Job ID = 9157933 sra ファイルのダウンロード中... Completed: 1025187K bytes transferred in 13 seconds (640838K bits/sec), in 1 file, 2 directories. 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 43174143 spots for /home/okishinya/chipatlas/results/dm3/SRX1837296/SRR3657652.sra Written 43174143 spots total 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:24 43174143 reads; of these: 43174143 (100.00%) were unpaired; of these: 4805891 (11.13%) aligned 0 times 14211979 (32.92%) aligned exactly 1 time 24156273 (55.95%) aligned >1 times 88.87% overall alignment rate Time searching: 00:21:24 Overall time: 00:21:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 11108092 / 38368252 = 0.2895 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 @ Tue, 27 Jun 2017 14:38:27: # Command line: callpeak -t SRX1837296.bam -f BAM -g dm -n SRX1837296.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837296.20 # format = BAM # ChIP-seq file = ['SRX1837296.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 14:38:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:38:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:38:27: # Command line: callpeak -t SRX1837296.bam -f BAM -g dm -n SRX1837296.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837296.05 # format = BAM # ChIP-seq file = ['SRX1837296.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 14:38:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:38:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:38:27: # Command line: callpeak -t SRX1837296.bam -f BAM -g dm -n SRX1837296.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837296.10 # format = BAM # ChIP-seq file = ['SRX1837296.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 27 Jun 2017 14:38:27: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:38:27: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:38:35: 1000000 INFO @ Tue, 27 Jun 2017 14:38:35: 1000000 INFO @ Tue, 27 Jun 2017 14:38:35: 1000000 INFO @ Tue, 27 Jun 2017 14:38:42: 2000000 INFO @ Tue, 27 Jun 2017 14:38:42: 2000000 INFO @ Tue, 27 Jun 2017 14:38:43: 2000000 INFO @ Tue, 27 Jun 2017 14:38:50: 3000000 INFO @ Tue, 27 Jun 2017 14:38:50: 3000000 INFO @ Tue, 27 Jun 2017 14:38:50: 3000000 INFO @ Tue, 27 Jun 2017 14:38:57: 4000000 INFO @ Tue, 27 Jun 2017 14:38:57: 4000000 INFO @ Tue, 27 Jun 2017 14:38:58: 4000000 INFO @ Tue, 27 Jun 2017 14:39:05: 5000000 INFO @ Tue, 27 Jun 2017 14:39:05: 5000000 INFO @ Tue, 27 Jun 2017 14:39:06: 5000000 INFO @ Tue, 27 Jun 2017 14:39:12: 6000000 INFO @ Tue, 27 Jun 2017 14:39:12: 6000000 INFO @ Tue, 27 Jun 2017 14:39:13: 6000000 INFO @ Tue, 27 Jun 2017 14:39:20: 7000000 INFO @ Tue, 27 Jun 2017 14:39:20: 7000000 INFO @ Tue, 27 Jun 2017 14:39:21: 7000000 INFO @ Tue, 27 Jun 2017 14:39:28: 8000000 INFO @ Tue, 27 Jun 2017 14:39:28: 8000000 INFO @ Tue, 27 Jun 2017 14:39:29: 8000000 INFO @ Tue, 27 Jun 2017 14:39:35: 9000000 INFO @ Tue, 27 Jun 2017 14:39:35: 9000000 INFO @ Tue, 27 Jun 2017 14:39:37: 9000000 INFO @ Tue, 27 Jun 2017 14:39:42: 10000000 INFO @ Tue, 27 Jun 2017 14:39:42: 10000000 INFO @ Tue, 27 Jun 2017 14:39:44: 10000000 INFO @ Tue, 27 Jun 2017 14:39:50: 11000000 INFO @ Tue, 27 Jun 2017 14:39:50: 11000000 INFO @ Tue, 27 Jun 2017 14:39:52: 11000000 INFO @ Tue, 27 Jun 2017 14:39:57: 12000000 INFO @ Tue, 27 Jun 2017 14:39:57: 12000000 INFO @ Tue, 27 Jun 2017 14:40:00: 12000000 INFO @ Tue, 27 Jun 2017 14:40:05: 13000000 INFO @ Tue, 27 Jun 2017 14:40:05: 13000000 INFO @ Tue, 27 Jun 2017 14:40:07: 13000000 INFO @ Tue, 27 Jun 2017 14:40:12: 14000000 INFO @ Tue, 27 Jun 2017 14:40:12: 14000000 INFO @ Tue, 27 Jun 2017 14:40:15: 14000000 INFO @ Tue, 27 Jun 2017 14:40:20: 15000000 INFO @ Tue, 27 Jun 2017 14:40:20: 15000000 INFO @ Tue, 27 Jun 2017 14:40:23: 15000000 INFO @ Tue, 27 Jun 2017 14:40:27: 16000000 INFO @ Tue, 27 Jun 2017 14:40:27: 16000000 INFO @ Tue, 27 Jun 2017 14:40:30: 16000000 INFO @ Tue, 27 Jun 2017 14:40:35: 17000000 INFO @ Tue, 27 Jun 2017 14:40:35: 17000000 INFO @ Tue, 27 Jun 2017 14:40:38: 17000000 INFO @ Tue, 27 Jun 2017 14:40:42: 18000000 INFO @ Tue, 27 Jun 2017 14:40:42: 18000000 INFO @ Tue, 27 Jun 2017 14:40:46: 18000000 INFO @ Tue, 27 Jun 2017 14:40:50: 19000000 INFO @ Tue, 27 Jun 2017 14:40:50: 19000000 INFO @ Tue, 27 Jun 2017 14:40:53: 19000000 INFO @ Tue, 27 Jun 2017 14:40:57: 20000000 INFO @ Tue, 27 Jun 2017 14:40:57: 20000000 INFO @ Tue, 27 Jun 2017 14:41:01: 20000000 INFO @ Tue, 27 Jun 2017 14:41:05: 21000000 INFO @ Tue, 27 Jun 2017 14:41:05: 21000000 INFO @ Tue, 27 Jun 2017 14:41:09: 21000000 INFO @ Tue, 27 Jun 2017 14:41:12: 22000000 INFO @ Tue, 27 Jun 2017 14:41:12: 22000000 INFO @ Tue, 27 Jun 2017 14:41:16: 22000000 INFO @ Tue, 27 Jun 2017 14:41:20: 23000000 INFO @ Tue, 27 Jun 2017 14:41:20: 23000000 INFO @ Tue, 27 Jun 2017 14:41:24: 23000000 INFO @ Tue, 27 Jun 2017 14:41:27: 24000000 INFO @ Tue, 27 Jun 2017 14:41:27: 24000000 INFO @ Tue, 27 Jun 2017 14:41:32: 24000000 INFO @ Tue, 27 Jun 2017 14:41:35: 25000000 INFO @ Tue, 27 Jun 2017 14:41:35: 25000000 INFO @ Tue, 27 Jun 2017 14:41:40: 25000000 INFO @ Tue, 27 Jun 2017 14:41:42: 26000000 INFO @ Tue, 27 Jun 2017 14:41:42: 26000000 INFO @ Tue, 27 Jun 2017 14:41:47: 26000000 INFO @ Tue, 27 Jun 2017 14:41:50: 27000000 INFO @ Tue, 27 Jun 2017 14:41:50: 27000000 INFO @ Tue, 27 Jun 2017 14:41:52: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:41:52: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:41:52: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:41:52: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:41:52: #1 total tags in treatment: 27260160 INFO @ Tue, 27 Jun 2017 14:41:52: #1 total tags in treatment: 27260160 INFO @ Tue, 27 Jun 2017 14:41:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:41:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:41:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:41:53: #1 tags after filtering in treatment: 27260160 INFO @ Tue, 27 Jun 2017 14:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:41:53: #1 finished! INFO @ Tue, 27 Jun 2017 14:41:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:41:53: #1 tags after filtering in treatment: 27260160 INFO @ Tue, 27 Jun 2017 14:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:41:53: #1 finished! INFO @ Tue, 27 Jun 2017 14:41:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:41:55: #2 number of paired peaks: 748 WARNING @ Tue, 27 Jun 2017 14:41:55: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Tue, 27 Jun 2017 14:41:55: start model_add_line... INFO @ Tue, 27 Jun 2017 14:41:55: #2 number of paired peaks: 748 WARNING @ Tue, 27 Jun 2017 14:41:55: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Tue, 27 Jun 2017 14:41:55: start model_add_line... INFO @ Tue, 27 Jun 2017 14:41:55: start X-correlation... INFO @ Tue, 27 Jun 2017 14:41:55: start X-correlation... INFO @ Tue, 27 Jun 2017 14:41:55: end of X-cor INFO @ Tue, 27 Jun 2017 14:41:55: end of X-cor INFO @ Tue, 27 Jun 2017 14:41:55: #2 finished! INFO @ Tue, 27 Jun 2017 14:41:55: #2 finished! INFO @ Tue, 27 Jun 2017 14:41:55: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 14:41:55: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 14:41:55: #2 