Job ID = 9157919 sra ファイルのダウンロード中... Completed: 648284K bytes transferred in 8 seconds (596838K 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 27124521 spots for /home/okishinya/chipatlas/results/dm3/SRX1837288/SRR3657644.sra Written 27124521 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: 00:14:23 27124521 reads; of these: 27124521 (100.00%) were unpaired; of these: 1293466 (4.77%) aligned 0 times 8987753 (33.14%) aligned exactly 1 time 16843302 (62.10%) aligned >1 times 95.23% overall alignment rate Time searching: 00:14:23 Overall time: 00:14:23 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 12 files... [bam_rmdupse_core] 7768001 / 25831055 = 0.3007 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 14:23:52: # Command line: callpeak -t SRX1837288.bam -f BAM -g dm -n SRX1837288.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837288.10 # format = BAM # ChIP-seq file = ['SRX1837288.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 14:23:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:23:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:23:52: # Command line: callpeak -t SRX1837288.bam -f BAM -g dm -n SRX1837288.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837288.20 # format = BAM # ChIP-seq file = ['SRX1837288.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 14:23:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:23:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:23:52: # Command line: callpeak -t SRX1837288.bam -f BAM -g dm -n SRX1837288.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837288.05 # format = BAM # ChIP-seq file = ['SRX1837288.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 14:23:52: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:23:52: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:23:59: 1000000 INFO @ Tue, 27 Jun 2017 14:24:00: 1000000 INFO @ Tue, 27 Jun 2017 14:24:00: 1000000 INFO @ Tue, 27 Jun 2017 14:24:06: 2000000 INFO @ Tue, 27 Jun 2017 14:24:08: 2000000 INFO @ Tue, 27 Jun 2017 14:24:08: 2000000 INFO @ Tue, 27 Jun 2017 14:24:13: 3000000 INFO @ Tue, 27 Jun 2017 14:24:15: 3000000 INFO @ Tue, 27 Jun 2017 14:24:15: 3000000 INFO @ Tue, 27 Jun 2017 14:24:20: 4000000 INFO @ Tue, 27 Jun 2017 14:24:23: 4000000 INFO @ Tue, 27 Jun 2017 14:24:23: 4000000 INFO @ Tue, 27 Jun 2017 14:24:27: 5000000 INFO @ Tue, 27 Jun 2017 14:24:31: 5000000 INFO @ Tue, 27 Jun 2017 14:24:31: 5000000 INFO @ Tue, 27 Jun 2017 14:24:33: 6000000 INFO @ Tue, 27 Jun 2017 14:24:38: 6000000 INFO @ Tue, 27 Jun 2017 14:24:38: 6000000 INFO @ Tue, 27 Jun 2017 14:24:40: 7000000 INFO @ Tue, 27 Jun 2017 14:24:46: 7000000 INFO @ Tue, 27 Jun 2017 14:24:46: 7000000 INFO @ Tue, 27 Jun 2017 14:24:47: 8000000 INFO @ Tue, 27 Jun 2017 14:24:54: 8000000 INFO @ Tue, 27 Jun 2017 14:24:54: 8000000 INFO @ Tue, 27 Jun 2017 14:24:54: 9000000 INFO @ Tue, 27 Jun 2017 14:25:00: 10000000 INFO @ Tue, 27 Jun 2017 14:25:01: 9000000 INFO @ Tue, 27 Jun 2017 14:25:01: 9000000 INFO @ Tue, 27 Jun 2017 14:25:07: 11000000 INFO @ Tue, 27 Jun 2017 14:25:09: 10000000 INFO @ Tue, 27 Jun 2017 14:25:09: 10000000 INFO @ Tue, 27 Jun 2017 14:25:14: 12000000 INFO @ Tue, 27 Jun 2017 14:25:16: 11000000 INFO @ Tue, 27 Jun 2017 14:25:16: 11000000 INFO @ Tue, 27 Jun 2017 14:25:21: 13000000 INFO @ Tue, 27 Jun 2017 14:25:24: 12000000 INFO @ Tue, 27 Jun 2017 14:25:24: 12000000 INFO @ Tue, 27 Jun 2017 14:25:28: 14000000 INFO @ Tue, 27 Jun 2017 14:25:32: 13000000 INFO @ Tue, 27 Jun 2017 14:25:32: 13000000 INFO @ Tue, 27 Jun 2017 14:25:34: 15000000 INFO @ Tue, 27 Jun 2017 14:25:39: 14000000 INFO @ Tue, 27 Jun 2017 14:25:39: 14000000 INFO @ Tue, 27 Jun 2017 14:25:41: 16000000 INFO @ Tue, 27 Jun 2017 14:25:47: 15000000 INFO @ Tue, 27 Jun 2017 14:25:47: 15000000 INFO @ Tue, 27 Jun 2017 14:25:48: 17000000 INFO @ Tue, 27 Jun 2017 14:25:55: 16000000 INFO @ Tue, 27 Jun 2017 14:25:55: 16000000 INFO @ Tue, 27 Jun 2017 14:25:55: 18000000 INFO @ Tue, 27 Jun 2017 14:25:55: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:25:55: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:25:55: #1 total tags in treatment: 18063054 INFO @ Tue, 27 Jun 2017 14:25:55: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:25:55: #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 14:25:56: #1 tags after filtering in treatment: 18063054 INFO @ Tue, 27 Jun 2017 14:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:25:56: #1 finished! INFO @ Tue, 27 Jun 2017 14:25:56: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:25:57: #2 number of paired peaks: 1068 INFO @ Tue, 27 Jun 2017 14:25:57: start model_add_line... INFO @ Tue, 27 Jun 2017 14:25:57: start X-correlation... INFO @ Tue, 27 Jun 2017 14:25:57: end of X-cor INFO @ Tue, 27 Jun 2017 14:25:57: #2 finished! INFO @ Tue, 27 Jun 2017 14:25:57: #2 predicted fragment length is 54 bps INFO @ Tue, 27 Jun 2017 14:25:57: #2 alternative fragment length(s) may be 3,54,560 bps INFO @ Tue, 27 Jun 