Job ID = 10194753 sra ファイルのダウンロード中... Completed: 490229K bytes transferred in 7 seconds (544883K 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 36600697 spots for /home/okishinya/chipatlas/results/rn6/SRX1091091/SRR2095968.sra Written 36600697 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:30 36600697 reads; of these: 36600697 (100.00%) were unpaired; of these: 1269795 (3.47%) aligned 0 times 25698500 (70.21%) aligned exactly 1 time 9632402 (26.32%) aligned >1 times 96.53% overall alignment rate Time searching: 00:27:33 Overall time: 00:27:33 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] 1297773 / 35330902 = 0.0367 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 @ Sat, 11 Nov 2017 00:55:31: # Command line: callpeak -t SRX1091091.bam -f BAM -g 2.15e9 -n SRX1091091.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1091091.20 # format = BAM # ChIP-seq file = ['SRX1091091.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, 11 Nov 2017 00:55:31: # Command line: callpeak -t SRX1091091.bam -f BAM -g 2.15e9 -n SRX1091091.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1091091.10 # format = BAM # ChIP-seq file = ['SRX1091091.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, 11 Nov 2017 00:55:31: # Command line: callpeak -t SRX1091091.bam -f BAM -g 2.15e9 -n SRX1091091.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1091091.05 # format = BAM # ChIP-seq file = ['SRX1091091.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, 11 Nov 2017 00:55:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:55:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:55:31: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:55:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:55:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:55:31: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:55:37: 1000000 INFO @ Sat, 11 Nov 2017 00:55:38: 1000000 INFO @ Sat, 11 Nov 2017 00:55:38: 1000000 INFO @ Sat, 11 Nov 2017 00:55:44: 2000000 INFO @ Sat, 11 Nov 2017 00:55:45: 2000000 INFO @ Sat, 11 Nov 2017 00:55:45: 2000000 INFO @ Sat, 11 Nov 2017 00:55:51: 3000000 INFO @ Sat, 11 Nov 2017 00:55:52: 3000000 INFO @ Sat, 11 Nov 2017 00:55:52: 3000000 INFO @ Sat, 11 Nov 2017 00:55:59: 4000000 INFO @ Sat, 11 Nov 2017 00:55:59: 4000000 INFO @ Sat, 11 Nov 2017 00:56:00: 4000000 INFO @ Sat, 11 Nov 2017 00:56:06: 5000000 INFO @ Sat, 11 Nov 2017 00:56:07: 5000000 INFO @ Sat, 11 Nov 2017 00:56:07: 5000000 INFO @ Sat, 11 Nov 2017 00:56:13: 6000000 INFO @ Sat, 11 Nov 2017 00:56:14: 6000000 INFO @ Sat, 11 Nov 2017 00:56:15: 6000000 INFO @ Sat, 11 Nov 2017 00:56:20: 7000000 INFO @ Sat, 11 Nov 2017 00:56:22: 7000000 INFO @ Sat, 11 Nov 2017 00:56:22: 7000000 INFO @ Sat, 11 Nov 2017 00:56:28: 8000000 INFO @ Sat, 11 Nov 2017 00:56:29: 8000000 INFO @ Sat, 11 Nov 2017 00:56:30: 8000000 INFO @ Sat, 11 Nov 2017 00:56:35: 9000000 INFO @ Sat, 11 Nov 2017 00:56:37: 9000000 INFO @ Sat, 11 Nov 2017 00:56:38: 9000000 INFO @ Sat, 11 Nov 2017 00:56:42: 10000000 INFO @ Sat, 11 Nov 2017 00:56:44: 10000000 INFO @ Sat, 11 Nov 2017 00:56:45: 10000000 INFO @ Sat, 11 Nov 2017 00:56:50: 11000000 INFO @ Sat, 11 Nov 2017 00:56:52: 11000000 INFO @ Sat, 11 Nov 2017 00:56:53: 11000000 INFO @ Sat, 11 Nov 2017 00:56:57: 12000000 INFO @ Sat, 11 Nov 2017 00:57:00: 12000000 INFO @ Sat, 11 Nov 2017 00:57:01: 12000000 INFO @ Sat, 11 Nov 2017 00:57:04: 13000000 INFO @ Sat, 11 Nov 2017 00:57:07: 13000000 INFO @ Sat, 11 Nov 2017 00:57:08: 13000000 INFO @ Sat, 11 Nov 2017 00:57:12: 14000000 INFO @ Sat, 11 Nov 2017 00:57:15: 14000000 INFO @ Sat, 11 Nov 2017 00:57:16: 14000000 INFO @ Sat, 11 Nov 2017 00:57:19: 15000000 INFO @ Sat, 11 Nov 2017 00:57:23: 15000000 INFO @ Sat, 11 Nov 2017 00:57:24: 15000000 INFO @ Sat, 11 Nov 2017 00:57:26: 16000000 INFO @ Sat, 11 Nov 2017 00:57:30: 16000000 INFO @ Sat, 11 Nov 2017 00:57:32: 16000000 INFO @ Sat, 11 Nov 2017 00:57:34: 17000000 INFO @ Sat, 11 