44: #2 alternative fragment length(s) may be 136 bps INFO @ Tue, 10 Dec 2019 13:48:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.20_model.r WARNING @ Tue, 10 Dec 2019 13:48:44: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:48:44: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Tue, 10 Dec 2019 13:48:44: #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 13:48:44: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:48:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:49:42: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460583/SRX5460583.20_summits.bed INFO @ Tue, 10 Dec 2019 13:50:11: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (2475 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。