Job ID = 2161354 sra ファイルのダウンロード中... Completed: 179914K bytes transferred in 5 seconds (292428K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 36769 0 36769 0 0 50221 0 --:--:-- --:--:-- --:--:-- 67964 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 10289917 spots for /home/okishinya/chipatlas/results/dm3/SRX022743/SRR059122.sra Written 10289917 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:01 10289917 reads; of these: 10289917 (100.00%) were unpaired; of these: 752013 (7.31%) aligned 0 times 7185867 (69.83%) aligned exactly 1 time 2352037 (22.86%) aligned >1 times 92.69% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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_rmdupse_core] 662065 / 9537904 = 0.0694 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, 21 Apr 2015 12:32:35: # Command line: callpeak -t SRX022743.bam -f BAM -g dm -n SRX022743.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX022743.10 # format = BAM # ChIP-seq file = ['SRX022743.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 INFO @ Tue, 21 Apr 2015 12:32:35: # Command line: callpeak -t SRX022743.bam -f BAM -g dm -n SRX022743.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX022743.05 # format = BAM # ChIP-seq file = ['SRX022743.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 INFO @ Tue, 21 Apr 2015 12:32:35: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:35: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:35: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:35: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:35: # Command line: callpeak -t SRX022743.bam -f BAM -g dm -n SRX022743.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX022743.20 # format = BAM # ChIP-seq file = ['SRX022743.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 INFO @ Tue, 21 Apr 2015 12:32:35: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:32:35: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:32:40: 1000000 INFO @ Tue, 21 Apr 2015 12:32:40: 1000000 INFO @ Tue, 21 Apr 2015 12:32:40: 1000000 INFO @ Tue, 21 Apr 2015 12:32:45: 2000000 INFO @ Tue, 21 Apr 2015 12:32:45: 2000000 INFO @ Tue, 21 Apr 2015 12:32:45: 2000000 INFO @ Tue, 21 Apr 2015 12:32:49: 3000000 INFO @ Tue, 21 Apr 2015 12:32:50: 3000000 INFO @ Tue, 21 Apr 2015 12:32:50: 3000000 INFO @ Tue, 21 Apr 2015 12:32:54: 4000000 INFO @ Tue, 21 Apr 2015 12:32:55: 4000000 INFO @ Tue, 21 Apr 2015 12:32:55: 4000000 INFO @ Tue, 21 Apr 2015 12:32:59: 5000000 INFO @ Tue, 21 Apr 2015 12:33:00: 5000000 INFO @ Tue, 21 Apr 2015 12:33:00: 5000000 INFO @ Tue, 21 Apr 2015 12:33:03: 6000000 INFO @ Tue, 21 Apr 2015 12:33:04: 6000000 INFO @ Tue, 21 Apr 2015 12:33:05: 6000000 INFO @ Tue, 21 Apr 2015 12:33:08: 7000000 INFO @ Tue, 21 Apr 2015 12:33:09: 7000000 INFO @ Tue, 21 Apr 2015 12:33:11: 7000000 INFO @ Tue, 21 Apr 2015 12:33:12: 8000000 INFO @ Tue, 21 Apr 2015 12:33:14: 8000000 INFO @ Tue, 21 Apr 2015 12:33:16: 8000000 INFO @ Tue, 21 Apr 2015 12:33:17: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:33:17: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:33:17: #1 total tags in treatment: 8875839 INFO @ Tue, 21 Apr 2015 12:33:17: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:33:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:33:18: #1 tags after filtering in treatment: 8875337 INFO @ Tue, 21 Apr 2015 12:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:18: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:18: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:33:19: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:33:19: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:33:19: #1 total tags in treatment: 8875839 INFO @ Tue, 21 Apr 2015 12:33:19: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:33:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:33:20: #2 number of paired peaks: 1108 INFO @ Tue, 21 Apr 2015 12:33:20: start model_add_line... INFO @ Tue, 21 Apr 2015 12:33:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:33:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:33:20: #1 total tags in treatment: 8875839 INFO @ Tue, 21 Apr 2015 12:33:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:33:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:33:20: #1 tags after filtering in treatment: 8875337 INFO @ Tue, 21 Apr 2015 12:33:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:20: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:20: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:33:22: #2 number of paired peaks: 1108 INFO @ Tue, 21 Apr 2015 12:33:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:33:22: #1 tags after filtering in treatment: 8875337 INFO @ Tue, 21 Apr 2015 12:33:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:22: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:33:24: #2 number of paired peaks: 1108 INFO @ Tue, 21 Apr 2015 12:33:24: start model_add_line... INFO @ Tue, 21 Apr 2015 12:33:27: start X-correlation... INFO @ Tue, 21 Apr 2015 12:33:27: end of X-cor INFO @ Tue, 21 Apr 2015 12:33:27: #2 finished! INFO @ Tue, 21 Apr 2015 12:33:27: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 12:33:27: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 12:33:27: #2.2 Generate R script for model : SRX022743.20_model.r WARNING @ Tue, 21 Apr 2015 12:33:27: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:33:27: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 12:33:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:33:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:33:29: start X-correlation... INFO @ Tue, 21 Apr 2015 12:33:29: end of X-cor INFO @ Tue, 21 Apr 2015 12:33:29: #2 finished! INFO @ Tue, 21 Apr 2015 12:33:29: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 12:33:29: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 12:33:29: #2.2 Generate R script for model : SRX022743.05_model.r WARNING @ Tue, 21 Apr 2015 12:33:29: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:33:29: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 12:33:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:33:29: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:33:31: start X-correlation... INFO @ Tue, 21 Apr 2015 12:33:31: end of X-cor INFO @ Tue, 21 Apr 2015 12:33:31: #2 finished! INFO @ Tue, 21 Apr 2015 12:33:31: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 12:33:31: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 12:33:31: #2.2 Generate R script for model : SRX022743.10_model.r WARNING @ Tue, 21 Apr 2015 12:33:31: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:33:31: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 12:33:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:33:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:33:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:34:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:34:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:34:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:34:52: #4 Write output xls file... SRX022743.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:52: #4 Write peak in narrowPeak format file... SRX022743.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:52: #4 Write summits bed file... SRX022743.20_summits.bed INFO @ Tue, 21 Apr 2015 12:34:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1937 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:34:53: #4 Write output xls file... SRX022743.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:53: #4 Write peak in narrowPeak format file... SRX022743.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:53: #4 Write summits bed file... SRX022743.10_summits.bed INFO @ Tue, 21 Apr 2015 12:34:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3780 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:34:57: #4 Write output xls file... SRX022743.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:34:57: #4 Write peak in narrowPeak format file... SRX022743.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:34:57: #4 Write summits bed file... SRX022743.05_summits.bed INFO @ Tue, 21 Apr 2015 12:34:57: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6378 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。