Job ID = 2640385 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 45,702,343 reads read : 45,702,343 reads written : 45,702,343 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: 00:00:00 Multiseed full-index search: 00:25:31 45702343 reads; of these: 45702343 (100.00%) were unpaired; of these: 140495 (0.31%) aligned 0 times 41503531 (90.81%) aligned exactly 1 time 4058317 (8.88%) aligned >1 times 99.69% overall alignment rate Time searching: 00:25:34 Overall time: 00:25:34 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] 737 / 45561848 = 0.0000 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.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 16:53:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:53:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:53:58: 1000000 INFO @ Sat, 24 Aug 2019 16:54:07: 2000000 INFO @ Sat, 24 Aug 2019 16:54:17: 3000000 INFO @ Sat, 24 Aug 2019 16:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.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 16:54:18: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:54:18: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:54:26: 4000000 INFO @ Sat, 24 Aug 2019 16:54:27: 1000000 INFO @ Sat, 24 Aug 2019 16:54:35: 5000000 INFO @ Sat, 24 Aug 2019 16:54:36: 2000000 INFO @ Sat, 24 Aug 2019 16:54:45: 3000000 INFO @ Sat, 24 Aug 2019 16:54:45: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.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 16:54:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:54:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:54:53: 4000000 INFO @ Sat, 24 Aug 2019 16:54:54: 7000000 INFO @ Sat, 24 Aug 2019 16:54:57: 1000000 INFO @ Sat, 24 Aug 2019 16:55:02: 5000000 INFO @ Sat, 24 Aug 2019 16:55:04: 8000000 INFO @ Sat, 24 Aug 2019 16:55:06: 2000000 INFO @ Sat, 24 Aug 2019 16:55:12: 6000000 INFO @ Sat, 24 Aug 2019 16:55:14: 9000000 INFO @ Sat, 24 Aug 2019 16:55:15: 3000000 INFO @ Sat, 24 Aug 2019 16:55:20: 7000000 INFO @ Sat, 24 Aug 2019 16:55:23: 10000000 INFO @ Sat, 24 Aug 2019 16:55:24: 4000000 INFO @ Sat, 24 Aug 2019 16:55:29: 8000000 INFO @ Sat, 24 Aug 2019 16:55:33: 11000000 INFO @ Sat, 24 Aug 2019 16:55:33: 5000000 INFO @ Sat, 24 Aug 2019 16:55:38: 9000000 INFO @ Sat, 24 Aug 2019 16:55:42: 12000000 INFO @ Sat, 24 Aug 2019 16:55:42: 6000000 INFO @ Sat, 24 Aug 2019 16:55:47: 10000000 INFO @ Sat, 24 Aug 2019 16:55:51: 7000000 INFO @ Sat, 24 Aug 2019 16:55:52: 13000000 INFO @ Sat, 24 Aug 2019 16:55:57: 11000000 INFO @ Sat, 24 Aug 2019 16:56:01: 8000000 INFO @ Sat, 24 Aug 2019 16:56:01: 14000000 INFO @ Sat, 24 Aug 2019 16:56:06: 12000000 INFO @ Sat, 24 Aug 2019 16:56:10: 9000000 INFO @ Sat, 24 Aug 2019 16:56:11: 15000000 INFO @ Sat, 24 Aug 2019 16:56:14: 13000000 INFO @ Sat, 24 Aug 2019 16:56:19: 10000000 INFO @ Sat, 24 Aug 2019 16:56:20: 16000000 INFO @ Sat, 24 Aug 2019 16:56:23: 14000000 INFO @ Sat, 24 Aug 2019 16:56:28: 11000000 INFO @ Sat, 24 Aug 2019 16:56:30: 17000000 INFO @ Sat, 24 Aug 2019 16:56:33: 15000000 INFO @ Sat, 24 Aug 2019 16:56:37: 12000000 INFO @ Sat, 24 Aug 2019 16:56:40: 18000000 INFO @ Sat, 24 Aug 2019 16:56:42: 16000000 INFO @ Sat, 24 Aug 2019 16:56:46: 13000000 INFO @ Sat, 24 Aug 2019 16:56:49: 19000000 INFO @ Sat, 24 Aug 2019 16:56:51: 17000000 INFO @ Sat, 24 Aug 2019 16:56:56: 14000000 INFO @ Sat, 24 Aug 2019 16:56:58: 20000000 INFO @ Sat, 24 Aug 2019 16:57:00: 18000000 INFO @ Sat, 24 Aug 2019 16:57:05: 15000000 INFO @ Sat, 24 Aug 2019 16:57:08: 21000000 INFO @ Sat, 24 Aug 2019 16:57:09: 19000000 INFO @ Sat, 24 Aug 2019 16:57:14: 16000000 INFO @ Sat, 24 Aug 2019 16:57:17: 22000000 INFO @ Sat, 24 Aug 2019 16:57:18: 20000000 INFO @ Sat, 24 Aug 2019 16:57:23: 17000000 INFO @ Sat, 24 Aug 2019 16:57:27: 23000000 INFO @ Sat, 24 Aug 2019 16:57:27: 21000000 INFO @ Sat, 24 Aug 2019 16:57:33: 18000000 INFO @ Sat, 24 Aug 2019 16:57:36: 22000000 INFO @ Sat, 24 Aug 2019 16:57:36: 24000000 INFO @ Sat, 24 Aug 2019 16:57:41: 19000000 INFO @ Sat, 24 Aug 2019 16:57:45: 23000000 INFO @ Sat, 24 Aug 2019 16:57:46: 25000000 INFO @ Sat, 24 Aug 2019 16:57:51: 20000000 INFO @ Sat, 24 Aug 2019 16:57:54: 24000000 INFO @ Sat, 24 Aug 2019 16:57:56: 26000000 INFO @ Sat, 24 Aug 2019 16:58:00: 21000000 INFO @ Sat, 24 Aug 2019 16:58:03: 25000000 INFO @ Sat, 24 Aug 2019 16:58:05: 27000000 INFO @ Sat, 24 Aug 2019 16:58:09: 22000000 INFO @ Sat, 24 Aug 2019 16:58:12: 26000000 INFO @ Sat, 24 Aug 2019 16:58:15: 28000000 INFO @ Sat, 24 Aug 2019 16:58:18: 23000000 INFO @ Sat, 24 Aug 2019 16:58:20: 27000000 INFO @ Sat, 24 Aug 2019 16:58:24: 29000000 INFO @ Sat, 24 Aug 2019 16:58:27: 24000000 INFO @ Sat, 24 Aug 2019 16:58:29: 28000000 INFO @ Sat, 24 Aug 2019 16:58:34: 30000000 INFO @ Sat, 24 Aug 2019 16:58:36: 25000000 INFO @ Sat, 24 Aug 2019 16:58:38: 29000000 INFO @ Sat, 24 Aug 2019 16:58:43: 31000000 INFO @ Sat, 24 Aug 2019 16:58:45: 26000000 INFO @ Sat, 24 Aug 2019 16:58:47: 30000000 INFO @ Sat, 24 Aug 2019 16:58:53: 32000000 INFO @ Sat, 24 Aug 2019 16:58:54: 27000000 INFO @ Sat, 24 Aug 2019 16:58:56: 31000000 INFO @ Sat, 24 Aug 2019 16:59:02: 33000000 INFO @ Sat, 24 Aug 2019 16:59:03: 28000000 INFO @ Sat, 24 Aug 2019 16:59:05: 32000000 INFO @ Sat, 24 Aug 2019 16:59:11: 34000000 INFO @ Sat, 24 Aug 2019 16:59:12: 29000000 INFO @ Sat, 24 Aug 2019 16:59:14: 33000000 INFO @ Sat, 24 Aug 2019 16:59:20: 35000000 INFO @ Sat, 24 Aug 2019 16:59:22: 30000000 INFO @ Sat, 24 Aug 2019 16:59:23: 34000000 INFO @ Sat, 24 Aug 2019 16:59:29: 36000000 INFO @ Sat, 24 Aug 2019 16:59:31: 31000000 INFO @ Sat, 24 Aug 2019 16:59:32: 35000000 INFO @ Sat, 24 Aug 2019 16:59:39: 37000000 INFO @ Sat, 24 Aug 2019 16:59:40: 32000000 INFO @ Sat, 24 Aug 2019 16:59:41: 36000000 INFO @ Sat, 24 Aug 2019 16:59:48: 38000000 INFO @ Sat, 24 Aug 2019 16:59:49: 33000000 INFO @ Sat, 24 Aug 2019 16:59:50: 37000000 INFO @ Sat, 24 Aug 2019 16:59:57: 39000000 INFO @ Sat, 24 Aug 2019 16:59:58: 34000000 INFO @ Sat, 24 Aug 2019 16:59:59: 38000000 INFO @ Sat, 24 Aug 2019 17:00:06: 40000000 INFO @ Sat, 24 Aug 2019 17:00:07: 35000000 INFO @ Sat, 24 Aug 2019 17:00:08: 39000000 INFO @ Sat, 24 Aug 2019 17:00:15: 41000000 INFO @ Sat, 24 Aug 2019 17:00:16: 36000000 INFO @ Sat, 24 Aug 2019 17:00:17: 40000000 INFO @ Sat, 24 Aug 2019 17:00:24: 42000000 INFO @ Sat, 24 Aug 2019 17:00:25: 37000000 INFO @ Sat, 24 Aug 2019 17:00:26: 41000000 INFO @ Sat, 24 Aug 2019 17:00:34: 43000000 INFO @ Sat, 24 Aug 2019 17:00:34: 38000000 INFO @ Sat, 24 Aug 2019 17:00:35: 42000000 INFO @ Sat, 24 Aug 2019 17:00:42: 44000000 INFO @ Sat, 24 Aug 2019 17:00:44: 39000000 INFO @ Sat, 24 Aug 2019 17:00:44: 43000000 INFO @ Sat, 24 Aug 2019 17:00:52: 45000000 INFO @ Sat, 24 Aug 2019 17:00:53: 44000000 INFO @ Sat, 24 Aug 2019 17:00:53: 40000000 INFO @ Sat, 24 Aug 2019 17:00:57: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:00:57: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:00:57: #1 total tags in treatment: 45561111 INFO @ Sat, 24 Aug 2019 17:00:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:00:57: #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 17:00:58: #1 tags after filtering in treatment: 45561010 INFO @ Sat, 24 Aug 2019 17:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:00:58: #1 finished! INFO @ Sat, 24 Aug 2019 17:00:58: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:01:02: 45000000 INFO @ Sat, 24 Aug 2019 17:01:02: 41000000 INFO @ Sat, 24 Aug 2019 17:01:03: #2 number of paired peaks: 536 WARNING @ Sat, 24 Aug 2019 17:01:03: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sat, 24 Aug 2019 17:01:03: start model_add_line... INFO @ Sat, 24 Aug 2019 17:01:03: start X-correlation... INFO @ Sat, 24 Aug 2019 17:01:03: end of X-cor INFO @ Sat, 24 Aug 2019 17:01:03: #2 finished! INFO @ Sat, 24 Aug 2019 17:01:03: #2 predicted fragment length is 49 bps INFO @ Sat, 24 Aug 2019 17:01:03: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 24 Aug 2019 17:01:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.05_model.r WARNING @ Sat, 24 Aug 2019 17:01:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:01:03: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 24 Aug 2019 17:01:03: #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 17:01:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:01:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:01:07: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:01:07: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:01:07: #1 total tags in treatment: 45561111 INFO @ Sat, 24 Aug 2019 17:01:07: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:01:07: #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 17:01:08: #1 tags after filtering in treatment: 45561010 INFO @ Sat, 24 Aug 2019 17:01:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:01:08: #1 finished! INFO @ Sat, 24 Aug 2019 17:01:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:01:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:01:11: 42000000 INFO @ Sat, 24 Aug 2019 17:01:13: #2 number of paired peaks: 536 WARNING @ Sat, 24 Aug 2019 17:01:13: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sat, 24 Aug 2019 17:01:13: start model_add_line... INFO @ Sat, 24 Aug 2019 17:01:13: start X-correlation... INFO @ Sat, 24 Aug 2019 17:01:13: end of X-cor INFO @ Sat, 24 Aug 2019 17:01:13: #2 finished! INFO @ Sat, 24 Aug 2019 17:01:13: #2 predicted fragment length is 49 bps INFO @ Sat, 24 Aug 2019 17:01:13: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 24 Aug 2019 17:01:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.10_model.r WARNING @ Sat, 24 Aug 2019 17:01:13: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:01:13: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 24 Aug 2019 17:01:13: #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 17:01:13: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:01:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:01:20: 43000000 INFO @ Sat, 24 Aug 2019 17:01:29: 44000000 INFO @ Sat, 24 Aug 2019 17:01:38: 45000000 INFO @ Sat, 24 Aug 2019 17:01:44: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:01:44: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:01:44: #1 total tags in treatment: 45561111 INFO @ Sat, 24 Aug 2019 17:01:44: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:01:44: #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 17:01:45: #1 tags after filtering in treatment: 45561010 INFO @ Sat, 24 Aug 2019 17:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:01:45: #1 finished! INFO @ Sat, 24 Aug 2019 17:01:45: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:01:49: #2 number of paired peaks: 536 WARNING @ Sat, 24 Aug 2019 17:01:49: Fewer paired peaks (536) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 536 pairs to build model! INFO @ Sat, 24 Aug 2019 17:01:49: start model_add_line... INFO @ Sat, 24 Aug 2019 17:01:50: start X-correlation... INFO @ Sat, 24 Aug 2019 17:01:50: end of X-cor INFO @ Sat, 24 Aug 2019 17:01:50: #2 finished! INFO @ Sat, 24 Aug 2019 17:01:50: #2 predicted fragment length is 49 bps INFO @ Sat, 24 Aug 2019 17:01:50: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 24 Aug 2019 17:01:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.20_model.r WARNING @ Sat, 24 Aug 2019 17:01:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:01:50: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 24 Aug 2019 17:01:50: #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 17:01:50: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:03:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:03:32: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:04:09: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:04:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:04:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:04:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.05_summits.bed INFO @ Sat, 24 Aug 2019 17:04:34: Done! pass1 - making usageList (23 chroms): 3 millis pass2 - checking and writing primary data (664 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.10_summits.bed INFO @ Sat, 24 Aug 2019 17:04:43: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (268 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:05:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:05:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:05:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX2901257/ERX2901257.20_summits.bed INFO @ Sat, 24 Aug 2019 17:05:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (80 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。