Job ID = 9157929 sra ファイルのダウンロード中... Completed: 732306K bytes transferred in 9 seconds (646476K 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 30561786 spots for /home/okishinya/chipatlas/results/dm3/SRX1837292/SRR3657648.sra Written 30561786 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: 00:17:11 30561786 reads; of these: 30561786 (100.00%) were unpaired; of these: 969755 (3.17%) aligned 0 times 11102438 (36.33%) aligned exactly 1 time 18489593 (60.50%) aligned >1 times 96.83% overall alignment rate Time searching: 00:17:11 Overall time: 00:17:11 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] 12807963 / 29592031 = 0.4328 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 14:28:36: # Command line: callpeak -t SRX1837292.bam -f BAM -g dm -n SRX1837292.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837292.10 # format = BAM # ChIP-seq file = ['SRX1837292.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 14:28:36: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:28:36: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:28:36: # Command line: callpeak -t SRX1837292.bam -f BAM -g dm -n SRX1837292.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837292.20 # format = BAM # ChIP-seq file = ['SRX1837292.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 14:28:36: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:28:36: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:28:36: # Command line: callpeak -t SRX1837292.bam -f BAM -g dm -n SRX1837292.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837292.05 # format = BAM # ChIP-seq file = ['SRX1837292.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 14:28:36: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:28:36: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:28:42: 1000000 INFO @ Tue, 27 Jun 2017 14:28:42: 1000000 INFO @ Tue, 27 Jun 2017 14:28:44: 1000000 INFO @ Tue, 27 Jun 2017 14:28:50: 2000000 INFO @ Tue, 27 Jun 2017 14:28:50: 2000000 INFO @ Tue, 27 Jun 2017 14:28:52: 2000000 INFO @ Tue, 27 Jun 2017 14:28:56: 3000000 INFO @ Tue, 27 Jun 2017 14:28:57: 3000000 INFO @ Tue, 27 Jun 2017 14:29:00: 3000000 INFO @ Tue, 27 Jun 2017 14:29:03: 4000000 INFO @ Tue, 27 Jun 2017 14:29:03: 4000000 INFO @ Tue, 27 Jun 2017 14:29:07: 4000000 INFO @ Tue, 27 Jun 2017 14:29:09: 5000000 INFO @ Tue, 27 Jun 2017 14:29:10: 5000000 INFO @ Tue, 27 Jun 2017 14:29:13: 5000000 INFO @ Tue, 27 Jun 2017 14:29:16: 6000000 INFO @ Tue, 27 Jun 2017 14:29:17: 6000000 INFO @ Tue, 27 Jun 2017 14:29:20: 6000000 INFO @ Tue, 27 Jun 2017 14:29:22: 7000000 INFO @ Tue, 27 Jun 2017 14:29:24: 7000000 INFO @ Tue, 27 Jun 2017 14:29:26: 7000000 INFO @ Tue, 27 Jun 2017 14:29:28: 8000000 INFO @ Tue, 27 Jun 2017 14:29:31: 8000000 INFO @ Tue, 27 Jun 2017 14:29:33: 8000000 INFO @ Tue, 27 Jun 2017 14:29:35: 9000000 INFO @ Tue, 27 Jun 2017 14:29:38: 9000000 INFO @ Tue, 27 Jun 2017 14:29:39: 9000000 INFO @ Tue, 27 Jun 2017 14:29:42: 10000000 INFO @ Tue, 27 Jun 2017 14:29:45: 10000000 INFO @ Tue, 27 Jun 2017 14:29:45: 10000000 INFO @ Tue, 27 Jun 2017 14:29:48: 11000000 INFO @ Tue, 27 Jun 2017 14:29:52: 11000000 INFO @ Tue, 27 Jun 2017 14:29:52: 11000000 INFO @ Tue, 27 Jun 2017 14:29:55: 12000000 INFO @ Tue, 27 Jun 2017 14:29:58: 12000000 INFO @ Tue, 27 Jun 2017 14:29:59: 12000000 INFO @ Tue, 27 Jun 2017 14:30:01: 13000000 INFO @ Tue, 27 Jun 2017 14:30:04: 13000000 INFO @ Tue, 27 Jun 2017 14:30:06: 13000000 INFO @ Tue, 27 Jun 2017 14:30:08: 14000000 INFO @ Tue, 27 Jun 2017 14:30:11: 14000000 INFO @ Tue, 27 Jun 2017 14:30:13: 14000000 INFO @ Tue, 27 Jun 2017 14:30:14: 15000000 INFO @ Tue, 27 Jun 2017 14:30:17: 15000000 INFO @ Tue, 27 Jun 2017 14:30:20: 15000000 INFO @ Tue, 27 Jun 2017 14:30:21: 16000000 INFO @ Tue, 27 Jun 2017 14:30:23: 16000000 INFO @ Tue, 27 Jun 2017 14:30:26: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:30:26: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:30:26: #1 total tags in treatment: 16784068 INFO @ Tue, 27 Jun 2017 14:30:26: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:30:26: #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 14:30:27: #1 tags after filtering in treatment: 16784068 INFO @ Tue, 27 Jun 2017 14:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:30:27: #1 finished! INFO @ Tue, 27 Jun 2017 14:30:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:30:27: 16000000 INFO @ Tue, 27 Jun 2017 14:30:28: #2 number of paired peaks: 778 WARNING @ Tue, 27 Jun 2017 14:30:28: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Tue, 27 Jun 2017 14:30:28: start model_add_line... INFO @ Tue, 27 Jun 2017 14:30:28: start X-correlation... INFO @ Tue, 27 Jun 2017 14:30:28: end of X-cor INFO @ Tue, 27 Jun 2017 14:30:28: #2 finished! INFO @ Tue, 27 Jun 2017 