Job ID = 6983661 sra ファイルのダウンロード中... Completed: 266609K bytes transferred in 5 seconds (366474K 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 10548 0 10548 0 0 12491 0 --:--:-- --:--:-- --:--:-- 21395 100 34978 0 34978 0 0 34314 0 --:--:-- 0:00:01 --:--:-- 52362 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 11385640 spots for /home/okishinya/chipatlas/results/dm3/SRX017471/SRR037528.sra Written 11385640 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: 00:03:23 11385640 reads; of these: 11385640 (100.00%) were unpaired; of these: 1474829 (12.95%) aligned 0 times 7467488 (65.59%) aligned exactly 1 time 2443323 (21.46%) aligned >1 times 87.05% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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_rmdupse_core] 1992989 / 9910811 = 0.2011 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 @ Sun, 05 Jun 2016 15:40:09: # Command line: callpeak -t SRX017471.bam -f BAM -g dm -n SRX017471.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017471.20 # format = BAM # ChIP-seq file = ['SRX017471.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 @ Sun, 05 Jun 2016 15:40:09: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:09: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:09: # Command line: callpeak -t SRX017471.bam -f BAM -g dm -n SRX017471.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017471.05 # format = BAM # ChIP-seq file = ['SRX017471.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 @ Sun, 05 Jun 2016 15:40:09: # Command line: callpeak -t SRX017471.bam -f BAM -g dm -n SRX017471.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017471.10 # format = BAM # ChIP-seq file = ['SRX017471.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 @ Sun, 05 Jun 2016 15:40:09: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:09: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:09: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:09: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:15: 1000000 INFO @ Sun, 05 Jun 2016 15:40:15: 1000000 INFO @ Sun, 05 Jun 2016 15:40:15: 1000000 INFO @ Sun, 05 Jun 2016 15:40:20: 2000000 INFO @ Sun, 05 Jun 2016 15:40:20: 2000000 INFO @ Sun, 05 Jun 2016 15:40:20: 2000000 INFO @ Sun, 05 Jun 2016 15:40:26: 3000000 INFO @ Sun, 05 Jun 2016 15:40:26: 3000000 INFO @ Sun, 05 Jun 2016 15:40:26: 3000000 INFO @ Sun, 05 Jun 2016 15:40:31: 4000000 INFO @ Sun, 05 Jun 2016 15:40:32: 4000000 INFO @ Sun, 05 Jun 2016 15:40:32: 4000000 INFO @ Sun, 05 Jun 2016 15:40:38: 5000000 INFO @ Sun, 05 Jun 2016 15:40:38: 5000000 INFO @ Sun, 05 Jun 2016 15:40:39: 5000000 INFO @ Sun, 05 Jun 2016 15:40:44: 6000000 INFO @ Sun, 05 Jun 2016 15:40:44: 6000000 INFO @ Sun, 05 Jun 2016 15:40:45: 6000000 INFO @ Sun, 05 Jun 2016 15:40:50: 7000000 INFO @ Sun, 05 Jun 2016 15:40:50: 7000000 INFO @ Sun, 05 Jun 2016 15:40:52: 7000000 INFO @ Sun, 05 Jun 2016 15:40:55: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:40:55: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:40:55: #1 total tags in treatment: 7917822 INFO @ Sun, 05 Jun 2016 15:40:55: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:40:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:40:56: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:40:56: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:40:56: #1 total tags in treatment: 7917822 INFO @ Sun, 05 Jun 2016 15:40:56: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:40:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:40:57: #1 tags after filtering in treatment: 7917293 INFO @ Sun, 05 Jun 2016 15:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:40:57: #1 finished! INFO @ Sun, 05 Jun 2016 15:40:57: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:40:57: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:40:57: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:40:57: #1 total tags in treatment: 7917822 INFO @ Sun, 05 Jun 2016 15:40:57: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:40:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 05 Jun 2016 15:40:57: #1 tags after filtering in treatment: 7917293 INFO @ Sun, 05 Jun 2016 15:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:40:57: #1 finished! INFO @ Sun, 05 Jun 2016 15:40:57: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:40:58: #2 number of paired peaks: 242 WARNING @ Sun, 05 Jun 2016 15:40:58: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 05 Jun 2016 15:40:58: start model_add_line... INFO @ Sun, 05 Jun 2016 15:40:58: #1 tags after filtering in treatment: 7917293 INFO @ Sun, 05 Jun 2016 15:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:40:58: #1 finished! INFO @ Sun, 05 Jun 2016 15:40:58: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:40:59: #2 number of paired peaks: 242 WARNING @ Sun, 05 Jun 2016 15:40:59: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 05 Jun 2016 15:40:59: start model_add_line... INFO @ Sun, 05 Jun 2016 15:41:00: #2 number of paired peaks: 242 WARNING @ Sun, 05 Jun 2016 15:41:00: Fewer paired peaks (242) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 242 pairs to build model! INFO @ Sun, 05 Jun 2016 15:41:00: start model_add_line... INFO @ Sun, 05 Jun 2016 15:41:00: start X-correlation... INFO @ Sun, 05 Jun 2016 15:41:00: end of X-cor INFO @ Sun, 05 Jun 2016 15:41:00: #2 finished! INFO @ Sun, 05 Jun 2016 15:41:00: #2 predicted fragment length is 60 bps INFO @ Sun, 05 Jun 2016 15:41:00: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 05 Jun 2016 15:41:00: #2.2 Generate R script for model : SRX017471.20_model.r WARNING @ Sun, 05 Jun 2016 15:41:00: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:41:00: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 05 Jun 2016 15:41:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:41:00: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:41:00: start X-correlation... INFO @ Sun, 05 Jun 2016 15:41:00: end of X-cor INFO @ Sun, 05 Jun 2016 15:41:00: #2 finished! INFO @ Sun, 05 Jun 2016 15:41:00: #2 predicted fragment length is 60 bps INFO @ Sun, 05 Jun 2016 15:41:00: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 05 Jun 2016 15:41:00: #2.2 Generate R script for model : SRX017471.05_model.r WARNING @ Sun, 05 Jun 2016 15:41:00: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:41:00: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 05 Jun 2016 15:41:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:41:00: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:41:01: start X-correlation... INFO @ Sun, 05 Jun 2016 15:41:01: end of X-cor INFO @ Sun, 05 Jun 2016 15:41:01: #2 finished! INFO @ Sun, 05 Jun 2016 15:41:01: #2 predicted fragment length is 60 bps INFO @ Sun, 05 Jun 2016 15:41:01: #2 alternative fragment length(s) may be 60 bps INFO @ Sun, 05 Jun 2016 15:41:01: #2.2 Generate R script for model : SRX017471.10_model.r WARNING @ Sun, 05 Jun 2016 15:41:01: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:41:01: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sun, 05 Jun 2016 15:41:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 05 Jun 2016 15:41:01: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:41:44: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:41:45: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:41:45: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:42:18: #4 Write output xls file... SRX017471.20_peaks.xls INFO @ Sun, 05 Jun 2016 15:42:18: #4 Write peak in narrowPeak format file... SRX017471.20_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:42:18: #4 Write summits bed file... SRX017471.20_summits.bed INFO @ Sun, 05 Jun 2016 15:42:18: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (706 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:42:18: #4 Write output xls file... SRX017471.10_peaks.xls INFO @ Sun, 05 Jun 2016 15:42:18: #4 Write peak in narrowPeak format file... SRX017471.10_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:42:18: #4 Write summits bed file... SRX017471.10_summits.bed INFO @ Sun, 05 Jun 2016 15:42:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2761 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:42:23: #4 Write output xls file... SRX017471.05_peaks.xls INFO @ Sun, 05 Jun 2016 15:42:23: #4 Write peak in narrowPeak format file... SRX017471.05_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:42:23: #4 Write summits bed file... SRX017471.05_summits.bed INFO @ Sun, 05 Jun 2016 15:42:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6280 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。