Job ID = 10194748 sra ファイルのダウンロード中... Completed: 519170K bytes transferred in 7 seconds (586557K 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 38889374 spots for /home/okishinya/chipatlas/results/rn6/SRX1091086/SRR2095963.sra Written 38889374 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: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:29:10 38889374 reads; of these: 38889374 (100.00%) were unpaired; of these: 1873503 (4.82%) aligned 0 times 26912992 (69.20%) aligned exactly 1 time 10102879 (25.98%) aligned >1 times 95.18% overall alignment rate Time searching: 00:29:15 Overall time: 00:29:15 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] 1833107 / 37015871 = 0.0495 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 00:47:11: # Command line: callpeak -t SRX1091086.bam -f BAM -g 2.15e9 -n SRX1091086.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1091086.20 # format = BAM # ChIP-seq file = ['SRX1091086.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 00:47:11: # Command line: callpeak -t SRX1091086.bam -f BAM -g 2.15e9 -n SRX1091086.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1091086.05 # format = BAM # ChIP-seq file = ['SRX1091086.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 00:47:11: # Command line: callpeak -t SRX1091086.bam -f BAM -g 2.15e9 -n SRX1091086.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1091086.10 # format = BAM # ChIP-seq file = ['SRX1091086.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 00:47:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:47:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:47:11: #1 read tag files... INFO @ Sat, 11 Nov 2017 00:47:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:47:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:47:11: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 00:47:18: 1000000 INFO @ Sat, 11 Nov 2017 00:47:19: 1000000 INFO @ Sat, 11 Nov 2017 00:47:19: 1000000 INFO @ Sat, 11 Nov 2017 00:47:25: 2000000 INFO @ Sat, 11 Nov 2017 00:47:26: 2000000 INFO @ Sat, 11 Nov 2017 00:47:26: 2000000 INFO @ Sat, 11 Nov 2017 00:47:32: 3000000 INFO @ Sat, 11 Nov 2017 00:47:34: 3000000 INFO @ Sat, 11 Nov 2017 00:47:34: 3000000 INFO @ Sat, 11 Nov 2017 00:47:39: 4000000 INFO @ Sat, 11 Nov 2017 00:47:41: 4000000 INFO @ Sat, 11 Nov 2017 00:47:41: 4000000 INFO @ Sat, 11 Nov 2017 00:47:46: 5000000 INFO @ Sat, 11 Nov 2017 00:47:48: 5000000 INFO @ Sat, 11 Nov 2017 00:47:48: 5000000 INFO @ Sat, 11 Nov 2017 00:47:53: 6000000 INFO @ Sat, 11 Nov 2017 00:47:56: 6000000 INFO @ Sat, 11 Nov 2017 00:47:56: 6000000 INFO @ Sat, 11 Nov 2017 00:48:00: 7000000 INFO @ Sat, 11 Nov 2017 00:48:03: 7000000 INFO @ Sat, 11 Nov 2017 00:48:03: 7000000 INFO @ Sat, 11 Nov 2017 00:48:06: 8000000 INFO @ Sat, 11 Nov 2017 00:48:11: 8000000 INFO @ Sat, 11 Nov 2017 00:48:11: 8000000 INFO @ Sat, 11 Nov 2017 00:48:13: 9000000 INFO @ Sat, 11 Nov 2017 00:48:18: 9000000 INFO @ Sat, 11 Nov 2017 00:48:18: 9000000 INFO @ Sat, 11 Nov 2017 00:48:20: 10000000 INFO @ Sat, 11 Nov 2017 00:48:25: 10000000 INFO @ Sat, 11 Nov 2017 00:48:25: 10000000 INFO @ Sat, 11 Nov 2017 00:48:27: 11000000 INFO @ Sat, 11 Nov 2017 00:48:33: 11000000 INFO @ Sat, 11 Nov 2017 00:48:33: 11000000 INFO @ Sat, 11 Nov 2017 00:48:34: 12000000 INFO @ Sat, 11 Nov 2017 00:48:40: 12000000 INFO @ Sat, 11 Nov 2017 00:48:40: 12000000 INFO @ Sat, 11 Nov 2017 00:48:41: 13000000 INFO @ Sat, 11 Nov 2017 00:48:48: 13000000 INFO @ Sat, 11 Nov 2017 00:48:48: 13000000 INFO @ Sat, 11 Nov 2017 00:48:48: 14000000 INFO @ Sat, 11 Nov 2017 00:48:55: 15000000 INFO @ Sat, 11 Nov 2017 00:48:55: 14000000 INFO @ Sat, 11 Nov 2017 00:48:55: 14000000 INFO @ Sat, 11 Nov 2017 00:49:02: 16000000 INFO @ Sat, 11 Nov 2017 00:49:02: 15000000 INFO @ Sat, 11 Nov 2017 00:49:02: 15000000 INFO @ Sat, 11 Nov 2017 00:49:09: 17000000 INFO @ Sat, 11 Nov 2017 00:49:10: 16000000 INFO @ Sat, 11 Nov 2017 00:49:10: 16000000 INFO @ Sat, 11 Nov 2017 00:49:16: 18000000 INFO @ Sat, 11 Nov 2017 00:49:17: 17000000 