Job ID = 9031179 sra ファイルのダウンロード中... Completed: 107179K bytes transferred in 4 seconds (206294K bits/sec), in 2 files, 3 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 22317 0 22317 0 0 2867 0 --:--:-- 0:00:07 --:--:-- 16716 100 46317 0 46317 0 0 5377 0 --:--:-- 0:00:08 --:--:-- 21393 100 48333 0 48333 0 0 5611 0 --:--:-- 0:00:08 --:--:-- 22314 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 3024052 spots for /home/okishinya/chipatlas/results/dm3/SRX330997/SRR947211.sra Written 3024052 spots total Written 5101822 spots for /home/okishinya/chipatlas/results/dm3/SRX330997/SRR947212.sra Written 5101822 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: 00:02:07 8125874 reads; of these: 8125874 (100.00%) were unpaired; of these: 2191553 (26.97%) aligned 0 times 4251084 (52.32%) aligned exactly 1 time 1683237 (20.71%) aligned >1 times 73.03% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 491844 / 5934321 = 0.0829 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 @ Sat, 03 Jun 2017 18:25:25: # Command line: callpeak -t SRX330997.bam -f BAM -g dm -n SRX330997.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX330997.20 # format = BAM # ChIP-seq file = ['SRX330997.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 @ Sat, 03 Jun 2017 18:25:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 18:25:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 18:25:25: # Command line: callpeak -t SRX330997.bam -f BAM -g dm -n SRX330997.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX330997.05 # format = BAM # ChIP-seq file = ['SRX330997.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 @ Sat, 03 Jun 2017 18:25:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 18:25:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 18:25:25: # Command line: callpeak -t SRX330997.bam -f BAM -g dm -n SRX330997.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX330997.10 # format = BAM # ChIP-seq file = ['SRX330997.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 @ Sat, 03 Jun 2017 18:25:25: #1 read tag files... INFO @ Sat, 03 Jun 2017 18:25:25: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 18:25:31: 1000000 INFO @ Sat, 03 Jun 2017 18:25:31: 1000000 INFO @ Sat, 03 Jun 2017 18:25:31: 1000000 INFO @ Sat, 03 Jun 2017 18:25:36: 2000000 INFO @ Sat, 03 Jun 2017 18:25:37: 2000000 INFO @ Sat, 03 Jun 2017 18:25:37: 2000000 INFO @ Sat, 03 Jun 2017 18:25:42: 3000000 INFO @ Sat, 03 Jun 2017 18:25:43: 3000000 INFO @ Sat, 03 Jun 2017 18:25:43: 3000000 INFO @ Sat, 03 Jun 2017 18:25:47: 4000000 INFO @ Sat, 03 Jun 2017 18:25:49: 4000000 INFO @ Sat, 03 Jun 2017 18:25:49: 4000000 INFO @ Sat, 03 Jun 2017 18:25:53: 5000000 INFO @ Sat, 03 Jun 2017 18:25:55: 5000000 INFO @ Sat, 03 Jun 2017 18:25:55: 5000000 INFO @ Sat, 03 Jun 2017 18:25:55: #1 tag size is determined as 28 bps INFO @ Sat, 03 Jun 2017 18:25:55: #1 tag size = 28 INFO @ Sat, 03 Jun 2017 18:25:55: #1 total tags in treatment: 5442477 INFO @ Sat, 03 Jun 2017 18:25:55: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 18:25:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 18:25:56: #1 tags after filtering in treatment: 5441762 INFO @ Sat, 03 Jun 2017 18:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 18:25:56: #1 finished! INFO @ Sat, 03 Jun 2017 18:25:56: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 18:25:57: #2 number of paired peaks: 534 WARNING @ Sat, 03 Jun 2017 18:25:57: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Sat, 03 Jun 2017 18:25:57: start model_add_line... INFO @ Sat, 03 Jun 2017 18:25:58: #1 tag size is determined as 28 bps INFO @ Sat, 03 Jun 2017 18:25:58: #1 tag size = 28 INFO @ Sat, 03 Jun 2017 18:25:58: #1 total tags in treatment: 5442477 INFO @ Sat, 03 Jun 2017 18:25:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 18:25:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 18:25:58: #1 tag size is determined as 28 bps INFO @ Sat, 03 Jun 2017 18:25:58: #1 tag size = 28 INFO @ Sat, 03 Jun 2017 18:25:58: #1 total tags in treatment: 5442477 INFO @ Sat, 03 Jun 2017 18:25:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 18:25:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 18:25:59: #1 tags after filtering in treatment: 5441762 INFO @ Sat, 03 Jun 2017 18:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 