Job ID = 10487599 sra ファイルのダウンロード中... Completed: 3718382K bytes transferred in 62 seconds (489644K 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 55347921 spots for /home/okishinya/chipatlas/results/rn6/SRX2611121/SRR5311165.sra Written 55347921 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: 00:00:01 Multiseed full-index search: 03:00:06 55347921 reads; of these: 55347921 (100.00%) were unpaired; of these: 13918327 (25.15%) aligned 0 times 35679316 (64.46%) aligned exactly 1 time 5750278 (10.39%) aligned >1 times 74.85% overall alignment rate Time searching: 03:00:09 Overall time: 03:00:09 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 32 files... [bam_rmdupse_core] 12088769 / 41429594 = 0.2918 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 @ Sun, 18 Mar 2018 13:14:40: # Command line: callpeak -t SRX2611121.bam -f BAM -g 2.15e9 -n SRX2611121.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611121.05 # format = BAM # ChIP-seq file = ['SRX2611121.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 @ Sun, 18 Mar 2018 13:14:40: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:14:40: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:14:40: # Command line: callpeak -t SRX2611121.bam -f BAM -g 2.15e9 -n SRX2611121.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611121.10 # format = BAM # ChIP-seq file = ['SRX2611121.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 @ Sun, 18 Mar 2018 13:14:40: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:14:40: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:14:40: # Command line: callpeak -t SRX2611121.bam -f BAM -g 2.15e9 -n SRX2611121.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611121.20 # format = BAM # ChIP-seq file = ['SRX2611121.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 @ Sun, 18 Mar 2018 13:14:40: #1 read tag files... INFO @ Sun, 18 Mar 2018 13:14:40: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 13:14:51: 1000000 INFO @ Sun, 18 Mar 2018 13:14:51: 1000000 INFO @ Sun, 18 Mar 2018 13:14:52: 1000000 INFO @ Sun, 18 Mar 2018 13:15:02: 2000000 INFO @ Sun, 18 Mar 2018 13:15:02: 2000000 INFO @ Sun, 18 Mar 2018 13:15:03: 2000000 INFO @ Sun, 18 Mar 2018 13:15:13: 3000000 INFO @ Sun, 18 Mar 2018 13:15:13: 3000000 INFO @ Sun, 18 Mar 2018 13:15:14: 3000000 INFO @ Sun, 18 Mar 2018 13:15:24: 4000000 INFO @ Sun, 18 Mar 2018 13:15:24: 4000000 INFO @ Sun, 18 Mar 2018 13:15:25: 4000000 INFO @ Sun, 18 Mar 2018 13:15:35: 5000000 INFO @ Sun, 18 Mar 2018 13:15:35: 5000000 INFO @ Sun, 18 Mar 2018 13:15:36: 5000000 INFO @ Sun, 18 Mar 2018 13:15:46: 6000000 INFO @ Sun, 18 Mar 2018 13:15:46: 6000000 INFO @ Sun, 18 Mar 2018 13:15:47: 6000000 INFO @ Sun, 18 Mar 2018 13:15:57: 7000000 INFO @ Sun, 18 Mar 2018 13:15:58: 7000000 INFO @ Sun, 18 Mar 2018 13:15:59: 7000000 INFO @ Sun, 18 Mar 2018 13:16:08: 8000000 INFO @ Sun, 18 Mar 2018 13:16:09: 8000000 INFO @ Sun, 18 Mar 2018 13:16:10: 8000000 INFO @ Sun, 18 Mar 2018 13:16:19: 9000000 INFO @ Sun, 18 Mar 2018 13:16:21: 9000000 INFO @ Sun, 18 Mar 2018 13:16:22: 9000000 INFO @ Sun, 18 Mar 2018 13:16:30: 10000000 INFO @ Sun, 18 Mar 2018 13:16:32: 10000000 INFO @ Sun, 18 Mar 2018 13:16:33: 10000000 INFO @ Sun, 18 Mar 2018 13:16:40: 11000000 INFO @ Sun, 18 Mar 2018 13:16:43: 11000000 INFO @ Sun, 18 Mar 2018 13:16:45: 11000000 INFO @ Sun, 18 Mar 2018 13:16:51: 12000000 INFO @ Sun, 18 Mar 2018 13:16:54: 12000000 INFO @ Sun, 18 Mar 2018 13:16:56: 12000000 INFO @ Sun, 18 Mar 2018 13:17:02: 13000000 INFO @ Sun, 18 Mar 2018 13:17:06: 13000000 INFO @ Sun, 18 Mar 2018 13:17:07: 13000000 INFO @ Sun, 18 Mar 2018 13:17:13: 14000000 INFO @ Sun, 18 Mar 2018 13:17:17: 14000000 INFO @ Sun, 18 Mar 2018 13:17:19: 14000000 INFO @ Sun, 18 Mar 2018 13:17:23: 15000000 INFO @ Sun, 18 Mar 2018 13:17:28: 