INFO @ Sat, 11 Nov 2017 00:49:17: 17000000 INFO @ Sat, 11 Nov 2017 00:49:23: 19000000 INFO @ Sat, 11 Nov 2017 00:49:24: 18000000 INFO @ Sat, 11 Nov 2017 00:49:24: 18000000 INFO @ Sat, 11 Nov 2017 00:49:30: 20000000 INFO @ Sat, 11 Nov 2017 00:49:31: 19000000 INFO @ Sat, 11 Nov 2017 00:49:31: 19000000 INFO @ Sat, 11 Nov 2017 00:49:37: 21000000 INFO @ Sat, 11 Nov 2017 00:49:39: 20000000 INFO @ Sat, 11 Nov 2017 00:49:39: 20000000 INFO @ Sat, 11 Nov 2017 00:49:44: 22000000 INFO @ Sat, 11 Nov 2017 00:49:46: 21000000 INFO @ Sat, 11 Nov 2017 00:49:46: 21000000 INFO @ Sat, 11 Nov 2017 00:49:51: 23000000 INFO @ Sat, 11 Nov 2017 00:49:53: 22000000 INFO @ Sat, 11 Nov 2017 00:49:54: 22000000 INFO @ Sat, 11 Nov 2017 00:49:58: 24000000 INFO @ Sat, 11 Nov 2017 00:50:00: 23000000 INFO @ Sat, 11 Nov 2017 00:50:01: 23000000 INFO @ Sat, 11 Nov 2017 00:50:05: 25000000 INFO @ Sat, 11 Nov 2017 00:50:08: 24000000 INFO @ Sat, 11 Nov 2017 00:50:08: 24000000 INFO @ Sat, 11 Nov 2017 00:50:12: 26000000 INFO @ Sat, 11 Nov 2017 00:50:15: 25000000 INFO @ Sat, 11 Nov 2017 00:50:16: 25000000 INFO @ Sat, 11 Nov 2017 00:50:19: 27000000 INFO @ Sat, 11 Nov 2017 00:50:23: 26000000 INFO @ Sat, 11 Nov 2017 00:50:24: 26000000 INFO @ Sat, 11 Nov 2017 00:50:26: 28000000 INFO @ Sat, 11 Nov 2017 00:50:30: 27000000 INFO @ Sat, 11 Nov 2017 00:50:31: 27000000 INFO @ Sat, 11 Nov 2017 00:50:33: 29000000 INFO @ Sat, 11 Nov 2017 00:50:37: 28000000 INFO @ Sat, 11 Nov 2017 00:50:39: 28000000 INFO @ Sat, 11 Nov 2017 00:50:40: 30000000 INFO @ Sat, 11 Nov 2017 00:50:45: 29000000 INFO @ Sat, 11 Nov 2017 00:50:46: 29000000 INFO @ Sat, 11 Nov 2017 00:50:47: 31000000 INFO @ Sat, 11 Nov 2017 00:50:52: 30000000 INFO @ Sat, 11 Nov 2017 00:50:54: 32000000 INFO @ Sat, 11 Nov 2017 00:50:54: 30000000 INFO @ Sat, 11 Nov 2017 00:51:00: 31000000 INFO @ Sat, 11 Nov 2017 00:51:01: 33000000 INFO @ Sat, 11 Nov 2017 00:51:02: 31000000 INFO @ Sat, 11 Nov 2017 00:51:08: 32000000 INFO @ Sat, 11 Nov 2017 00:51:08: 34000000 INFO @ Sat, 11 Nov 2017 00:51:10: 32000000 INFO @ Sat, 11 Nov 2017 00:51:15: 35000000 INFO @ Sat, 11 Nov 2017 00:51:15: 33000000 INFO @ Sat, 11 Nov 2017 00:51:16: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:51:16: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:51:16: #1 total tags in treatment: 35182764 INFO @ Sat, 11 Nov 2017 00:51:16: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:51:16: #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 00:51:17: #1 tags after filtering in treatment: 35182693 INFO @ Sat, 11 Nov 2017 00:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:51:17: #1 finished! INFO @ Sat, 11 Nov 2017 00:51:17: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:51:17: 33000000 INFO @ Sat, 11 Nov 2017 00:51:21: #2 number of paired peaks: 5976 INFO @ Sat, 11 Nov 2017 00:51:21: start model_add_line... INFO @ Sat, 11 Nov 2017 00:51:21: start X-correlation... INFO @ Sat, 11 Nov 2017 00:51:21: end of X-cor INFO @ Sat, 11 Nov 2017 00:51:21: #2 finished! INFO @ Sat, 11 Nov 2017 00:51:21: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Nov 2017 00:51:21: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Nov 2017 00:51:21: #2.2 Generate R script for model : SRX1091086.20_model.r WARNING @ Sat, 11 Nov 2017 00:51:21: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:51:21: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Nov 2017 00:51:21: #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 00:51:21: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:51:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:51:23: 34000000 INFO @ Sat, 11 Nov 2017 00:51:25: 34000000 INFO @ Sat, 11 Nov 2017 00:51:31: 35000000 INFO @ Sat, 11 Nov 2017 00:51:33: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:51:33: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:51:33: #1 total tags in treatment: 35182764 INFO @ Sat, 11 Nov 2017 00:51:33: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:51:33: #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 