Job ID = 2162392 sra ファイルのダウンロード中... Completed: 358181K bytes transferred in 5 seconds (499946K 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 --:--:-- --:--:-- --:--:-- 0 101 5460 0 5460 0 0 9922 0 --:--:-- --:--:-- --:--:-- 15208 100 35641 0 35641 0 0 48168 0 --:--:-- --:--:-- --:--:-- 64919 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 24636309 spots for /home/okishinya/chipatlas/results/dm3/SRX079914/SRR298656.sra Written 24636309 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: 00:04:09 24636309 reads; of these: 24636309 (100.00%) were unpaired; of these: 14610924 (59.31%) aligned 0 times 7108831 (28.86%) aligned exactly 1 time 2916554 (11.84%) aligned >1 times 40.69% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 8104810 / 10025385 = 0.8084 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 13:48:25: # Command line: callpeak -t SRX079914.bam -f BAM -g dm -n SRX079914.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX079914.10 # format = BAM # ChIP-seq file = ['SRX079914.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 13:48:25: # Command line: callpeak -t SRX079914.bam -f BAM -g dm -n SRX079914.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX079914.20 # format = BAM # ChIP-seq file = ['SRX079914.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 13:48:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:48:25: # Command line: callpeak -t SRX079914.bam -f BAM -g dm -n SRX079914.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX079914.05 # format = BAM # ChIP-seq file = ['SRX079914.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 13:48:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:48:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:48:25: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:48:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:48:25: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:48:30: 1000000 INFO @ Tue, 21 Apr 2015 13:48:30: 1000000 INFO @ Tue, 21 Apr 2015 13:48:30: 1000000 INFO @ Tue, 21 Apr 2015 13:48:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:48:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:48:34: #1 total tags in treatment: 1920575 INFO @ Tue, 21 Apr 2015 13:48:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:48:34: #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 13:48:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:48:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:48:35: #1 total tags in treatment: 1920575 INFO @ Tue, 21 Apr 2015 13:48:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:48:35: #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 13:48:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:48:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:48:35: #1 total tags in treatment: 1920575 INFO @ Tue, 21 Apr 2015 13:48:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:48:35: #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 13:48:35: #1 tags after filtering in treatment: 1920067 INFO @ Tue, 21 Apr 2015 13:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:48:35: #1 finished! INFO @ Tue, 21 Apr 2015 13:48:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:48:35: #1 tags after filtering in treatment: 1920067 INFO @ Tue, 21 Apr 2015 13:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:48:35: #1 finished! INFO @ Tue, 21 Apr 2015 13:48:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:48:35: #1 tags after filtering in treatment: 1920067 INFO @ Tue, 21 Apr 2015 13:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:48:35: #1 finished! INFO @ Tue, 21 Apr 2015 13:48:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:48:35: #2 number of paired peaks: 853 WARNING @ Tue, 21 Apr 2015 13:48:35: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Tue, 21 Apr 2015 13:48:35: start model_add_line... INFO @ Tue, 21 Apr 2015 13:48:35: #2 number of paired peaks: 853 WARNING @ Tue, 21 Apr 2015 13:48:35: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Tue, 21 Apr 2015 13:48:35: start model_add_line... INFO @ Tue, 21 Apr 2015 13:48:35: #2 number of paired peaks: 853 WARNING @ Tue, 21 Apr 2015 13:48:35: Fewer paired peaks (853) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 853 pairs to build model! INFO @ Tue, 21 Apr 2015 13:48:35: start model_add_line... INFO @ Tue, 21 Apr 2015 13:48:37: start X-correlation... INFO @ Tue, 21 Apr 2015 13:48:37: end of X-cor INFO @ Tue, 21 Apr 2015 13:48:37: #2 finished! INFO @ Tue, 21 Apr 2015 13:48:37: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 13:48:37: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 13:48:37: #2.2 Generate R script for model : SRX079914.10_model.r WARNING @ Tue, 21 Apr 2015 13:48:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:48:37: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 13:48:37: #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 13:48:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:48:37: start X-correlation... INFO @ Tue, 21 Apr 2015 13:48:37: end of X-cor INFO @ Tue, 21 Apr 2015 13:48:37: #2 finished! INFO @ Tue, 21 Apr 2015 13:48:37: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 13:48:37: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 13:48:37: #2.2 Generate R script for model : SRX079914.05_model.r WARNING @ Tue, 21 Apr 2015 13:48:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:48:37: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 13:48:37: #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 13:48:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:48:37: start X-correlation... INFO @ Tue, 21 Apr 2015 13:48:37: end of X-cor INFO @ Tue, 21 Apr 2015 13:48:37: #2 finished! INFO @ Tue, 21 Apr 2015 13:48:37: #2 predicted fragment length is 41 bps INFO @ Tue, 21 Apr 2015 13:48:37: #2 alternative fragment length(s) may be 41 bps INFO @ Tue, 21 Apr 2015 13:48:37: #2.2 Generate R script for model : SRX079914.20_model.r WARNING @ Tue, 21 Apr 2015 13:48:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:48:37: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Tue, 21 Apr 2015 13:48:37: #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 13:48:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:48:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:48:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:48:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:48:56: #4 Write output xls file... SRX079914.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:48:56: #4 Write peak in narrowPeak format file... SRX079914.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:48:56: #4 Write summits bed file... SRX079914.10_summits.bed INFO @ Tue, 21 Apr 2015 13:48:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (711 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:48:56: #4 Write output xls file... SRX079914.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:48:56: #4 Write peak in narrowPeak format file... SRX079914.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:48:56: #4 Write summits bed file... SRX079914.20_summits.bed INFO @ Tue, 21 Apr 2015 13:48:56: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:48:57: #4 Write output xls file... SRX079914.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:48:57: #4 Write peak in narrowPeak format file... SRX079914.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:48:57: #4 Write summits bed file... SRX079914.05_summits.bed INFO @ Tue, 21 Apr 2015 13:48:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1299 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。