Job ID = 2161415 sra ファイルのダウンロード中... Completed: 47963K bytes transferred in 3 seconds (100393K 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 44409 0 44409 0 0 48426 0 --:--:-- --:--:-- --:--:-- 61169 100 44409 0 44409 0 0 48384 0 --:--:-- --:--:-- --:--:-- 61085 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 1826540 spots for /home/okishinya/chipatlas/results/dm3/SRX025488/SRR063892.sra Written 1826540 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: 00:00:35 1826540 reads; of these: 1826540 (100.00%) were unpaired; of these: 122005 (6.68%) aligned 0 times 1215611 (66.55%) aligned exactly 1 time 488924 (26.77%) aligned >1 times 93.32% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 71291 / 1704535 = 0.0418 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 12:35:46: # Command line: callpeak -t SRX025488.bam -f BAM -g dm -n SRX025488.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025488.10 # format = BAM # ChIP-seq file = ['SRX025488.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 12:35:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:35:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:35:46: # Command line: callpeak -t SRX025488.bam -f BAM -g dm -n SRX025488.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025488.20 # format = BAM # ChIP-seq file = ['SRX025488.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 12:35:46: # Command line: callpeak -t SRX025488.bam -f BAM -g dm -n SRX025488.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025488.05 # format = BAM # ChIP-seq file = ['SRX025488.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 12:35:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:35:46: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:35:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:35:46: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:35:52: 1000000 INFO @ Tue, 21 Apr 2015 12:35:52: 1000000 INFO @ Tue, 21 Apr 2015 12:35:52: 1000000 INFO @ Tue, 21 Apr 2015 12:35:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:35:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:35:55: #1 total tags in treatment: 1633244 INFO @ Tue, 21 Apr 2015 12:35:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:35:55: #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 12:35:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:35:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:35:55: #1 total tags in treatment: 1633244 INFO @ Tue, 21 Apr 2015 12:35:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:35:55: #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 12:35:56: #1 tags after filtering in treatment: 1633191 INFO @ Tue, 21 Apr 2015 12:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:35:56: #1 finished! INFO @ Tue, 21 Apr 2015 12:35:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:35:56: #1 tags after filtering in treatment: 1633191 INFO @ Tue, 21 Apr 2015 12:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:35:56: #1 finished! INFO @ Tue, 21 Apr 2015 12:35:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:35:56: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:35:56: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:35:56: #1 total tags in treatment: 1633244 INFO @ Tue, 21 Apr 2015 12:35:56: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:35:56: #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 12:35:56: #1 tags after filtering in treatment: 1633191 INFO @ Tue, 21 Apr 2015 12:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:35:56: #1 finished! INFO @ Tue, 21 Apr 2015 12:35:56: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:35:56: #2 number of paired peaks: 428 WARNING @ Tue, 21 Apr 2015 12:35:56: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 21 Apr 2015 12:35:56: start model_add_line... INFO @ Tue, 21 Apr 2015 12:35:56: #2 number of paired peaks: 428 WARNING @ Tue, 21 Apr 2015 12:35:56: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 21 Apr 2015 12:35:56: start model_add_line... INFO @ Tue, 21 Apr 2015 12:35:56: #2 number of paired peaks: 428 WARNING @ Tue, 21 Apr 2015 12:35:56: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Tue, 21 Apr 2015 12:35:56: start model_add_line... INFO @ Tue, 21 Apr 2015 12:35:57: start X-correlation... INFO @ Tue, 21 Apr 2015 12:35:57: end of X-cor INFO @ Tue, 21 Apr 2015 12:35:57: #2 finished! INFO @ Tue, 21 Apr 2015 12:35:57: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:35:57: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:35:57: #2.2 Generate R script for model : SRX025488.05_model.r WARNING @ Tue, 21 Apr 2015 12:35:57: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:35:57: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:35:57: #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 12:35:57: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:35:57: start X-correlation... INFO @ Tue, 21 Apr 2015 12:35:57: end of X-cor INFO @ Tue, 21 Apr 2015 12:35:57: #2 finished! INFO @ Tue, 21 Apr 2015 12:35:57: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:35:57: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:35:57: #2.2 Generate R script for model : SRX025488.10_model.r WARNING @ Tue, 21 Apr 2015 12:35:57: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:35:57: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:35:57: #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 12:35:57: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:35:57: start X-correlation... INFO @ Tue, 21 Apr 2015 12:35:57: end of X-cor INFO @ Tue, 21 Apr 2015 12:35:57: #2 finished! INFO @ Tue, 21 Apr 2015 12:35:57: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:35:57: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:35:57: #2.2 Generate R script for model : SRX025488.20_model.r WARNING @ Tue, 21 Apr 2015 12:35:57: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:35:57: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:35:57: #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 12:35:57: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:36:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:36:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:36:07: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write output xls file... SRX025488.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write peak in narrowPeak format file... SRX025488.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write summits bed file... SRX025488.05_summits.bed INFO @ Tue, 21 Apr 2015 12:36:14: Done! INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write output xls file... SRX025488.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write peak in narrowPeak format file... SRX025488.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write summits bed file... SRX025488.20_summits.bed INFO @ Tue, 21 Apr 2015 12:36:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (866 records, 4 fields): 3 millis pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write output xls file... SRX025488.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write peak in narrowPeak format file... SRX025488.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:36:14: #4 Write summits bed file... SRX025488.10_summits.bed INFO @ Tue, 21 Apr 2015 12:36:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。