15000000 INFO @ Sun, 18 Mar 2018 13:17:30: 15000000 INFO @ Sun, 18 Mar 2018 13:17:34: 16000000 INFO @ Sun, 18 Mar 2018 13:17:39: 16000000 INFO @ Sun, 18 Mar 2018 13:17:41: 16000000 INFO @ Sun, 18 Mar 2018 13:17:45: 17000000 INFO @ Sun, 18 Mar 2018 13:17:50: 17000000 INFO @ Sun, 18 Mar 2018 13:17:53: 17000000 INFO @ Sun, 18 Mar 2018 13:17:55: 18000000 INFO @ Sun, 18 Mar 2018 13:18:02: 18000000 INFO @ Sun, 18 Mar 2018 13:18:04: 18000000 INFO @ Sun, 18 Mar 2018 13:18:06: 19000000 INFO @ Sun, 18 Mar 2018 13:18:13: 19000000 INFO @ Sun, 18 Mar 2018 13:18:15: 19000000 INFO @ Sun, 18 Mar 2018 13:18:17: 20000000 INFO @ Sun, 18 Mar 2018 13:18:24: 20000000 INFO @ Sun, 18 Mar 2018 13:18:26: 20000000 INFO @ Sun, 18 Mar 2018 13:18:27: 21000000 INFO @ Sun, 18 Mar 2018 13:18:35: 21000000 INFO @ Sun, 18 Mar 2018 13:18:38: 21000000 INFO @ Sun, 18 Mar 2018 13:18:38: 22000000 INFO @ Sun, 18 Mar 2018 13:18:46: 22000000 INFO @ Sun, 18 Mar 2018 13:18:49: 23000000 INFO @ Sun, 18 Mar 2018 13:18:49: 22000000 INFO @ Sun, 18 Mar 2018 13:18:58: 23000000 INFO @ Sun, 18 Mar 2018 13:19:00: 24000000 INFO @ Sun, 18 Mar 2018 13:19:00: 23000000 INFO @ Sun, 18 Mar 2018 13:19:09: 24000000 INFO @ Sun, 18 Mar 2018 13:19:10: 25000000 INFO @ Sun, 18 Mar 2018 13:19:12: 24000000 INFO @ Sun, 18 Mar 2018 13:19:21: 25000000 INFO @ Sun, 18 Mar 2018 13:19:21: 26000000 INFO @ Sun, 18 Mar 2018 13:19:24: 25000000 INFO @ Sun, 18 Mar 2018 13:19:32: 27000000 INFO @ Sun, 18 Mar 2018 13:19:32: 26000000 INFO @ Sun, 18 Mar 2018 13:19:35: 26000000 INFO @ Sun, 18 Mar 2018 13:19:42: 28000000 INFO @ Sun, 18 Mar 2018 13:19:43: 27000000 INFO @ Sun, 18 Mar 2018 13:19:47: 27000000 INFO @ Sun, 18 Mar 2018 13:19:53: 29000000 INFO @ Sun, 18 Mar 2018 13:19:54: 28000000 INFO @ Sun, 18 Mar 2018 13:19:57: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:19:57: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:19:57: #1 total tags in treatment: 29340825 INFO @ Sun, 18 Mar 2018 13:19:57: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:19:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:19:58: 28000000 INFO @ Sun, 18 Mar 2018 13:19:58: #1 tags after filtering in treatment: 29340720 INFO @ Sun, 18 Mar 2018 13:19:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:19:58: #1 finished! INFO @ Sun, 18 Mar 2018 13:19:58: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:19:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:20:01: #2 number of paired peaks: 12762 INFO @ Sun, 18 Mar 2018 13:20:01: start model_add_line... INFO @ Sun, 18 Mar 2018 13:20:01: start X-correlation... INFO @ Sun, 18 Mar 2018 13:20:01: end of X-cor INFO @ Sun, 18 Mar 2018 13:20:01: #2 finished! INFO @ Sun, 18 Mar 2018 13:20:01: #2 predicted fragment length is 162 bps INFO @ Sun, 18 Mar 2018 13:20:01: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 18 Mar 2018 13:20:01: #2.2 Generate R script for model : SRX2611121.05_model.r WARNING @ Sun, 18 Mar 2018 13:20:01: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:20:01: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Sun, 18 Mar 2018 13:20:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:20:01: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:20:06: 29000000 INFO @ Sun, 18 Mar 2018 13:20:09: 29000000 INFO @ Sun, 18 Mar 2018 13:20:10: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:20:10: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:20:10: #1 total tags in treatment: 29340825 INFO @ Sun, 18 Mar 2018 13:20:10: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:20:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:20:11: #1 tags after filtering in treatment: 29340720 INFO @ Sun, 18 Mar 2018 13:20:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:20:11: #1 finished! INFO @ Sun, 18 Mar 2018 