Job ID = 2161334 sra ファイルのダウンロード中... Completed: 445189K bytes transferred in 6 seconds (527033K bits/sec), in 3 files, 4 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 6920 0 6920 0 0 12437 0 --:--:-- --:--:-- --:--:-- 19010 100 35998 0 35998 0 0 48112 0 --:--:-- --:--:-- --:--:-- 64744 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 4742892 spots for /home/okishinya/chipatlas/results/dm3/SRX018630/SRR039098.sra Written 4742892 spots total Written 5452372 spots for /home/okishinya/chipatlas/results/dm3/SRX018630/SRR039096.sra Written 5452372 spots total Written 5930026 spots for /home/okishinya/chipatlas/results/dm3/SRX018630/SRR039097.sra Written 5930026 spots total 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: 00:03:49 16125290 reads; of these: 16125290 (100.00%) were unpaired; of these: 5649035 (35.03%) aligned 0 times 7199769 (44.65%) aligned exactly 1 time 3276486 (20.32%) aligned >1 times 64.97% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 690325 / 10476255 = 0.0659 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 12:29:48: # Command line: callpeak -t SRX018630.bam -f BAM -g dm -n SRX018630.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX018630.10 # format = BAM # ChIP-seq file = ['SRX018630.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 12:29:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:29:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:29:48: # Command line: callpeak -t SRX018630.bam -f BAM -g dm -n SRX018630.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX018630.05 # format = BAM # ChIP-seq file = ['SRX018630.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 12:29:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:29:48: # Command line: callpeak -t SRX018630.bam -f BAM -g dm -n SRX018630.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX018630.20 # format = BAM # ChIP-seq file = ['SRX018630.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 12:29:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:29:48: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:29:48: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:29:54: 1000000 INFO @ Tue, 21 Apr 2015 12:29:54: 1000000 INFO @ Tue, 21 Apr 2015 12:29:54: 1000000 INFO @ Tue, 21 Apr 2015 12:29:59: 2000000 INFO @ Tue, 21 Apr 2015 12:29:59: 2000000 INFO @ Tue, 21 Apr 2015 12:29:59: 2000000 INFO @ Tue, 21 Apr 2015 12:30:04: 3000000 INFO @ Tue, 21 Apr 2015 12:30:05: 3000000 INFO @ Tue, 21 Apr 2015 12:30:05: 3000000 INFO @ Tue, 21 Apr 2015 12:30:10: 4000000 INFO @ Tue, 21 Apr 2015 12:30:10: 4000000 INFO @ Tue, 21 Apr 2015 12:30:10: 4000000 INFO @ Tue, 21 Apr 2015 12:30:15: 5000000 INFO @ Tue, 21 Apr 2015 12:30:16: 5000000 INFO @ Tue, 21 Apr 2015 12:30:16: 5000000 INFO @ Tue, 21 Apr 2015 12:30:21: 6000000 INFO @ Tue, 21 Apr 2015 12:30:21: 6000000 INFO @ Tue, 21 Apr 2015 12:30:22: 6000000 INFO @ Tue, 21 Apr 2015 12:30:26: 7000000 INFO @ Tue, 21 Apr 2015 12:30:27: 7000000 INFO @ Tue, 21 Apr 2015 12:30:28: 7000000 INFO @ Tue, 21 Apr 2015 12:30:31: 8000000 INFO @ Tue, 21 Apr 2015 12:30:33: 8000000 INFO @ Tue, 21 Apr 2015 12:30:34: 8000000 INFO @ Tue, 21 Apr 2015 12:30:37: 9000000 INFO @ Tue, 21 Apr 2015 12:30:39: 9000000 INFO @ Tue, 21 Apr 2015 12:30:39: 9000000 INFO @ Tue, 21 Apr 2015 12:30:41: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:30:41: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:30:41: #1 total tags in treatment: 9785930 INFO @ Tue, 21 Apr 2015 12:30:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:30:41: #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 12:30:43: #1 tags after filtering in treatment: 9785074 INFO @ Tue, 21 Apr 2015 12:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:30:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:30:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:30:43: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:30:43: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:30:43: #1 total tags in treatment: 9785930 INFO @ Tue, 21 Apr 2015 12:30:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:30:43: #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 12:30:44: #1 tag size is determined as 39 bps INFO @ Tue, 21 Apr 2015 12:30:44: #1 tag size = 39 INFO @ Tue, 21 Apr 2015 12:30:44: #1 total tags in treatment: 9785930 INFO @ Tue, 21 Apr 2015 12:30:44: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:30:44: #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 12:30:44: #2 