Job ID = 2161302 sra ファイルのダウンロード中... Completed: 235224K bytes transferred in 5 seconds (372791K 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 14928 0 14928 0 0 21591 0 --:--:-- --:--:-- --:--:-- 29915 100 34347 0 34347 0 0 49620 0 --:--:-- --:--:-- --:--:-- 68831 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 9329497 spots for /home/okishinya/chipatlas/results/dm3/SRX016168/SRR034736.sra Written 9329497 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: 00:01:56 9329497 reads; of these: 9329497 (100.00%) were unpaired; of these: 2103541 (22.55%) aligned 0 times 6032934 (64.67%) aligned exactly 1 time 1193022 (12.79%) aligned >1 times 77.45% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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] 480009 / 7225956 = 0.0664 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 12:18:42: # Command line: callpeak -t SRX016168.bam -f BAM -g dm -n SRX016168.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016168.10 # format = BAM # ChIP-seq file = ['SRX016168.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 12:18:42: # Command line: callpeak -t SRX016168.bam -f BAM -g dm -n SRX016168.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016168.05 # format = BAM # ChIP-seq file = ['SRX016168.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 12:18:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:42: # Command line: callpeak -t SRX016168.bam -f BAM -g dm -n SRX016168.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016168.20 # format = BAM # ChIP-seq file = ['SRX016168.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 12:18:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:18:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:18:48: 1000000 INFO @ Tue, 21 Apr 2015 12:18:48: 1000000 INFO @ Tue, 21 Apr 2015 12:18:48: 1000000 INFO @ Tue, 21 Apr 2015 12:18:53: 2000000 INFO @ Tue, 21 Apr 2015 12:18:54: 2000000 INFO @ Tue, 21 Apr 2015 12:18:54: 2000000 INFO @ Tue, 21 Apr 2015 12:18:59: 3000000 INFO @ Tue, 21 Apr 2015 12:18:59: 3000000 INFO @ Tue, 21 Apr 2015 12:18:59: 3000000 INFO @ Tue, 21 Apr 2015 12:19:05: 4000000 INFO @ Tue, 21 Apr 2015 12:19:05: 4000000 INFO @ Tue, 21 Apr 2015 12:19:05: 4000000 INFO @ Tue, 21 Apr 2015 12:19:10: 5000000 INFO @ Tue, 21 Apr 2015 12:19:11: 5000000 INFO @ Tue, 21 Apr 2015 12:19:11: 5000000 INFO @ Tue, 21 Apr 2015 12:19:16: 6000000 INFO @ Tue, 21 Apr 2015 12:19:16: 6000000 INFO @ Tue, 21 Apr 2015 12:19:16: 6000000 INFO @ Tue, 21 Apr 2015 12:19:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:20: #1 total tags in treatment: 6745947 INFO @ Tue, 21 Apr 2015 12:19:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:20: #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 12:19:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:21: #1 total tags in treatment: 6745947 INFO @ Tue, 21 Apr 2015 12:19:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:21: #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 12:19:21: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:19:21: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:19:21: #1 total tags in treatment: 6745947 INFO @ Tue, 21 Apr 2015 12:19:21: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:19:21: #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 12:19:21: #1 tags after filtering in treatment: 6745065 INFO @ Tue, 21 Apr 2015 12:19:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:21: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:21: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:22: #1 tags after filtering in treatment: 6745065 INFO @ Tue, 21 Apr 2015 12:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:22: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:22: #1 tags after filtering in treatment: 6745065 INFO @ Tue, 21 Apr 2015 12:19:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:19:22: #1 finished! INFO @ Tue, 21 Apr 2015 12:19:22: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:19:22: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:19:22: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:22: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:23: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:19:23: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:23: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 12:19:23: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 12:19:23: #2.2 Generate R script for model : SRX016168.20_model.r WARNING @ Tue, 21 Apr 2015 12:19:23: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:19:23: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 12:19:23: #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 12:19:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:19:23: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:19:23: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Tue, 21 Apr 2015 12:19:23: start model_add_line... INFO @ Tue, 21 Apr 2015 12:19:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:24: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 12:19:24: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 12:19:24: #2.2 Generate R script for model : SRX016168.10_model.r WARNING @ Tue, 21 Apr 2015 12:19:24: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:19:24: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 12:19:24: #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 12:19:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:19:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:19:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:19:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:19:24: #2 predicted fragment length is 36 bps INFO @ Tue, 21 Apr 2015 12:19:24: #2 alternative fragment length(s) may be 36 bps INFO @ Tue, 21 Apr 2015 12:19:24: #2.2 Generate R script for model : SRX016168.05_model.r WARNING @ Tue, 21 Apr 2015 12:19:24: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:19:24: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Tue, 21 Apr 2015 12:19:24: #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 12:19:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:20:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:20:28: #4 Write output xls file... SRX016168.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:20:28: #4 Write peak in narrowPeak format file... SRX016168.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:20:28: #4 Write summits bed file... SRX016168.20_summits.bed INFO @ Tue, 21 Apr 2015 12:20:28: Done! pass1 - making usageList (4 chroms): 4 millis pass2 - checking and writing primary data (331 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:20:29: #4 Write output xls file... SRX016168.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:20:29: #4 Write peak in narrowPeak format file... SRX016168.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:20:29: #4 Write summits bed file... SRX016168.10_summits.bed INFO @ Tue, 21 Apr 2015 12:20:29: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:20:31: #4 Write output xls file... SRX016168.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:20:31: #4 Write peak in narrowPeak format file... SRX016168.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:20:31: #4 Write summits bed file... SRX016168.05_summits.bed INFO @ Tue, 21 Apr 2015 12:20:31: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (462 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。