Job ID = 6983658 sra ファイルのダウンロード中... Completed: 333975K bytes transferred in 7 seconds (375660K 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 5639 0 5639 0 0 5888 0 --:--:-- --:--:-- --:--:-- 9305 100 35556 0 35556 0 0 21571 0 --:--:-- 0:00:01 --:--:-- 27456 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 16425261 spots for /home/okishinya/chipatlas/results/dm3/SRX017468/SRR037525.sra Written 16425261 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: 00:04:42 16425261 reads; of these: 16425261 (100.00%) were unpaired; of these: 1285110 (7.82%) aligned 0 times 11184810 (68.10%) aligned exactly 1 time 3955341 (24.08%) aligned >1 times 92.18% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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] 3489288 / 15140151 = 0.2305 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 15:40:47: # Command line: callpeak -t SRX017468.bam -f BAM -g dm -n SRX017468.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX017468.10 # format = BAM # ChIP-seq file = ['SRX017468.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 15:40:47: # Command line: callpeak -t SRX017468.bam -f BAM -g dm -n SRX017468.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX017468.05 # format = BAM # ChIP-seq file = ['SRX017468.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 15:40:47: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:47: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:47: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:47: # Command line: callpeak -t SRX017468.bam -f BAM -g dm -n SRX017468.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX017468.20 # format = BAM # ChIP-seq file = ['SRX017468.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 15:40:47: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:47: #1 read tag files... INFO @ Sun, 05 Jun 2016 15:40:47: #1 read treatment tags... INFO @ Sun, 05 Jun 2016 15:40:53: 1000000 INFO @ Sun, 05 Jun 2016 15:40:53: 1000000 INFO @ Sun, 05 Jun 2016 15:40:53: 1000000 INFO @ Sun, 05 Jun 2016 15:40:58: 2000000 INFO @ Sun, 05 Jun 2016 15:40:58: 2000000 INFO @ Sun, 05 Jun 2016 15:40:58: 2000000 INFO @ Sun, 05 Jun 2016 15:41:03: 3000000 INFO @ Sun, 05 Jun 2016 15:41:03: 3000000 INFO @ Sun, 05 Jun 2016 15:41:04: 3000000 INFO @ Sun, 05 Jun 2016 15:41:08: 4000000 INFO @ Sun, 05 Jun 2016 15:41:09: 4000000 INFO @ Sun, 05 Jun 2016 15:41:09: 4000000 INFO @ Sun, 05 Jun 2016 15:41:14: 5000000 INFO @ Sun, 05 Jun 2016 15:41:14: 5000000 INFO @ Sun, 05 Jun 2016 15:41:14: 5000000 INFO @ Sun, 05 Jun 2016 15:41:19: 6000000 INFO @ Sun, 05 Jun 2016 15:41:19: 6000000 INFO @ Sun, 05 Jun 2016 15:41:20: 6000000 INFO @ Sun, 05 Jun 2016 15:41:24: 7000000 INFO @ Sun, 05 Jun 2016 15:41:25: 7000000 INFO @ Sun, 05 Jun 2016 15:41:25: 7000000 INFO @ Sun, 05 Jun 2016 15:41:30: 8000000 INFO @ Sun, 05 Jun 2016 15:41:30: 8000000 INFO @ Sun, 05 Jun 2016 15:41:31: 8000000 INFO @ Sun, 05 Jun 2016 15:41:36: 9000000 INFO @ Sun, 05 Jun 2016 15:41:36: 9000000 INFO @ Sun, 05 Jun 2016 15:41:37: 9000000 INFO @ Sun, 05 Jun 2016 15:41:41: 10000000 INFO @ Sun, 05 Jun 2016 15:41:41: 10000000 INFO @ Sun, 05 Jun 2016 15:41:43: 10000000 INFO @ Sun, 05 Jun 2016 15:41:46: 11000000 INFO @ Sun, 05 Jun 2016 15:41:47: 11000000 INFO @ Sun, 05 Jun 2016 15:41:49: 11000000 INFO @ Sun, 05 Jun 2016 15:41:50: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:41:50: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:41:50: #1 total tags in treatment: 11650863 INFO @ Sun, 05 Jun 2016 15:41:50: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:41:50: #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 15:41:51: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:41:51: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:41:51: #1 total tags in treatment: 11650863 INFO @ Sun, 05 Jun 2016 15:41:51: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:41:51: #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 15:41:52: #1 tags after filtering in treatment: 11649258 INFO @ Sun, 05 Jun 2016 15:41:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:41:52: #1 finished! INFO @ Sun, 05 Jun 2016 15:41:52: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:41:52: #1 tag size is determined as 36 bps INFO @ Sun, 05 Jun 2016 15:41:52: #1 tag size = 36 INFO @ Sun, 05 Jun 2016 15:41:52: #1 total tags in treatment: 11650863 INFO @ Sun, 05 Jun 2016 15:41:52: #1 user defined the maximum tags... INFO @ Sun, 05 Jun 2016 15:41:52: #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 15:41:53: #1 tags after filtering in treatment: 11649258 INFO @ Sun, 05 Jun 2016 15:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:41:53: #1 finished! INFO @ Sun, 05 Jun 2016 15:41:53: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:41:54: #2 number of paired peaks: 248 WARNING @ Sun, 05 Jun 2016 15:41:54: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 05 Jun 2016 15:41:54: start model_add_line... INFO @ Sun, 05 Jun 2016 15:41:55: #1 tags after filtering in treatment: 11649258 INFO @ Sun, 05 Jun 2016 15:41:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 05 Jun 2016 15:41:55: #1 finished! INFO @ Sun, 05 Jun 2016 15:41:55: #2 Build Peak Model... INFO @ Sun, 05 Jun 2016 15:41:55: #2 number of paired peaks: 248 WARNING @ Sun, 05 Jun 2016 15:41:55: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 05 Jun 2016 15:41:55: start model_add_line... INFO @ Sun, 05 Jun 2016 15:41:56: start X-correlation... INFO @ Sun, 05 Jun 2016 15:41:56: end of X-cor INFO @ Sun, 05 Jun 2016 15:41:56: #2 finished! INFO @ Sun, 05 Jun 2016 15:41:56: #2 predicted fragment length is 70 bps INFO @ Sun, 05 Jun 2016 15:41:56: #2 alternative fragment length(s) may be 70 bps INFO @ Sun, 05 Jun 2016 15:41:56: #2.2 Generate R script for model : SRX017468.20_model.r WARNING @ Sun, 05 Jun 2016 15:41:56: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:41:56: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Sun, 05 Jun 2016 15:41:56: #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 15:41:56: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:41:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:41:57: #2 number of paired peaks: 248 WARNING @ Sun, 05 Jun 2016 15:41:57: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Sun, 05 Jun 2016 15:41:57: start model_add_line... INFO @ Sun, 05 Jun 2016 15:41:58: start X-correlation... INFO @ Sun, 05 Jun 2016 15:41:58: end of X-cor INFO @ Sun, 05 Jun 2016 15:41:58: #2 finished! INFO @ Sun, 05 Jun 2016 15:41:58: #2 predicted fragment length is 70 bps INFO @ Sun, 05 Jun 2016 15:41:58: #2 alternative fragment length(s) may be 70 bps INFO @ Sun, 05 Jun 2016 15:41:58: #2.2 Generate R script for model : SRX017468.10_model.r WARNING @ Sun, 05 Jun 2016 15:41:58: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:41:58: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Sun, 05 Jun 2016 15:41:58: #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 15:41:58: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:41:59: start X-correlation... INFO @ Sun, 05 Jun 2016 15:41:59: end of X-cor INFO @ Sun, 05 Jun 2016 15:41:59: #2 finished! INFO @ Sun, 05 Jun 2016 15:41:59: #2 predicted fragment length is 70 bps INFO @ Sun, 05 Jun 2016 15:41:59: #2 alternative fragment length(s) may be 70 bps INFO @ Sun, 05 Jun 2016 15:41:59: #2.2 Generate R script for model : SRX017468.05_model.r WARNING @ Sun, 05 Jun 2016 15:41:59: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 05 Jun 2016 15:41:59: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Sun, 05 Jun 2016 15:41:59: #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 15:41:59: #3 Call peaks... INFO @ Sun, 05 Jun 2016 15:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 05 Jun 2016 15:43:00: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:43:01: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:43:01: #3 Call peaks for each chromosome... INFO @ Sun, 05 Jun 2016 15:43:48: #4 Write output xls file... SRX017468.10_peaks.xls INFO @ Sun, 05 Jun 2016 15:43:48: #4 Write peak in narrowPeak format file... SRX017468.10_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:43:48: #4 Write summits bed file... SRX017468.10_summits.bed INFO @ Sun, 05 Jun 2016 15:43:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3396 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:43:49: #4 Write output xls file... SRX017468.20_peaks.xls INFO @ Sun, 05 Jun 2016 15:43:49: #4 Write peak in narrowPeak format file... SRX017468.20_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:43:49: #4 Write summits bed file... SRX017468.20_summits.bed INFO @ Sun, 05 Jun 2016 15:43:49: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1115 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 05 Jun 2016 15:43:50: #4 Write output xls file... SRX017468.05_peaks.xls INFO @ Sun, 05 Jun 2016 15:43:50: #4 Write peak in narrowPeak format file... SRX017468.05_peaks.narrowPeak INFO @ Sun, 05 Jun 2016 15:43:50: #4 Write summits bed file... SRX017468.05_summits.bed INFO @ Sun, 05 Jun 2016 15:43:51: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7593 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。