number of paired peaks: 667 WARNING @ Tue, 21 Apr 2015 12:30:44: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Tue, 21 Apr 2015 12:30:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:30:45: #1 tags after filtering in treatment: 9785074 INFO @ Tue, 21 Apr 2015 12:30:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:30:45: #1 finished! INFO @ Tue, 21 Apr 2015 12:30:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:30:46: #1 tags after filtering in treatment: 9785074 INFO @ Tue, 21 Apr 2015 12:30:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:30:46: #1 finished! INFO @ Tue, 21 Apr 2015 12:30:46: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:30:47: #2 number of paired peaks: 667 WARNING @ Tue, 21 Apr 2015 12:30:47: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Tue, 21 Apr 2015 12:30:47: start model_add_line... INFO @ Tue, 21 Apr 2015 12:30:47: #2 number of paired peaks: 667 WARNING @ Tue, 21 Apr 2015 12:30:47: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Tue, 21 Apr 2015 12:30:47: start model_add_line... INFO @ Tue, 21 Apr 2015 12:30:49: start X-correlation... INFO @ Tue, 21 Apr 2015 12:30:49: end of X-cor INFO @ Tue, 21 Apr 2015 12:30:49: #2 finished! INFO @ Tue, 21 Apr 2015 12:30:49: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 12:30:49: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 12:30:49: #2.2 Generate R script for model : SRX018630.20_model.r WARNING @ Tue, 21 Apr 2015 12:30:49: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:30:49: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 12:30:49: #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 12:30:49: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:30:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:30:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:30:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:30:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:30:51: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 12:30:51: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 12:30:51: #2.2 Generate R script for model : SRX018630.10_model.r WARNING @ Tue, 21 Apr 2015 12:30:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:30:51: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 12:30:51: #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 12:30:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:30:52: start X-correlation... INFO @ Tue, 21 Apr 2015 12:30:52: end of X-cor INFO @ Tue, 21 Apr 2015 12:30:52: #2 finished! INFO @ Tue, 21 Apr 2015 12:30:52: #2 predicted fragment length is 47 bps INFO @ Tue, 21 Apr 2015 12:30:52: #2 alternative fragment length(s) may be 47 bps INFO @ Tue, 21 Apr 2015 12:30:52: #2.2 Generate R script for model : SRX018630.05_model.r WARNING @ Tue, 21 Apr 2015 12:30:52: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:30:52: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Tue, 21 Apr 2015 12:30:52: #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 12:30:52: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:31:40: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:31:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:31:44: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:32:18: #4 Write output xls file... SRX018630.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:18: #4 Write peak in narrowPeak format file... SRX018630.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:18: #4 Write summits bed file... SRX018630.20_summits.bed INFO @ Tue, 21 Apr 2015 12:32:18: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (891 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:32:21: #4 Write output xls file... SRX018630.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:21: #4 Write peak in narrowPeak format file... SRX018630.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:21: #4 Write summits bed file... SRX018630.10_summits.bed INFO @ Tue, 21 Apr 2015 12:32:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1866 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:32:23: #4 Write output xls file... SRX018630.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:32:23: #4 Write peak in narrowPeak format file... SRX018630.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:32:23: #4 Write summits bed file... SRX018630.05_summits.bed INFO @ Tue, 21 Apr 2015 12:32:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3288 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。