Job ID = 10194804 sra ファイルのダウンロード中... Completed: 1601894K bytes transferred in 24 seconds (546005K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 59041751 spots for /home/okishinya/chipatlas/results/rn6/SRX1819030/SRR3624106.sra Written 59041751 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:57:26 59041751 reads; of these: 59041751 (100.00%) were unpaired; of these: 5137259 (8.70%) aligned 0 times 40298181 (68.25%) aligned exactly 1 time 13606311 (23.05%) aligned >1 times 91.30% overall alignment rate Time searching: 00:57:31 Overall time: 00:57:31 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 16 files... [bam_rmdupse_core] 11004123 / 53904492 = 0.2041 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 10 Nov 2017 22:55:47: # Command line: callpeak -t SRX1819030.bam -f BAM -g 2.15e9 -n SRX1819030.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1819030.05 # format = BAM # ChIP-seq file = ['SRX1819030.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 @ Fri, 10 Nov 2017 22:55:47: # Command line: callpeak -t SRX1819030.bam -f BAM -g 2.15e9 -n SRX1819030.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1819030.20 # format = BAM # ChIP-seq file = ['SRX1819030.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 @ Fri, 10 Nov 2017 22:55:47: # Command line: callpeak -t SRX1819030.bam -f BAM -g 2.15e9 -n SRX1819030.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1819030.10 # format = BAM # ChIP-seq file = ['SRX1819030.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 @ Fri, 10 Nov 2017 22:55:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:55:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:55:47: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:55:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:55:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:55:47: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:56:05: 1000000 INFO @ Fri, 10 Nov 2017 22:56:07: 1000000 INFO @ Fri, 10 Nov 2017 22:56:07: 1000000 INFO @ Fri, 10 Nov 2017 22:56:24: 2000000 INFO @ Fri, 10 Nov 2017 22:56:26: 2000000 INFO @ Fri, 10 Nov 2017 22:56:26: 2000000 INFO @ Fri, 10 Nov 2017 22:56:42: 3000000 INFO @ Fri, 10 Nov 2017 22:56:44: 3000000 INFO @ Fri, 10 Nov 2017 22:56:44: 3000000 INFO @ Fri, 10 Nov 2017 22:56:59: 4000000 INFO @ Fri, 10 Nov 2017 22:57:02: 4000000 INFO @ Fri, 10 Nov 2017 22:57:04: 4000000 INFO @ Fri, 10 Nov 2017 22:57:17: 5000000 INFO @ Fri, 10 Nov 2017 22:57:21: 5000000 INFO @ Fri, 10 Nov 2017 22:57:23: 5000000 INFO @ Fri, 10 Nov 2017 22:57:35: 6000000 INFO @ Fri, 10 Nov 2017 22:57:36: 6000000 INFO @ Fri, 10 Nov 2017 22:57:40: 6000000 INFO @ Fri, 10 Nov 2017 22:57:51: 7000000 INFO @ Fri, 10 Nov 2017 22:57:55: 7000000 INFO @ Fri, 10 Nov 2017 22:57:59: 7000000 INFO @ Fri, 10 Nov 2017 22:58:04: 8000000 INFO @ Fri, 10 Nov 2017 22:58:15: 8000000 INFO @ Fri, 10 Nov 2017 22:58:17: 9000000 INFO @ Fri, 10 Nov 2017 22:58:18: 8000000 INFO @ Fri, 10 Nov 2017 22:58:30: 10000000 INFO @ Fri, 10 Nov 2017 22:58:35: 9000000 INFO @ Fri, 10 Nov 2017 22:58:35: 9000000 INFO @ Fri, 10 Nov 2017 22:58:43: 11000000 INFO @ Fri, 10 Nov 2017 22:58:53: 10000000 INFO @ Fri, 10 Nov 2017 22:58:55: 10000000 INFO @ Fri, 10 Nov 2017 22:58:58: 12000000 INFO @ Fri, 10 Nov 2017 22:59:11: 