Job ID = 9157923 sra ファイルのダウンロード中... Completed: 769789K bytes transferred in 9 seconds (655652K 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 32535360 spots for /home/okishinya/chipatlas/results/dm3/SRX1837290/SRR3657646.sra Written 32535360 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: 00:14:27 32535360 reads; of these: 32535360 (100.00%) were unpaired; of these: 4941568 (15.19%) aligned 0 times 13095968 (40.25%) aligned exactly 1 time 14497824 (44.56%) aligned >1 times 84.81% overall alignment rate Time searching: 00:14:27 Overall time: 00:14:27 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] 10149625 / 27593792 = 0.3678 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 14:25:02: # Command line: callpeak -t SRX1837290.bam -f BAM -g dm -n SRX1837290.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1837290.20 # format = BAM # ChIP-seq file = ['SRX1837290.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 14:25:02: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:25:02: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:25:02: # Command line: callpeak -t SRX1837290.bam -f BAM -g dm -n SRX1837290.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1837290.05 # format = BAM # ChIP-seq file = ['SRX1837290.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 14:25:02: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:25:02: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:25:02: # Command line: callpeak -t SRX1837290.bam -f BAM -g dm -n SRX1837290.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1837290.10 # format = BAM # ChIP-seq file = ['SRX1837290.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 14:25:02: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:25:02: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:25:09: 1000000 INFO @ Tue, 27 Jun 2017 14:25:10: 1000000 INFO @ Tue, 27 Jun 2017 14:25:10: 1000000 INFO @ Tue, 27 Jun 2017 14:25:16: 2000000 INFO @ Tue, 27 Jun 2017 14:25:17: 2000000 INFO @ Tue, 27 Jun 2017 14:25:17: 2000000 INFO @ Tue, 27 Jun 2017 14:25:23: 3000000 INFO @ Tue, 27 Jun 2017 14:25:24: 3000000 INFO @ Tue, 27 Jun 2017 14:25:24: 3000000 INFO @ Tue, 27 Jun 2017 14:25:30: 4000000 INFO @ Tue, 27 Jun 2017 14:25:31: 4000000 INFO @ Tue, 27 Jun 2017 14:25:31: 4000000 INFO @ Tue, 27 Jun 2017 14:25:36: 5000000 INFO @ Tue, 27 Jun 2017 14:25:38: 5000000 INFO @ Tue, 27 Jun 2017 14:25:38: 5000000 INFO @ Tue, 27 Jun 2017 14:25:43: 6000000 INFO @ Tue, 27 Jun 2017 14:25:45: 6000000 INFO @ Tue, 27 Jun 2017 14:25:45: 6000000 INFO @ Tue, 27 Jun 2017 14:25:50: 7000000 INFO @ Tue, 27 Jun 2017 14:25:52: 7000000 INFO @ Tue, 27 Jun 2017 14:25:52: 7000000 INFO @ Tue, 27 Jun 2017 14:25:57: 8000000 INFO @ Tue, 27 Jun 2017 14:25:59: 8000000 INFO @ Tue, 27 Jun 2017 14:26:00: 8000000 INFO @ Tue, 27 Jun 2017 14:26:03: 9000000 INFO @ Tue, 27 Jun 2017 14:26:06: 9000000 INFO @ Tue, 27 Jun 2017 14:26:07: 9000000 INFO @ Tue, 27 Jun 2017 14:26:10: 10000000 INFO @ Tue, 27 Jun 2017 14:26:13: 10000000 INFO @ Tue, 27 Jun 2017 14:26:14: 10000000 INFO @ Tue, 27 Jun 2017 14:26:17: 11000000 INFO @ Tue, 27 Jun 2017 14:26:21: 11000000 INFO @ Tue, 27 Jun 2017 14:26:22: 11000000 INFO @ Tue, 27 Jun 2017 14:26:23: 12000000 INFO @ Tue, 27 Jun 2017 14:26:28: 12000000 INFO @ Tue, 27 Jun 2017 14:26:30: 12000000 INFO @ Tue, 27 Jun 2017 14:26:30: 13000000 INFO @ Tue, 27 Jun 2017 14:26:36: 13000000 INFO @ Tue, 27 Jun 2017 14:26:37: 14000000 INFO @ Tue, 27 Jun 2017 14:26:37: 13000000 INFO @ Tue, 27 Jun 2017 14:26:44: 14000000 INFO @ Tue, 27 Jun 2017 14:26:44: 15000000 INFO @ Tue, 27 Jun 2017 14:26:45: 14000000 INFO @ Tue, 27 Jun 2017 14:26:51: 16000000 INFO @ Tue, 27 Jun 2017 14:26:52: 15000000 INFO @ Tue, 27 Jun 2017 14:26:53: 15000000 INFO @ Tue, 27 Jun 2017 14:26:58: 17000000 INFO @ Tue, 27 Jun 2017 14:27:00: 16000000 INFO @ Tue, 27 Jun 2017 14:27:01: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:27:01: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:27:01: #1 total tags in treatment: 17444167 INFO @ Tue, 27 Jun 2017 14:27:01: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:27:01: #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 14:27:01: 16000000 INFO @ Tue, 27 Jun 2017 14:27:01: #1 tags after filtering in treatment: 17444167 INFO @ Tue, 27 Jun 2017 14:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:27:01: #1 finished! INFO @ Tue, 27 Jun 2017 14:27:01: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:27:03: #2 number of paired peaks: 710 WARNING @ Tue, 27 Jun 2017 14:27:03: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Tue, 27 Jun 2017 14:27:03: start model_add_line... INFO @ Tue, 27 Jun 2017 14:27:03: start X-correlation... INFO @ Tue, 27 Jun 2017 14:27:03: end of X-cor INFO @ Tue, 27 Jun 2017 14:27:03: #2 finished! INFO @ Tue, 27 Jun 2017 14:27:03: #2 predicted fragment length is 68 bps INFO @ Tue, 27 Jun 2017 14:27:03: #2 alternative fragment