alternative fragment length(s) may be 1,35 bps INFO @ Tue, 27 Jun 2017 14:41:55: #2 alternative fragment length(s) may be 1,35 bps INFO @ Tue, 27 Jun 2017 14:41:55: #2.2 Generate R script for model : SRX1837296.20_model.r INFO @ Tue, 27 Jun 2017 14:41:55: #2.2 Generate R script for model : SRX1837296.05_model.r WARNING @ Tue, 27 Jun 2017 14:41:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:41:55: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Tue, 27 Jun 2017 14:41:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:41:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Tue, 27 Jun 2017 14:41:55: #2 You may need to consider one of the other alternative d(s): 1,35 INFO @ Tue, 27 Jun 2017 14:41:55: #3 Call peaks... WARNING @ Tue, 27 Jun 2017 14:41:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 14:41:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:41:55: 27000000 INFO @ Tue, 27 Jun 2017 14:41:57: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:41:57: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:41:57: #1 total tags in treatment: 27260160 INFO @ Tue, 27 Jun 2017 14:41:57: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:41:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 14:41:58: #1 tags after filtering in treatment: 27260160 INFO @ Tue, 27 Jun 2017 14:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:41:58: #1 finished! INFO @ Tue, 27 Jun 2017 14:41:58: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:41:59: #2 number of paired peaks: 748 WARNING @ Tue, 27 Jun 2017 14:41:59: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Tue, 27 Jun 2017 14:41:59: start model_add_line... INFO @ Tue, 27 Jun 2017 14:42:00: start X-correlation... INFO @ Tue, 27 Jun 2017 14:42:00: end of X-cor INFO @ Tue, 27 Jun 2017 14:42:00: #2 finished! INFO @ Tue, 27 Jun 2017 14:42:00: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 14:42:00: #2 alternative fragment length(s) may be 1,35 bps INFO @ Tue, 27 Jun 2017 14:42:00: #2.2 Generate R script for model : SRX1837296.10_model.r WARNING @ Tue, 27 Jun 2017 14:42:00: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:42:00: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Tue, 27 Jun 2017 14:42:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 14:42:00: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:42:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:42:37: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:42:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:42:57: #4 Write output xls file... SRX1837296.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:42:57: #4 Write output xls file... SRX1837296.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:42:57: #4 Write peak in narrowPeak format file... SRX1837296.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:42:57: #4 Write peak in narrowPeak format file... SRX1837296.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:42:57: #4 Write summits bed file... SRX1837296.20_summits.bed INFO @ Tue, 27 Jun 2017 14:42:57: #4 Write summits bed file... SRX1837296.05_summits.bed INFO @ Tue, 27 Jun 2017 14:42:57: Done! INFO @ Tue, 27 Jun 2017 14:42:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:43:05: #4 Write output xls file... SRX1837296.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:43:05: #4 Write peak in narrowPeak format file... SRX1837296.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:43:05: #4 Write summits bed file... SRX1837296.10_summits.bed INFO @ Tue, 27 Jun 2017 14:43:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。