14:30:28: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 14:30:28: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 27 Jun 2017 14:30:28: #2.2 Generate R script for model : SRX1837292.05_model.r WARNING @ Tue, 27 Jun 2017 14:30:28: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:30:28: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 27 Jun 2017 14:30:28: #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 14:30:28: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:30:28: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:30:28: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:30:28: #1 total tags in treatment: 16784068 INFO @ Tue, 27 Jun 2017 14:30:28: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:30:28: #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 14:30:29: #1 tags after filtering in treatment: 16784068 INFO @ Tue, 27 Jun 2017 14:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:30:29: #1 finished! INFO @ Tue, 27 Jun 2017 14:30:29: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:30:30: #2 number of paired peaks: 778 WARNING @ Tue, 27 Jun 2017 14:30:30: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Tue, 27 Jun 2017 14:30:30: start model_add_line... INFO @ Tue, 27 Jun 2017 14:30:30: start X-correlation... INFO @ Tue, 27 Jun 2017 14:30:30: end of X-cor INFO @ Tue, 27 Jun 2017 14:30:30: #2 finished! INFO @ Tue, 27 Jun 2017 14:30:30: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 14:30:30: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 27 Jun 2017 14:30:30: #2.2 Generate R script for model : SRX1837292.20_model.r WARNING @ Tue, 27 Jun 2017 14:30:30: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:30:30: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 27 Jun 2017 14:30:30: #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 14:30:30: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:30:32: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:30:32: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:30:32: #1 total tags in treatment: 16784068 INFO @ Tue, 27 Jun 2017 14:30:32: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:30:32: #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 14:30:33: #1 tags after filtering in treatment: 16784068 INFO @ Tue, 27 Jun 2017 14:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:30:33: #1 finished! INFO @ Tue, 27 Jun 2017 14:30:33: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:30:34: #2 number of paired peaks: 778 WARNING @ Tue, 27 Jun 2017 14:30:34: Fewer paired peaks (778) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 778 pairs to build model! INFO @ Tue, 27 Jun 2017 14:30:34: start model_add_line... INFO @ Tue, 27 Jun 2017 14:30:34: start X-correlation... INFO @ Tue, 27 Jun 2017 14:30:34: end of X-cor INFO @ Tue, 27 Jun 2017 14:30:34: #2 finished! INFO @ Tue, 27 Jun 2017 14:30:34: #2 predicted fragment length is 51 bps INFO @ Tue, 27 Jun 2017 14:30:34: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 27 Jun 2017 14:30:34: #2.2 Generate R script for model : SRX1837292.10_model.r WARNING @ Tue, 27 Jun 2017 14:30:34: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:30:34: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 27 Jun 2017 14:30:34: #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 14:30:34: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:31:03: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:31:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:31:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:31:23: #4 Write output xls file... SRX1837292.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:31:23: #4 Write peak in narrowPeak format file... SRX1837292.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:31:23: #4 Write summits bed file... SRX1837292.05_summits.bed INFO @ Tue, 27 Jun 2017 14:31:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8758 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:31:25: #4 Write output xls file... SRX1837292.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:31:25: #4 Write peak in narrowPeak format file... SRX1837292.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:31:25: #4 Write summits bed file... SRX1837292.20_summits.bed INFO @ Tue, 27 Jun 2017 14:31:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (993 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:31:29: #4 Write output xls file... SRX1837292.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:31:29: #4 Write peak in narrowPeak format file... SRX1837292.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:31:29: #4 Write summits bed file... SRX1837292.10_summits.bed INFO @ Tue, 27 Jun 2017 14:31:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2643 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。