13:20:11: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:20:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:20:13: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 13:20:13: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 13:20:13: #1 total tags in treatment: 29340825 INFO @ Sun, 18 Mar 2018 13:20:13: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 13:20:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 13:20:14: #2 number of paired peaks: 12762 INFO @ Sun, 18 Mar 2018 13:20:14: start model_add_line... INFO @ Sun, 18 Mar 2018 13:20:14: #1 tags after filtering in treatment: 29340720 INFO @ Sun, 18 Mar 2018 13:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 13:20:14: #1 finished! INFO @ Sun, 18 Mar 2018 13:20:14: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 13:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 13:20:14: start X-correlation... INFO @ Sun, 18 Mar 2018 13:20:14: end of X-cor INFO @ Sun, 18 Mar 2018 13:20:14: #2 finished! INFO @ Sun, 18 Mar 2018 13:20:14: #2 predicted fragment length is 162 bps INFO @ Sun, 18 Mar 2018 13:20:14: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 18 Mar 2018 13:20:14: #2.2 Generate R script for model : SRX2611121.20_model.r WARNING @ Sun, 18 Mar 2018 13:20:14: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:20:14: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Sun, 18 Mar 2018 13:20:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:20:14: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:20:18: #2 number of paired peaks: 12762 INFO @ Sun, 18 Mar 2018 13:20:18: start model_add_line... INFO @ Sun, 18 Mar 2018 13:20:18: start X-correlation... INFO @ Sun, 18 Mar 2018 13:20:18: end of X-cor INFO @ Sun, 18 Mar 2018 13:20:18: #2 finished! INFO @ Sun, 18 Mar 2018 13:20:18: #2 predicted fragment length is 162 bps INFO @ Sun, 18 Mar 2018 13:20:18: #2 alternative fragment length(s) may be 162 bps INFO @ Sun, 18 Mar 2018 13:20:18: #2.2 Generate R script for model : SRX2611121.10_model.r WARNING @ Sun, 18 Mar 2018 13:20:18: #2 Since the d (162) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 13:20:18: #2 You may need to consider one of the other alternative d(s): 162 WARNING @ Sun, 18 Mar 2018 13:20:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 13:20:18: #3 Call peaks... INFO @ Sun, 18 Mar 2018 13:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 13:21:12: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:21:31: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:21:32: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 13:21:54: #4 Write output xls file... SRX2611121.05_peaks.xls INFO @ Sun, 18 Mar 2018 13:21:54: #4 Write peak in narrowPeak format file... SRX2611121.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:21:54: #4 Write summits bed file... SRX2611121.05_summits.bed INFO @ Sun, 18 Mar 2018 13:21:54: Done! pass1 - making usageList (53 chroms): 12 millis pass2 - checking and writing primary data (2747 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:22:11: #4 Write output xls file... SRX2611121.20_peaks.xls INFO @ Sun, 18 Mar 2018 13:22:11: #4 Write peak in narrowPeak format file... SRX2611121.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:22:11: #4 Write summits bed file... SRX2611121.20_summits.bed INFO @ Sun, 18 Mar 2018 13:22:11: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 13:22:19: #4 Write output xls file... SRX2611121.10_peaks.xls INFO @ Sun, 18 Mar 2018 13:22:19: #4 Write peak in narrowPeak format file... SRX2611121.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 13:22:19: #4 Write summits bed file... SRX2611121.10_summits.bed INFO @ Sun, 18 Mar 2018 13:22:19: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (881 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。