Job ID = 2640393 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 74,644,174 reads read : 74,644,174 reads written : 74,644,174 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: 00:53:38 74644174 reads; of these: 74644174 (100.00%) were unpaired; of these: 11405002 (15.28%) aligned 0 times 45470748 (60.92%) aligned exactly 1 time 17768424 (23.80%) aligned >1 times 84.72% overall alignment rate Time searching: 00:53:41 Overall time: 00:53:41 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 28 files... [bam_rmdupse_core] 26079804 / 63239172 = 0.4124 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:35:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.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 17:35:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:35:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:35:44: 1000000 INFO @ Sat, 24 Aug 2019 17:35:51: 2000000 INFO @ Sat, 24 Aug 2019 17:35:57: 3000000 INFO @ Sat, 24 Aug 2019 17:36:04: 4000000 INFO @ Sat, 24 Aug 2019 17:36:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.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 17:36:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:36:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:36:10: 5000000 INFO @ Sat, 24 Aug 2019 17:36:16: 1000000 INFO @ Sat, 24 Aug 2019 17:36:16: 6000000 INFO @ Sat, 24 Aug 2019 17:36:23: 7000000 INFO @ Sat, 24 Aug 2019 17:36:24: 2000000 INFO @ Sat, 24 Aug 2019 17:36:29: 8000000 INFO @ Sat, 24 Aug 2019 17:36:31: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:36:36: 9000000 INFO @ Sat, 24 Aug 2019 17:36:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.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 17:36:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:36:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:36:39: 4000000 INFO @ Sat, 24 Aug 2019 17:36:42: 10000000 INFO @ Sat, 24 Aug 2019 17:36:46: 1000000 INFO @ Sat, 24 Aug 2019 17:36:47: 5000000 INFO @ Sat, 24 Aug 2019 17:36:49: 11000000 INFO @ Sat, 24 Aug 2019 17:36:54: 2000000 INFO @ Sat, 24 Aug 2019 17:36:54: 6000000 INFO @ Sat, 24 Aug 2019 17:36:55: 12000000 INFO @ Sat, 24 Aug 2019 17:37:01: 3000000 INFO @ Sat, 24 Aug 2019 17:37:02: 13000000 INFO @ Sat, 24 Aug 2019 17:37:02: 7000000 INFO @ Sat, 24 Aug 2019 17:37:08: 14000000 INFO @ Sat, 24 Aug 2019 17:37:09: 4000000 INFO @ Sat, 24 Aug 2019 17:37:10: 8000000 INFO @ Sat, 24 Aug 2019 17:37:15: 15000000 INFO @ Sat, 24 Aug 2019 17:37:17: 5000000 INFO @ Sat, 24 Aug 2019 17:37:18: 9000000 INFO @ Sat, 24 Aug 2019 17:37:21: 16000000 INFO @ Sat, 24 Aug 2019 17:37:25: 6000000 INFO @ Sat, 24 Aug 2019 17:37:25: 10000000 INFO @ Sat, 24 Aug 2019 17:37:28: 17000000 INFO @ Sat, 24 Aug 2019 17:37:32: 7000000 INFO @ Sat, 24 Aug 2019 17:37:33: 11000000 INFO @ Sat, 24 Aug 2019 17:37:34: 18000000 INFO @ Sat, 24 Aug 2019 17:37:40: 8000000 INFO @ Sat, 24 Aug 2019 17:37:41: 19000000 INFO @ Sat, 24 Aug 2019 17:37:41: 12000000 INFO @ Sat, 24 Aug 2019 17:37:47: 20000000 INFO @ Sat, 24 Aug 2019 17:37:48: 9000000 INFO @ Sat, 24 Aug 2019 17:37:49: 13000000 INFO @ Sat, 24 Aug 2019 17:37:54: 21000000 INFO @ Sat, 24 Aug 2019 17:37:56: 10000000 INFO @ Sat, 24 Aug 2019 17:37:56: 14000000 INFO @ Sat, 24 Aug 2019 17:38:00: 22000000 INFO @ Sat, 24 Aug 2019 17:38:03: 11000000 INFO @ Sat, 24 Aug 2019 17:38:04: 15000000 INFO @ Sat, 24 Aug 2019 17:38:07: 23000000 INFO @ Sat, 24 Aug 2019 17:38:11: 12000000 INFO @ Sat, 24 Aug 2019 17:38:12: 16000000 INFO @ Sat, 24 Aug 2019 17:38:13: 24000000 INFO @ Sat, 24 Aug 2019 17:38:19: 13000000 INFO @ Sat, 24 Aug 2019 17:38:19: 17000000 INFO @ Sat, 24 Aug 2019 17:38:20: 25000000 INFO @ Sat, 24 Aug 2019 17:38:26: 26000000 INFO @ Sat, 24 Aug 2019 17:38:26: 14000000 INFO @ Sat, 24 Aug 2019 17:38:27: 18000000 INFO @ Sat, 24 Aug 2019 17:38:32: 27000000 INFO @ Sat, 24 Aug 2019 17:38:34: 15000000 INFO @ Sat, 24 Aug 2019 17:38:35: 19000000 INFO @ Sat, 24 Aug 2019 17:38:39: 28000000 INFO @ Sat, 24 Aug 2019 17:38:42: 16000000 INFO @ Sat, 24 Aug 2019 17:38:42: 20000000 INFO @ Sat, 24 Aug 2019 17:38:45: 29000000 INFO @ Sat, 24 Aug 2019 17:38:50: 17000000 INFO @ Sat, 24 Aug 2019 17:38:50: 21000000 INFO @ Sat, 24 Aug 2019 17:38:52: 30000000 INFO @ Sat, 24 Aug 2019 17:38:57: 18000000 INFO @ Sat, 24 Aug 2019 17:38:58: 22000000 INFO @ Sat, 24 Aug 2019 17:38:58: 31000000 INFO @ Sat, 24 Aug 2019 17:39:04: 32000000 INFO @ Sat, 24 Aug 2019 17:39:05: 19000000 INFO @ Sat, 24 Aug 2019 17:39:05: 23000000 INFO @ Sat, 24 Aug 2019 17:39:11: 33000000 INFO @ Sat, 24 Aug 2019 17:39:12: 20000000 INFO @ Sat, 24 Aug 2019 17:39:13: 24000000 INFO @ Sat, 24 Aug 2019 17:39:17: 34000000 INFO @ Sat, 24 Aug 2019 17:39:20: 21000000 INFO @ Sat, 24 Aug 2019 17:39:20: 25000000 INFO @ Sat, 24 Aug 2019 17:39:24: 35000000 INFO @ Sat, 24 Aug 2019 17:39:28: 22000000 INFO @ Sat, 24 Aug 2019 17:39:28: 26000000 INFO @ Sat, 24 Aug 2019 17:39:30: 36000000 INFO @ Sat, 24 Aug 2019 17:39:35: 23000000 INFO @ Sat, 24 Aug 2019 17:39:36: 27000000 INFO @ Sat, 24 Aug 2019 17:39:37: 37000000 INFO @ Sat, 24 Aug 2019 17:39:38: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:39:38: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:39:38: #1 total tags in treatment: 37159368 INFO @ Sat, 24 Aug 2019 17:39:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:39:38: #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 17:39:39: #1 tags after filtering in treatment: 37159302 INFO @ Sat, 24 Aug 2019 17:39:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:39:39: #1 finished! INFO @ Sat, 24 Aug 2019 17:39:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:39:43: 24000000 INFO @ Sat, 24 Aug 2019 17:39:43: 28000000 INFO @ Sat, 24 Aug 2019 17:39:43: #2 number of paired peaks: 5825 INFO @ Sat, 24 Aug 2019 17:39:43: start model_add_line... INFO @ Sat, 24 Aug 2019 17:39:44: start X-correlation... INFO @ Sat, 24 Aug 2019 17:39:44: end of X-cor INFO @ Sat, 24 Aug 2019 17:39:44: #2 finished! INFO @ Sat, 24 Aug 2019 17:39:44: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 17:39:44: #2 alternative fragment length(s) may be 51,408 bps INFO @ Sat, 24 Aug 2019 17:39:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.05_model.r WARNING @ Sat, 24 Aug 2019 17:39:44: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:39:44: #2 You may need to consider one of the other alternative d(s): 51,408 WARNING @ Sat, 24 Aug 2019 17:39:44: #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 17:39:44: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:39:51: 25000000 INFO @ Sat, 24 Aug 2019 17:39:51: 29000000 INFO @ Sat, 24 Aug 2019 17:39:58: 26000000 INFO @ Sat, 24 Aug 2019 17:39:58: 30000000 INFO @ Sat, 24 Aug 2019 17:40:06: 27000000 INFO @ Sat, 24 Aug 2019 17:40:06: 31000000 INFO @ Sat, 24 Aug 2019 17:40:13: 28000000 INFO @ Sat, 24 Aug 2019 17:40:14: 32000000 INFO @ Sat, 24 Aug 2019 17:40:21: 29000000 INFO @ Sat, 24 Aug 2019 17:40:21: 33000000 INFO @ Sat, 24 Aug 2019 17:40:29: 30000000 INFO @ Sat, 24 Aug 2019 17:40:29: 34000000 INFO @ Sat, 24 Aug 2019 17:40:36: 31000000 INFO @ Sat, 24 Aug 2019 17:40:37: 35000000 INFO @ Sat, 24 Aug 2019 17:40:44: 32000000 INFO @ Sat, 24 Aug 2019 17:40:44: 36000000 INFO @ Sat, 24 Aug 2019 17:40:51: 33000000 INFO @ Sat, 24 Aug 2019 17:40:52: 37000000 INFO @ Sat, 24 Aug 2019 17:40:54: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:40:54: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:40:54: #1 total tags in treatment: 37159368 INFO @ Sat, 24 Aug 2019 