Nov 2017 00:57:38: 17000000 INFO @ Sat, 11 Nov 2017 00:57:39: 17000000 INFO @ Sat, 11 Nov 2017 00:57:41: 18000000 INFO @ Sat, 11 Nov 2017 00:57:46: 18000000 INFO @ Sat, 11 Nov 2017 00:57:47: 18000000 INFO @ Sat, 11 Nov 2017 00:57:48: 19000000 INFO @ Sat, 11 Nov 2017 00:57:53: 19000000 INFO @ Sat, 11 Nov 2017 00:57:55: 19000000 INFO @ Sat, 11 Nov 2017 00:57:56: 20000000 INFO @ Sat, 11 Nov 2017 00:58:01: 20000000 INFO @ Sat, 11 Nov 2017 00:58:03: 20000000 INFO @ Sat, 11 Nov 2017 00:58:03: 21000000 INFO @ Sat, 11 Nov 2017 00:58:09: 21000000 INFO @ Sat, 11 Nov 2017 00:58:10: 21000000 INFO @ Sat, 11 Nov 2017 00:58:10: 22000000 INFO @ Sat, 11 Nov 2017 00:58:16: 22000000 INFO @ Sat, 11 Nov 2017 00:58:18: 23000000 INFO @ Sat, 11 Nov 2017 00:58:18: 22000000 INFO @ Sat, 11 Nov 2017 00:58:24: 23000000 INFO @ Sat, 11 Nov 2017 00:58:25: 24000000 INFO @ Sat, 11 Nov 2017 00:58:26: 23000000 INFO @ Sat, 11 Nov 2017 00:58:32: 24000000 INFO @ Sat, 11 Nov 2017 00:58:33: 25000000 INFO @ Sat, 11 Nov 2017 00:58:34: 24000000 INFO @ Sat, 11 Nov 2017 00:58:40: 25000000 INFO @ Sat, 11 Nov 2017 00:58:40: 26000000 INFO @ Sat, 11 Nov 2017 00:58:41: 25000000 INFO @ Sat, 11 Nov 2017 00:58:47: 27000000 INFO @ Sat, 11 Nov 2017 00:58:47: 26000000 INFO @ Sat, 11 Nov 2017 00:58:49: 26000000 INFO @ Sat, 11 Nov 2017 00:58:55: 28000000 INFO @ Sat, 11 Nov 2017 00:58:55: 27000000 INFO @ Sat, 11 Nov 2017 00:58:57: 27000000 INFO @ Sat, 11 Nov 2017 00:59:02: 29000000 INFO @ Sat, 11 Nov 2017 00:59:03: 28000000 INFO @ Sat, 11 Nov 2017 00:59:04: 28000000 INFO @ Sat, 11 Nov 2017 00:59:09: 30000000 INFO @ Sat, 11 Nov 2017 00:59:10: 29000000 INFO @ Sat, 11 Nov 2017 00:59:12: 29000000 INFO @ Sat, 11 Nov 2017 00:59:17: 31000000 INFO @ Sat, 11 Nov 2017 00:59:18: 30000000 INFO @ Sat, 11 Nov 2017 00:59:20: 30000000 INFO @ Sat, 11 Nov 2017 00:59:24: 32000000 INFO @ Sat, 11 Nov 2017 00:59:26: 31000000 INFO @ Sat, 11 Nov 2017 00:59:28: 31000000 INFO @ Sat, 11 Nov 2017 00:59:32: 33000000 INFO @ Sat, 11 Nov 2017 00:59:34: 32000000 INFO @ Sat, 11 Nov 2017 00:59:35: 32000000 INFO @ Sat, 11 Nov 2017 00:59:39: 34000000 INFO @ Sat, 11 Nov 2017 00:59:40: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:59:40: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:59:40: #1 total tags in treatment: 34033129 INFO @ Sat, 11 Nov 2017 00:59:40: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:59:41: #1 tags after filtering in treatment: 34033052 INFO @ Sat, 11 Nov 2017 00:59:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:41: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:41: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:41: 33000000 INFO @ Sat, 11 Nov 2017 00:59:43: 33000000 INFO @ Sat, 11 Nov 2017 00:59:44: #2 number of paired peaks: 4871 INFO @ Sat, 11 Nov 2017 00:59:44: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:44: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:44: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:44: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:44: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:59:44: #2 alternative fragment length(s) may be 50,216,410 bps INFO @ Sat, 11 Nov 2017 00:59:44: #2.2 Generate R script for model : SRX1091091.05_model.r WARNING @ Sat, 11 Nov 2017 00:59:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:59:44: #2 You may need to consider one of the other alternative d(s): 50,216,410 WARNING @ Sat, 11 Nov 2017 00:59:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:59:44: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:48: 34000000 INFO @ Sat, 11 Nov 2017 00:59:49: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:59:49: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:59:49: #1 total tags in treatment: 34033129 INFO @ Sat, 11 Nov 2017 00:59:49: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:59:50: #1 tags after filtering in treatment: 34033052 INFO @ Sat, 11 Nov 2017 