length(s) may be 4,68 bps INFO @ Tue, 27 Jun 2017 14:27:03: #2.2 Generate R script for model : SRX1837290.10_model.r WARNING @ Tue, 27 Jun 2017 14:27:03: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:27:03: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Tue, 27 Jun 2017 14:27:03: #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 14:27:03: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:27:07: 17000000 INFO @ Tue, 27 Jun 2017 14:27:09: 17000000 INFO @ Tue, 27 Jun 2017 14:27:11: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:27:11: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:27:11: #1 total tags in treatment: 17444167 INFO @ Tue, 27 Jun 2017 14:27:11: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:27:11: #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 14:27:11: #1 tags after filtering in treatment: 17444167 INFO @ Tue, 27 Jun 2017 14:27:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:27:11: #1 finished! INFO @ Tue, 27 Jun 2017 14:27:11: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:27:12: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 14:27:12: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 14:27:12: #1 total tags in treatment: 17444167 INFO @ Tue, 27 Jun 2017 14:27:12: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:27:12: #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 14:27:12: #1 tags after filtering in treatment: 17444167 INFO @ Tue, 27 Jun 2017 14:27:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:27:12: #1 finished! INFO @ Tue, 27 Jun 2017 14:27:12: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:27:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:27:13: #2 number of paired peaks: 710 WARNING @ Tue, 27 Jun 2017 14:27:13: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Tue, 27 Jun 2017 14:27:13: start model_add_line... INFO @ Tue, 27 Jun 2017 14:27:13: start X-correlation... INFO @ Tue, 27 Jun 2017 14:27:13: end of X-cor INFO @ Tue, 27 Jun 2017 14:27:13: #2 finished! INFO @ Tue, 27 Jun 2017 14:27:13: #2 predicted fragment length is 68 bps INFO @ Tue, 27 Jun 2017 14:27:13: #2 alternative fragment length(s) may be 4,68 bps INFO @ Tue, 27 Jun 2017 14:27:13: #2.2 Generate R script for model : SRX1837290.05_model.r WARNING @ Tue, 27 Jun 2017 14:27:13: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:27:13: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Tue, 27 Jun 2017 14:27:13: #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 14:27:13: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:27:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:27:14: #2 number of paired peaks: 710 WARNING @ Tue, 27 Jun 2017 14:27:14: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Tue, 27 Jun 2017 14:27:14: start model_add_line... INFO @ Tue, 27 Jun 2017 14:27:14: start X-correlation... INFO @ Tue, 27 Jun 2017 14:27:14: end of X-cor INFO @ Tue, 27 Jun 2017 14:27:14: #2 finished! INFO @ Tue, 27 Jun 2017 14:27:14: #2 predicted fragment length is 68 bps INFO @ Tue, 27 Jun 2017 14:27:14: #2 alternative fragment length(s) may be 4,68 bps INFO @ Tue, 27 Jun 2017 14:27:14: #2.2 Generate R script for model : SRX1837290.20_model.r WARNING @ Tue, 27 Jun 2017 14:27:14: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:27:14: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Tue, 27 Jun 2017 14:27:14: #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 14:27:14: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:27:41: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:27:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:27:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:28:04: #4 Write output xls file... SRX1837290.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:28:04: #4 Write peak in narrowPeak format file... SRX1837290.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:28:04: #4 Write summits bed file... SRX1837290.10_summits.bed INFO @ Tue, 27 Jun 2017 14:28:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3689 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:28:12: #4 Write output xls file... SRX1837290.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:28:12: #4 Write peak in narrowPeak format file... SRX1837290.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:28:12: #4 Write summits bed file... SRX1837290.05_summits.bed INFO @ Tue, 27 Jun 2017 14:28:12: Done! INFO @ Tue, 27 Jun 2017 14:28:13: #4 Write output xls file... SRX1837290.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:28:13: #4 Write peak in narrowPeak format file... SRX1837290.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:28:13: #4 Write summits bed file... SRX1837290.20_summits.bed INFO @ Tue, 27 Jun 2017 14:28:13: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1232 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10164 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。