17:40:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:40:54: #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 17:40:55: #1 tags after filtering in treatment: 37159302 INFO @ Sat, 24 Aug 2019 17:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:40:55: #1 finished! INFO @ Sat, 24 Aug 2019 17:40:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:40:59: #2 number of paired peaks: 5825 INFO @ Sat, 24 Aug 2019 17:40:59: start model_add_line... INFO @ Sat, 24 Aug 2019 17:40:59: 34000000 INFO @ Sat, 24 Aug 2019 17:40:59: start X-correlation... INFO @ Sat, 24 Aug 2019 17:40:59: end of X-cor INFO @ Sat, 24 Aug 2019 17:40:59: #2 finished! INFO @ Sat, 24 Aug 2019 17:40:59: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 17:40:59: #2 alternative fragment length(s) may be 51,408 bps INFO @ Sat, 24 Aug 2019 17:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.10_model.r WARNING @ Sat, 24 Aug 2019 17:40:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:40:59: #2 You may need to consider one of the other alternative d(s): 51,408 WARNING @ Sat, 24 Aug 2019 17:40:59: #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 17:40:59: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:41:07: 35000000 INFO @ Sat, 24 Aug 2019 17:41:14: 36000000 INFO @ Sat, 24 Aug 2019 17:41:22: 37000000 INFO @ Sat, 24 Aug 2019 17:41:24: #1 tag size is determined as 50 bps INFO @ Sat, 24 Aug 2019 17:41:24: #1 tag size = 50 INFO @ Sat, 24 Aug 2019 17:41:24: #1 total tags in treatment: 37159368 INFO @ Sat, 24 Aug 2019 17:41:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:41:24: #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 17:41:25: #1 tags after filtering in treatment: 37159302 INFO @ Sat, 24 Aug 2019 17:41:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:41:25: #1 finished! INFO @ Sat, 24 Aug 2019 17:41:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:41:29: #2 number of paired peaks: 5825 INFO @ Sat, 24 Aug 2019 17:41:29: start model_add_line... INFO @ Sat, 24 Aug 2019 17:41:29: start X-correlation... INFO @ Sat, 24 Aug 2019 17:41:29: end of X-cor INFO @ Sat, 24 Aug 2019 17:41:29: #2 finished! INFO @ Sat, 24 Aug 2019 17:41:29: #2 predicted fragment length is 51 bps INFO @ Sat, 24 Aug 2019 17:41:29: #2 alternative fragment length(s) may be 51,408 bps INFO @ Sat, 24 Aug 2019 17:41:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.20_model.r WARNING @ Sat, 24 Aug 2019 17:41:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 17:41:29: #2 You may need to consider one of the other alternative d(s): 51,408 WARNING @ Sat, 24 Aug 2019 17:41:29: #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 17:41:29: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:41:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:41:37: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.05_summits.bed INFO @ Sat, 24 Aug 2019 17:42:31: Done! pass1 - making usageList (63 chroms): 3 millis pass2 - checking and writing primary data (3074 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:42:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:43:24: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:43:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.10_summits.bed INFO @ Sat, 24 Aug 2019 17:43:48: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (1626 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:44:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:44:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:44:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX337076/ERX337076.20_summits.bed INFO @ Sat, 24 Aug 2019 17:44:18: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (778 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。