Job ID = 2640735 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 42,439,666 reads read : 42,439,666 reads written : 42,439,666 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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 01:22:19 42439666 reads; of these: 42439666 (100.00%) were unpaired; of these: 2224867 (5.24%) aligned 0 times 29346215 (69.15%) aligned exactly 1 time 10868584 (25.61%) aligned >1 times 94.76% overall alignment rate Time searching: 01:22:23 Overall time: 01:22:23 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 20 files... [bam_rmdupse_core] 2928056 / 40214799 = 0.0728 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.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 @ Sat, 24 Aug 2019 21:18:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:18:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:18:14: 1000000 INFO @ Sat, 24 Aug 2019 21:18:24: 2000000 INFO @ Sat, 24 Aug 2019 21:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.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 @ Sat, 24 Aug 2019 21:18:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:18:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:18:34: 3000000 INFO @ Sat, 24 Aug 2019 21:18:43: 1000000 INFO @ Sat, 24 Aug 2019 21:18:45: 4000000 INFO @ Sat, 24 Aug 2019 21:18:54: 2000000 INFO @ Sat, 24 Aug 2019 21:18:55: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.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 @ Sat, 24 Aug 2019 21:19:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:19:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:19:04: 3000000 INFO @ Sat, 24 Aug 2019 21:19:05: 6000000 INFO @ Sat, 24 Aug 2019 21:19:12: 1000000 INFO @ Sat, 24 Aug 2019 21:19:14: 4000000 INFO @ Sat, 24 Aug 2019 21:19:15: 7000000 INFO @ Sat, 24 Aug 2019 21:19:22: 2000000 INFO @ Sat, 24 Aug 2019 21:19:25: 5000000 INFO @ Sat, 24 Aug 2019 21:19:25: 8000000 INFO @ Sat, 24 Aug 2019 21:19:32: 3000000 INFO @ Sat, 24 Aug 2019 21:19:35: 6000000 INFO @ Sat, 24 Aug 2019 21:19:36: 9000000 INFO @ Sat, 24 Aug 2019 21:19:42: 4000000 INFO @ Sat, 24 Aug 2019 21:19:45: 7000000 INFO @ Sat, 24 Aug 2019 21:19:46: 10000000 INFO @ Sat, 24 Aug 2019 21:19:52: 5000000 INFO @ Sat, 24 Aug 2019 21:19:56: 8000000 INFO @ Sat, 24 Aug 2019 21:19:56: 11000000 INFO @ Sat, 24 Aug 2019 21:20:02: 6000000 INFO @ Sat, 24 Aug 2019 21:20:06: 9000000 INFO @ Sat, 24 Aug 2019 21:20:07: 12000000 INFO @ Sat, 24 Aug 2019 21:20:13: 7000000 INFO @ Sat, 24 Aug 2019 21:20:16: 10000000 INFO @ Sat, 24 Aug 2019 21:20:17: 13000000 INFO @ Sat, 24 Aug 2019 21:20:23: 8000000 INFO @ Sat, 24 Aug 2019 21:20:27: 11000000 INFO @ Sat, 24 Aug 2019 21:20:27: 14000000 INFO @ Sat, 24 Aug 2019 21:20:34: 9000000 INFO @ Sat, 24 Aug 2019 21:20:39: 12000000 INFO @ Sat, 24 Aug 2019 21:20:39: 15000000 INFO @ Sat, 24 Aug 2019 21:20:46: 10000000 INFO @ Sat, 24 Aug 2019 21:20:51: 13000000 INFO @ Sat, 24 Aug 2019 21:20:51: 16000000 INFO @ Sat, 24 Aug 2019 21:20:58: 11000000 INFO @ Sat, 24 Aug 2019 21:21:02: 14000000 INFO @ Sat, 24 Aug 2019 21:21:03: 17000000 INFO @ Sat, 24 Aug 2019 21:21:10: 12000000 INFO @ Sat, 24 Aug 2019 21:21:15: 15000000 INFO @ Sat, 24 Aug 2019 21:21:16: 18000000 INFO @ Sat, 24 Aug 2019 21:21:22: 13000000 INFO @ Sat, 24 Aug 2019 21:21:24: 16000000 INFO @ Sat, 24 Aug 2019 21:21:26: 19000000 INFO @ Sat, 24 Aug 2019 21:21:32: 14000000 INFO @ Sat, 24 Aug 2019 21:21:34: 17000000 INFO @ Sat, 24 Aug 2019 21:21:36: 20000000 INFO @ Sat, 24 Aug 2019 21:21:43: 15000000 INFO @ Sat, 24 Aug 2019 21:21:45: 18000000 INFO @ Sat, 24 Aug 2019 21:21:46: 21000000 INFO @ Sat, 24 Aug 2019 21:21:53: 16000000 INFO @ Sat, 24 Aug 2019 21:21:55: 19000000 INFO @ Sat, 24 Aug 2019 21:21:57: 22000000 INFO @ Sat, 24 Aug 2019 21:22:04: 17000000 INFO @ Sat, 24 Aug 2019 21:22:06: 20000000 INFO @ Sat, 24 Aug 2019 21:22:07: 23000000 INFO @ Sat, 24 