13000000 INFO @ Fri, 10 Nov 2017 22:59:11: 11000000 INFO @ Fri, 10 Nov 2017 22:59:16: 11000000 INFO @ Fri, 10 Nov 2017 22:59:24: 14000000 INFO @ Fri, 10 Nov 2017 22:59:30: 12000000 INFO @ Fri, 10 Nov 2017 22:59:36: 12000000 INFO @ Fri, 10 Nov 2017 22:59:38: 15000000 INFO @ Fri, 10 Nov 2017 22:59:49: 13000000 INFO @ Fri, 10 Nov 2017 22:59:49: 16000000 INFO @ Fri, 10 Nov 2017 22:59:56: 13000000 INFO @ Fri, 10 Nov 2017 23:00:02: 17000000 INFO @ Fri, 10 Nov 2017 23:00:07: 14000000 INFO @ Fri, 10 Nov 2017 23:00:16: 14000000 INFO @ Fri, 10 Nov 2017 23:00:16: 18000000 INFO @ Fri, 10 Nov 2017 23:00:25: 15000000 INFO @ Fri, 10 Nov 2017 23:00:31: 19000000 INFO @ Fri, 10 Nov 2017 23:00:36: 15000000 INFO @ Fri, 10 Nov 2017 23:00:47: 16000000 INFO @ Fri, 10 Nov 2017 23:00:50: 20000000 INFO @ Fri, 10 Nov 2017 23:00:57: 16000000 INFO @ Fri, 10 Nov 2017 23:01:08: 17000000 INFO @ Fri, 10 Nov 2017 23:01:10: 21000000 INFO @ Fri, 10 Nov 2017 23:01:18: 17000000 INFO @ Fri, 10 Nov 2017 23:01:28: 22000000 INFO @ Fri, 10 Nov 2017 23:01:31: 18000000 INFO @ Fri, 10 Nov 2017 23:01:37: 18000000 INFO @ Fri, 10 Nov 2017 23:01:44: 23000000 INFO @ Fri, 10 Nov 2017 23:01:50: 19000000 INFO @ Fri, 10 Nov 2017 23:01:59: 19000000 INFO @ Fri, 10 Nov 2017 23:02:02: 24000000 INFO @ Fri, 10 Nov 2017 23:02:08: 20000000 INFO @ Fri, 10 Nov 2017 23:02:20: 25000000 INFO @ Fri, 10 Nov 2017 23:02:21: 20000000 INFO @ Fri, 10 Nov 2017 23:02:25: 21000000 INFO @ Fri, 10 Nov 2017 23:02:37: 26000000 INFO @ Fri, 10 Nov 2017 23:02:42: 22000000 INFO @ Fri, 10 Nov 2017 23:02:44: 21000000 INFO @ Fri, 10 Nov 2017 23:02:55: 27000000 INFO @ Fri, 10 Nov 2017 23:03:00: 23000000 INFO @ Fri, 10 Nov 2017 23:03:06: 22000000 INFO @ Fri, 10 Nov 2017 23:03:15: 28000000 INFO @ Fri, 10 Nov 2017 23:03:16: 24000000 INFO @ Fri, 10 Nov 2017 23:03:28: 23000000 INFO @ Fri, 10 Nov 2017 23:03:33: 25000000 INFO @ Fri, 10 Nov 2017 23:03:34: 29000000 INFO @ Fri, 10 Nov 2017 23:03:49: 24000000 INFO @ Fri, 10 Nov 2017 23:03:50: 26000000 INFO @ Fri, 10 Nov 2017 23:03:54: 30000000 INFO @ Fri, 10 Nov 2017 23:04:07: 27000000 INFO @ Fri, 10 Nov 2017 23:04:11: 25000000 INFO @ Fri, 10 Nov 2017 23:04:14: 31000000 INFO @ Fri, 10 Nov 2017 23:04:24: 28000000 INFO @ Fri, 10 Nov 2017 23:04:32: 26000000 INFO @ Fri, 10 Nov 2017 23:04:32: 32000000 INFO @ Fri, 10 Nov 2017 23:04:41: 29000000 INFO @ Fri, 10 Nov 2017 23:04:50: 27000000 INFO @ Fri, 10 Nov 2017 23:04:51: 33000000 INFO @ Fri, 10 Nov 2017 23:04:59: 30000000 INFO @ Fri, 10 Nov 2017 23:05:07: 28000000 INFO @ Fri, 10 Nov 2017 23:05:09: 34000000 INFO @ Fri, 10 Nov 2017 23:05:19: 31000000 INFO @ Fri, 10 Nov 2017 23:05:24: 29000000 INFO @ Fri, 10 Nov 2017 23:05:25: 35000000 INFO @ Fri, 10 Nov 2017 23:05:39: 32000000 INFO @ Fri, 10 Nov 2017 23:05:42: 36000000 INFO @ Fri, 10 Nov 2017 23:05:43: 30000000 INFO @ Fri, 10 Nov 2017 23:05:55: 37000000 INFO @ Fri, 10 Nov 2017 23:05:59: 33000000 INFO @ Fri, 10 Nov 2017 23:06:01: 31000000 INFO @ Fri, 10 Nov 2017 23:06:12: 38000000 INFO @ Fri, 10 Nov 2017 23:06:19: 32000000 INFO @ Fri, 10 Nov 2017 23:06:19: 34000000 INFO @ Fri, 10 Nov 2017 23:06:25: 39000000 INFO @ Fri, 10 Nov 2017 23:06:36: 33000000 INFO @ Fri, 10 Nov 2017 23:06:40: 35000000 INFO @ Fri, 10 Nov 2017 23:06:42: 40000000 INFO @ Fri, 10 Nov 