00:51:33: 35000000 INFO @ Sat, 11 Nov 2017 00:51:34: #1 tags after filtering in treatment: 35182693 INFO @ Sat, 11 Nov 2017 00:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:51:34: #1 finished! INFO @ Sat, 11 Nov 2017 00:51:34: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:51:35: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 00:51:35: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 00:51:35: #1 total tags in treatment: 35182764 INFO @ Sat, 11 Nov 2017 00:51:35: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 00:51:35: #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 00:51:36: #1 tags after filtering in treatment: 35182693 INFO @ Sat, 11 Nov 2017 00:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 00:51:36: #1 finished! INFO @ Sat, 11 Nov 2017 00:51:36: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 00:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 00:51:37: #2 number of paired peaks: 5976 INFO @ Sat, 11 Nov 2017 00:51:37: start model_add_line... INFO @ Sat, 11 Nov 2017 00:51:37: start X-correlation... INFO @ Sat, 11 Nov 2017 00:51:37: end of X-cor INFO @ Sat, 11 Nov 2017 00:51:37: #2 finished! INFO @ Sat, 11 Nov 2017 00:51:37: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Nov 2017 00:51:37: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Nov 2017 00:51:37: #2.2 Generate R script for model : SRX1091086.05_model.r WARNING @ Sat, 11 Nov 2017 00:51:37: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:51:37: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Nov 2017 00:51:37: #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 00:51:37: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:51:39: #2 number of paired peaks: 5976 INFO @ Sat, 11 Nov 2017 00:51:39: start model_add_line... INFO @ Sat, 11 Nov 2017 00:51:39: start X-correlation... INFO @ Sat, 11 Nov 2017 00:51:39: end of X-cor INFO @ Sat, 11 Nov 2017 00:51:39: #2 finished! INFO @ Sat, 11 Nov 2017 00:51:39: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Nov 2017 00:51:39: #2 alternative fragment length(s) may be 57 bps INFO @ Sat, 11 Nov 2017 00:51:39: #2.2 Generate R script for model : SRX1091086.10_model.r WARNING @ Sat, 11 Nov 2017 00:51:39: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 00:51:39: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sat, 11 Nov 2017 00:51:39: #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 00:51:39: #3 Call peaks... INFO @ Sat, 11 Nov 2017 00:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 00:52:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:53:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:53:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 00:53:34: #4 Write output xls file... SRX1091086.20_peaks.xls INFO @ Sat, 11 Nov 2017 00:53:34: #4 Write peak in narrowPeak format file... SRX1091086.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:53:34: #4 Write summits bed file... SRX1091086.20_summits.bed INFO @ Sat, 11 Nov 2017 00:53:34: Done! pass1 - making usageList (39 chroms): 0 millis pass2 - checking and writing primary data (768 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:53:53: #4 Write output xls file... SRX1091086.10_peaks.xls INFO @ Sat, 11 Nov 2017 00:53:53: #4 Write peak in narrowPeak format file... SRX1091086.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:53:53: #4 Write summits bed file... SRX1091086.10_summits.bed INFO @ Sat, 11 Nov 2017 00:53:53: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1843 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 00:53:56: #4 Write output xls file... SRX1091086.05_peaks.xls INFO @ Sat, 11 Nov 2017 00:53:56: #4 Write peak in narrowPeak format file... SRX1091086.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 00:53:56: #4 Write summits bed file... SRX1091086.05_summits.bed INFO @ Sat, 11 Nov 2017 00:53:56: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (3147 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。