Aug 2019 21:22:15: 18000000 INFO @ Sat, 24 Aug 2019 21:22:16: 21000000 INFO @ Sat, 24 Aug 2019 21:22:17: 24000000 INFO @ Sat, 24 Aug 2019 21:22:26: 19000000 INFO @ Sat, 24 Aug 2019 21:22:27: 22000000 INFO @ Sat, 24 Aug 2019 21:22:27: 25000000 INFO @ Sat, 24 Aug 2019 21:22:37: 20000000 INFO @ Sat, 24 Aug 2019 21:22:37: 23000000 INFO @ Sat, 24 Aug 2019 21:22:38: 26000000 INFO @ Sat, 24 Aug 2019 21:22:47: 21000000 INFO @ Sat, 24 Aug 2019 21:22:47: 24000000 INFO @ Sat, 24 Aug 2019 21:22:48: 27000000 INFO @ Sat, 24 Aug 2019 21:22:58: 25000000 INFO @ Sat, 24 Aug 2019 21:22:58: 22000000 INFO @ Sat, 24 Aug 2019 21:22:59: 28000000 INFO @ Sat, 24 Aug 2019 21:23:08: 26000000 INFO @ Sat, 24 Aug 2019 21:23:09: 23000000 INFO @ Sat, 24 Aug 2019 21:23:09: 29000000 INFO @ Sat, 24 Aug 2019 21:23:19: 27000000 INFO @ Sat, 24 Aug 2019 21:23:19: 30000000 INFO @ Sat, 24 Aug 2019 21:23:20: 24000000 INFO @ Sat, 24 Aug 2019 21:23:29: 28000000 INFO @ Sat, 24 Aug 2019 21:23:30: 31000000 INFO @ Sat, 24 Aug 2019 21:23:30: 25000000 INFO @ Sat, 24 Aug 2019 21:23:40: 29000000 INFO @ Sat, 24 Aug 2019 21:23:40: 32000000 INFO @ Sat, 24 Aug 2019 21:23:41: 26000000 INFO @ Sat, 24 Aug 2019 21:23:50: 30000000 INFO @ Sat, 24 Aug 2019 21:23:50: 33000000 INFO @ Sat, 24 Aug 2019 21:23:52: 27000000 INFO @ Sat, 24 Aug 2019 21:24:01: 31000000 INFO @ Sat, 24 Aug 2019 21:24:01: 34000000 INFO @ Sat, 24 Aug 2019 21:24:03: 28000000 INFO @ Sat, 24 Aug 2019 21:24:11: 32000000 INFO @ Sat, 24 Aug 2019 21:24:11: 35000000 INFO @ Sat, 24 Aug 2019 21:24:14: 29000000 INFO @ Sat, 24 Aug 2019 21:24:21: 33000000 INFO @ Sat, 24 Aug 2019 21:24:22: 36000000 INFO @ Sat, 24 Aug 2019 21:24:25: 30000000 INFO @ Sat, 24 Aug 2019 21:24:32: 34000000 INFO @ Sat, 24 Aug 2019 21:24:32: 37000000 INFO @ Sat, 24 Aug 2019 21:24:35: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:24:35: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:24:35: #1 total tags in treatment: 37286743 INFO @ Sat, 24 Aug 2019 21:24:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:24:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:24:36: 31000000 INFO @ Sat, 24 Aug 2019 21:24:36: #1 tags after filtering in treatment: 37286655 INFO @ Sat, 24 Aug 2019 21:24:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:24:36: #1 finished! INFO @ Sat, 24 Aug 2019 21:24:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:24:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:24:40: #2 number of paired peaks: 6230 INFO @ Sat, 24 Aug 2019 21:24:40: start model_add_line... INFO @ Sat, 24 Aug 2019 21:24:41: start X-correlation... INFO @ Sat, 24 Aug 2019 21:24:41: end of X-cor INFO @ Sat, 24 Aug 2019 21:24:41: #2 finished! INFO @ Sat, 24 Aug 2019 21:24:41: #2 predicted fragment length is 100 bps INFO @ Sat, 24 Aug 2019 21:24:41: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 24 Aug 2019 21:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.05_model.r WARNING @ Sat, 24 Aug 2019 21:24:41: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:24:41: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 24 Aug 2019 21:24:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 21:24:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:24:42: 35000000 INFO @ Sat, 24 Aug 2019 21:24:46: 32000000 INFO @ Sat, 24 Aug 2019 21:24:52: 36000000 INFO @ Sat, 24 Aug 2019 21:24:57: 33000000 INFO @ Sat, 24 Aug 2019 21:25:03: 37000000 INFO @ Sat, 24 Aug 2019 21:25:06: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:25:06: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:25:06: #1 total tags in treatment: 37286743 INFO @ Sat, 24 Aug 2019 21:25:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:25:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:25:07: #1 tags after filtering in treatment: 37286655 INFO @ Sat, 24 Aug 2019 21:25:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:25:07: #1 finished! INFO @ Sat, 24 Aug 2019 21:25:07: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:25:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:25:08: 34000000 INFO @ Sat, 24 Aug 2019 21:25:11: #2 number of paired peaks: 6230 INFO @ Sat, 24 Aug 2019 21:25:11: start model_add_line... INFO @ Sat, 24 Aug 2019 21:25:12: start X-correlation... INFO @ Sat, 24 Aug 2019 21:25:12: end of X-cor INFO @ Sat, 24 Aug 2019 21:25:12: #2 finished! INFO @ Sat, 24 Aug 2019 21:25:12: #2 predicted fragment length is 100 bps INFO @ Sat, 24 Aug 2019 21:25:12: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 24 Aug 2019 21:25:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.10_model.r WARNING @ Sat, 24 Aug 2019 21:25:12: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:25:12: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 24 Aug 2019 21:25:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 21:25:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:25:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:25:19: 35000000 INFO @ Sat, 24 Aug 2019 21:25:29: 36000000 INFO @ Sat, 24 Aug 2019 21:25:40: 37000000 INFO @ Sat, 24 Aug 2019 21:25:43: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:25:43: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:25:43: #1 total tags in treatment: 37286743 INFO @ Sat, 24 Aug 2019 21:25:43: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:25:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:25:44: #1 tags after filtering in treatment: 37286655 INFO @ Sat, 24 Aug 2019 21:25:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 21:25:44: #1 finished! INFO @ Sat, 24 Aug 2019 21:25:44: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:25:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:25:49: #2 number of paired peaks: 6230 INFO @ Sat, 24 Aug 2019 21:25:49: start model_add_line... INFO @ Sat, 24 Aug 2019 21:25:49: start X-correlation... INFO @ Sat, 24 Aug 2019 21:25:49: end of X-cor INFO @ Sat, 24 Aug 2019 21:25:49: #2 finished! INFO @ Sat, 24 Aug 2019 21:25:49: #2 predicted fragment length is 100 bps INFO @ Sat, 24 Aug 2019 21:25:49: #2 alternative fragment length(s) may be 100 bps INFO @ Sat, 24 Aug 2019 21:25:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.20_model.r WARNING @ Sat, 24 Aug 2019 21:25:49: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 21:25:49: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Sat, 24 Aug 2019 21:25:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 21:25:49: #3 Call peaks... INFO @ Sat, 24 Aug 2019 21:25:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 21:26:41: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:27:11: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:27:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.05_peaks.xls INFO @ Sat, 24 Aug 2019 21:27:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:27:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.05_summits.bed INFO @ Sat, 24 Aug 2019 21:27:39: Done! pass1 - making usageList (69 chroms): 3 millis pass2 - checking and writing primary data (3135 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:27:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 21:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.10_peaks.xls INFO @ Sat, 24 Aug 2019 21:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.10_summits.bed INFO @ Sat, 24 Aug 2019 21:28:08: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1277 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.20_peaks.xls INFO @ Sat, 24 Aug 2019 21:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 21:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX754757/SRX754757.20_summits.bed INFO @ Sat, 24 Aug 2019 21:28:47: Done! pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (603 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。