00:59:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:50: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:50: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:50: 34000000 INFO @ Sat, 11 Nov 2017 00:59:50: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:59:50: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:59:50: #1 total tags in treatment: 34033129 INFO @ Sat, 11 Nov 2017 00:59:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:59:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 00:59:51: #1 tags after filtering in treatment: 34033052 INFO @ Sat, 11 Nov 2017 00:59:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:59:51: #1 finished! INFO @ Sat, 11 Nov 2017 00:59:51: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:59:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:59:53: #2 number of paired peaks: 4871 INFO @ Sat, 11 Nov 2017 00:59:53: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:53: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:53: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:53: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:53: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:59:53: #2 alternative fragment length(s) may be 50,216,410 bps INFO @ Sat, 11 Nov 2017 00:59:53: #2.2 Generate R script for model : SRX1091091.10_model.r WARNING @ Sat, 11 Nov 2017 00:59:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:59:53: #2 You may need to consider one of the other alternative d(s): 50,216,410 WARNING @ Sat, 11 Nov 2017 00:59:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:59:53: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:59:54: #2 number of paired peaks: 4871 INFO @ Sat, 11 Nov 2017 00:59:54: start model_add_line... INFO @ Sat, 11 Nov 2017 00:59:55: start X-correlation... INFO @ Sat, 11 Nov 2017 00:59:55: end of X-cor INFO @ Sat, 11 Nov 2017 00:59:55: #2 finished! INFO @ Sat, 11 Nov 2017 00:59:55: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Nov 2017 00:59:55: #2 alternative fragment length(s) may be 50,216,410 bps INFO @ Sat, 11 Nov 2017 00:59:55: #2.2 Generate R script for model : SRX1091091.20_model.r WARNING @ Sat, 11 Nov 2017 00:59:55: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:59:55: #2 You may need to consider one of the other alternative d(s): 50,216,410 WARNING @ Sat, 11 Nov 2017 00:59:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 00:59:55: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:59:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:01:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:01:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:01:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:02:04: #4 Write output xls file... SRX1091091.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:04: #4 Write peak in narrowPeak format file... SRX1091091.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:04: #4 Write summits bed file... SRX1091091.05_summits.bed INFO @ Sat, 11 Nov 2017 01:02:04: Done! INFO @ Sat, 11 Nov 2017 01:02:04: #4 Write output xls file... SRX1091091.10_peaks.xls pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1851 records, 4 fields): 6 millis INFO @ Sat, 11 Nov 2017 01:02:04: #4 Write peak in narrowPeak format file... SRX1091091.10_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:02:04: #4 Write summits bed file... SRX1091091.10_summits.bed INFO @ Sat, 11 Nov 2017 01:02:04: Done! pass1 - making usageList (37 chroms): 0 millis pass2 - checking and writing primary data (1066 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:02:05: #4 Write output xls file... SRX1091091.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:02:05: #4 Write peak in narrowPeak format file... SRX1091091.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:02:05: #4 Write summits bed file... SRX1091091.20_summits.bed INFO @ Sat, 11 Nov 2017 01:02:05: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。