2017 14:25:57: #2.2 Generate R script for model : SRX1837288.05_model.r WARNING @ Tue, 27 Jun 2017 14:25:57: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:25:57: #2 You may need to consider one of the other alternative d(s): 3,54,560 WARNING @ Tue, 27 Jun 2017 14:25:57: #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 14:25:57: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:25:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:26:02: 17000000 INFO @ Tue, 27 Jun 2017 14:26:02: 17000000 INFO @ Tue, 27 Jun 2017 14:26:10: 18000000 INFO @ Tue, 27 Jun 2017 14:26:10: 18000000 INFO @ Tue, 27 Jun 2017 14:26:10: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:26:10: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:26:10: #1 total tags in treatment: 18063054 INFO @ Tue, 27 Jun 2017 14:26:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:26:10: #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 14:26:10: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:26:10: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:26:10: #1 total tags in treatment: 18063054 INFO @ Tue, 27 Jun 2017 14:26:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:26:10: #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 14:26:11: #1 tags after filtering in treatment: 18063054 INFO @ Tue, 27 Jun 2017 14:26:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:26:11: #1 finished! INFO @ Tue, 27 Jun 2017 14:26:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:26:11: #1 tags after filtering in treatment: 18063054 INFO @ Tue, 27 Jun 2017 14:26:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:26:11: #1 finished! INFO @ Tue, 27 Jun 2017 14:26:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:26:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:26:12: #2 number of paired peaks: 1068 INFO @ Tue, 27 Jun 2017 14:26:12: start model_add_line... INFO @ Tue, 27 Jun 2017 14:26:12: #2 number of paired peaks: 1068 INFO @ Tue, 27 Jun 2017 14:26:12: start model_add_line... INFO @ Tue, 27 Jun 2017 14:26:12: start X-correlation... INFO @ Tue, 27 Jun 2017 14:26:12: end of X-cor INFO @ Tue, 27 Jun 2017 14:26:12: #2 finished! INFO @ Tue, 27 Jun 2017 14:26:12: #2 predicted fragment length is 54 bps INFO @ Tue, 27 Jun 2017 14:26:12: #2 alternative fragment length(s) may be 3,54,560 bps INFO @ Tue, 27 Jun 2017 14:26:12: #2.2 Generate R script for model : SRX1837288.20_model.r WARNING @ Tue, 27 Jun 2017 14:26:12: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:26:12: #2 You may need to consider one of the other alternative d(s): 3,54,560 WARNING @ Tue, 27 Jun 2017 14:26:12: #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 14:26:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:26:12: start X-correlation... INFO @ Tue, 27 Jun 2017 14:26:12: end of X-cor INFO @ Tue, 27 Jun 2017 14:26:12: #2 finished! INFO @ Tue, 27 Jun 2017 14:26:12: #2 predicted fragment length is 54 bps INFO @ Tue, 27 Jun 2017 14:26:12: #2 alternative fragment length(s) may be 3,54,560 bps INFO @ Tue, 27 Jun 2017 14:26:12: #2.2 Generate R script for model : SRX1837288.10_model.r WARNING @ Tue, 27 Jun 2017 14:26:12: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:26:12: #2 You may need to consider one of the other alternative d(s): 3,54,560 WARNING @ Tue, 27 Jun 2017 14:26:12: #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 14:26:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:26:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:26:31: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:26:47: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:26:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:26:53: #4 Write output xls file... SRX1837288.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:26:53: #4 Write peak in narrowPeak format file... SRX1837288.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:26:53: #4 Write summits bed file... SRX1837288.05_summits.bed INFO @ Tue, 27 Jun 2017 14:26:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9483 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:27:08: #4 Write output xls file... SRX1837288.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:27:08: #4 Write peak in narrowPeak format file... SRX1837288.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:27:08: #4 Write summits bed file... SRX1837288.10_summits.bed INFO @ Tue, 27 Jun 2017 14:27:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3006 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:27:08: #4 Write output xls file... SRX1837288.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:27:09: #4 Write peak in narrowPeak format file... SRX1837288.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:27:09: #4 Write summits bed file... SRX1837288.20_summits.bed INFO @ Tue, 27 Jun 2017 14:27:09: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1059 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。