2017 23:06:53: 34000000 INFO @ Fri, 10 Nov 2017 23:06:59: 41000000 INFO @ Fri, 10 Nov 2017 23:07:01: 36000000 INFO @ Fri, 10 Nov 2017 23:07:11: 35000000 INFO @ Fri, 10 Nov 2017 23:07:14: 42000000 INFO @ Fri, 10 Nov 2017 23:07:23: 37000000 INFO @ Fri, 10 Nov 2017 23:07:29: 36000000 INFO @ Fri, 10 Nov 2017 23:07:31: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 23:07:31: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 23:07:31: #1 total tags in treatment: 42900369 INFO @ Fri, 10 Nov 2017 23:07:31: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:07:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:07:33: #1 tags after filtering in treatment: 42900303 INFO @ Fri, 10 Nov 2017 23:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:07:33: #1 finished! INFO @ Fri, 10 Nov 2017 23:07:33: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:07:38: #2 number of paired peaks: 4485 INFO @ Fri, 10 Nov 2017 23:07:38: start model_add_line... INFO @ Fri, 10 Nov 2017 23:07:38: start X-correlation... INFO @ Fri, 10 Nov 2017 23:07:38: end of X-cor INFO @ Fri, 10 Nov 2017 23:07:38: #2 finished! INFO @ Fri, 10 Nov 2017 23:07:38: #2 predicted fragment length is 40 bps INFO @ Fri, 10 Nov 2017 23:07:38: #2 alternative fragment length(s) may be 40,575 bps INFO @ Fri, 10 Nov 2017 23:07:38: #2.2 Generate R script for model : SRX1819030.10_model.r WARNING @ Fri, 10 Nov 2017 23:07:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:07:38: #2 You may need to consider one of the other alternative d(s): 40,575 WARNING @ Fri, 10 Nov 2017 23:07:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:07:38: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:07:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:07:44: 38000000 INFO @ Fri, 10 Nov 2017 23:07:47: 37000000 INFO @ Fri, 10 Nov 2017 23:08:06: 39000000 INFO @ Fri, 10 Nov 2017 23:08:13: 38000000 INFO @ Fri, 10 Nov 2017 23:08:25: 40000000 INFO @ Fri, 10 Nov 2017 23:08:39: 39000000 INFO @ Fri, 10 Nov 2017 23:08:44: 41000000 INFO @ Fri, 10 Nov 2017 23:09:04: 42000000 INFO @ Fri, 10 Nov 2017 23:09:05: 40000000 INFO @ Fri, 10 Nov 2017 23:09:21: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 23:09:21: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 23:09:21: #1 total tags in treatment: 42900369 INFO @ Fri, 10 Nov 2017 23:09:21: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:09:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:09:23: #1 tags after filtering in treatment: 42900303 INFO @ Fri, 10 Nov 2017 23:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:09:23: #1 finished! INFO @ Fri, 10 Nov 2017 23:09:23: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:09:28: #2 number of paired peaks: 4485 INFO @ Fri, 10 Nov 2017 23:09:28: start model_add_line... INFO @ Fri, 10 Nov 2017 23:09:29: start X-correlation... INFO @ Fri, 10 Nov 2017 23:09:29: end of X-cor INFO @ Fri, 10 Nov 2017 23:09:29: #2 finished! INFO @ Fri, 10 Nov 2017 23:09:29: #2 predicted fragment length is 40 bps INFO @ Fri, 10 Nov 2017 23:09:29: #2 alternative fragment length(s) may be 40,575 bps INFO @ Fri, 10 Nov 2017 23:09:29: #2.2 Generate R script for model : SRX1819030.20_model.r WARNING @ Fri, 10 Nov 2017 23:09:29: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:09:29: #2 You may need to consider one of the other alternative d(s): 40,575 WARNING @ Fri, 10 Nov 2017 23:09:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:09:29: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:09:30: 41000000 INFO @ Fri, 10 Nov 2017 23:09:56: 42000000 INFO @ Fri, 10 Nov 2017 23:10:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:10:19: #1 tag size is determined as 40 bps INFO @ Fri, 10 Nov 2017 23:10:19: #1 tag size = 40 INFO @ Fri, 10 Nov 2017 23:10:19: #1 total tags in treatment: 42900369 INFO @ Fri, 10 Nov 2017 23:10:19: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:10:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 23:10:20: #1 tags after filtering in treatment: 42900303 INFO @ Fri, 10 Nov 2017 23:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:10:20: #1 finished! INFO @ Fri, 10 Nov 2017 23:10:20: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:10:25: #2 number of paired peaks: 4485 INFO @ Fri, 10 Nov 2017 23:10:25: start model_add_line... INFO @ Fri, 10 Nov 2017 23:10:26: start X-correlation... INFO @ Fri, 10 Nov 2017 23:10:26: end of X-cor INFO @ Fri, 10 Nov 2017 23:10:26: #2 finished! INFO @ Fri, 10 Nov 2017 23:10:26: #2 predicted fragment length is 40 bps INFO @ Fri, 10 Nov 2017 23:10:26: #2 alternative fragment length(s) may be 40,575 bps INFO @ Fri, 10 Nov 2017 23:10:26: #2.2 Generate R script for model : SRX1819030.05_model.r WARNING @ Fri, 10 Nov 2017 23:10:26: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 23:10:26: #2 You may need to consider one of the other alternative d(s): 40,575 WARNING @ Fri, 10 Nov 2017 23:10:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 23:10:26: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:10:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:11:26: #4 Write output xls file... SRX1819030.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:11:26: #4 Write peak in narrowPeak format file... SRX1819030.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:11:26: #4 Write summits bed file... SRX1819030.10_summits.bed INFO @ Fri, 10 Nov 2017 23:11:26: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (1181 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:11:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:12:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:13:00: #4 Write output xls file... SRX1819030.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:13:00: #4 Write peak in narrowPeak format file... SRX1819030.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:13:00: #4 Write summits bed file... SRX1819030.20_summits.bed INFO @ Fri, 10 Nov 2017 23:13:00: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (538 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:13:57: #4 Write output xls file... SRX1819030.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:13:57: #4 Write peak in narrowPeak format file... SRX1819030.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:13:57: #4 Write summits bed file... SRX1819030.05_summits.bed INFO @ Fri, 10 Nov 2017 23:13:57: Done! pass1 - making usageList (45 chroms): 2 millis pass2 - checking and writing primary data (2036 records, 4 fields): 634 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。