18:25:59: #1 finished! INFO @ Sat, 03 Jun 2017 18:25:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 18:25:59: #1 tags after filtering in treatment: 5441762 INFO @ Sat, 03 Jun 2017 18:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 18:25:59: #1 finished! INFO @ Sat, 03 Jun 2017 18:25:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 18:26:00: #2 number of paired peaks: 534 WARNING @ Sat, 03 Jun 2017 18:26:00: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Sat, 03 Jun 2017 18:26:00: start model_add_line... INFO @ Sat, 03 Jun 2017 18:26:00: #2 number of paired peaks: 534 WARNING @ Sat, 03 Jun 2017 18:26:00: Fewer paired peaks (534) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 534 pairs to build model! INFO @ Sat, 03 Jun 2017 18:26:00: start model_add_line... INFO @ Sat, 03 Jun 2017 18:26:00: start X-correlation... INFO @ Sat, 03 Jun 2017 18:26:00: end of X-cor INFO @ Sat, 03 Jun 2017 18:26:00: #2 finished! INFO @ Sat, 03 Jun 2017 18:26:00: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 18:26:00: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 18:26:00: #2.2 Generate R script for model : SRX330997.05_model.r WARNING @ Sat, 03 Jun 2017 18:26:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 18:26:00: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 18:26:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 18:26:00: #3 Call peaks... INFO @ Sat, 03 Jun 2017 18:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 18:26:02: start X-correlation... INFO @ Sat, 03 Jun 2017 18:26:02: end of X-cor INFO @ Sat, 03 Jun 2017 18:26:02: #2 finished! INFO @ Sat, 03 Jun 2017 18:26:02: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 18:26:02: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 18:26:02: #2.2 Generate R script for model : SRX330997.20_model.r WARNING @ Sat, 03 Jun 2017 18:26:02: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 18:26:02: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 18:26:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 18:26:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 18:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 18:26:02: start X-correlation... INFO @ Sat, 03 Jun 2017 18:26:02: end of X-cor INFO @ Sat, 03 Jun 2017 18:26:02: #2 finished! INFO @ Sat, 03 Jun 2017 18:26:02: #2 predicted fragment length is 53 bps INFO @ Sat, 03 Jun 2017 18:26:02: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 03 Jun 2017 18:26:02: #2.2 Generate R script for model : SRX330997.10_model.r WARNING @ Sat, 03 Jun 2017 18:26:02: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 18:26:02: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 03 Jun 2017 18:26:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 18:26:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 18:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 18:26:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 18:26:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 18:26:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 18:26:54: #4 Write output xls file... SRX330997.20_peaks.xls INFO @ Sat, 03 Jun 2017 18:26:54: #4 Write peak in narrowPeak format file... SRX330997.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 18:26:54: #4 Write summits bed file... SRX330997.20_summits.bed INFO @ Sat, 03 Jun 2017 18:26:54: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (294 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 18:26:56: #4 Write output xls file... SRX330997.05_peaks.xls INFO @ Sat, 03 Jun 2017 18:26:56: #4 Write peak in narrowPeak format file... SRX330997.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 18:26:56: #4 Write summits bed file... SRX330997.05_summits.bed INFO @ Sat, 03 Jun 2017 18:26:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1631 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 18:26:58: #4 Write output xls file... SRX330997.10_peaks.xls INFO @ Sat, 03 Jun 2017 18:26:58: #4 Write peak in narrowPeak format file... SRX330997.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 18:26:58: #4 Write summits bed file... SRX330997.10_summits.bed INFO @ Sat, 03 Jun 2017 18:26:58: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (689 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。