Job ID = 2161578 sra ファイルのダウンロード中... Completed: 485685K bytes transferred in 8 seconds (460981K 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 14916 0 14916 0 0 19886 0 --:--:-- --:--:-- --:--:-- 26635 100 44903 0 44903 0 0 47782 0 --:--:-- --:--:-- --:--:-- 59950 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 23836399 spots for /home/okishinya/chipatlas/results/dm3/SRX032115/SRR073935.sra Written 23836399 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:13 23836399 reads; of these: 23836399 (100.00%) were unpaired; of these: 766273 (3.21%) aligned 0 times 15513137 (65.08%) aligned exactly 1 time 7556989 (31.70%) aligned >1 times 96.79% overall alignment rate Time searching: 00:09:14 Overall time: 00:09:14 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4066557 / 23070126 = 0.1763 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 13:11:18: # Command line: callpeak -t SRX032115.bam -f BAM -g dm -n SRX032115.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX032115.05 # format = BAM # ChIP-seq file = ['SRX032115.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 13:11:18: # Command line: callpeak -t SRX032115.bam -f BAM -g dm -n SRX032115.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX032115.10 # format = BAM # ChIP-seq file = ['SRX032115.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 13:11:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:18: # Command line: callpeak -t SRX032115.bam -f BAM -g dm -n SRX032115.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX032115.20 # format = BAM # ChIP-seq file = ['SRX032115.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 13:11:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:18: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:11:18: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:11:24: 1000000 INFO @ Tue, 21 Apr 2015 13:11:24: 1000000 INFO @ Tue, 21 Apr 2015 13:11:24: 1000000 INFO @ Tue, 21 Apr 2015 13:11:30: 2000000 INFO @ Tue, 21 Apr 2015 13:11:30: 2000000 INFO @ Tue, 21 Apr 2015 13:11:30: 2000000 INFO @ Tue, 21 Apr 2015 13:11:37: 3000000 INFO @ Tue, 21 Apr 2015 13:11:37: 3000000 INFO @ Tue, 21 Apr 2015 13:11:37: 3000000 INFO @ Tue, 21 Apr 2015 13:11:43: 4000000 INFO @ Tue, 21 Apr 2015 13:11:43: 4000000 INFO @ Tue, 21 Apr 2015 13:11:44: 4000000 INFO @ Tue, 21 Apr 2015 13:11:50: 5000000 INFO @ Tue, 21 Apr 2015 13:11:50: 5000000 INFO @ Tue, 21 Apr 2015 13:11:51: 5000000 INFO @ Tue, 21 Apr 2015 13:11:57: 6000000 INFO @ Tue, 21 Apr 2015 13:11:57: 6000000 INFO @ Tue, 21 Apr 2015 13:11:59: 6000000 INFO @ Tue, 21 Apr 2015 13:12:04: 7000000 INFO @ Tue, 21 Apr 2015 13:12:04: 7000000 INFO @ Tue, 21 Apr 2015 13:12:07: 7000000 INFO @ Tue, 21 Apr 2015 13:12:11: 8000000 INFO @ Tue, 21 Apr 2015 13:12:11: 8000000 INFO @ Tue, 21 Apr 2015 13:12:14: 8000000 INFO @ Tue, 21 Apr 2015 13:12:17: 9000000 INFO @ Tue, 21 Apr 2015 13:12:18: 9000000 INFO @ Tue, 21 Apr 2015 13:12:22: 9000000 INFO @ Tue, 21 Apr 2015 13:12:24: 10000000 INFO @ Tue, 21 Apr 2015 13:12:25: 10000000 INFO @ Tue, 21 Apr 2015 13:12:30: 10000000 INFO @ Tue, 21 Apr 2015 13:12:31: 11000000 INFO @ Tue, 21 Apr 2015 13:12:31: 11000000 INFO @ Tue, 21 Apr 2015 13:12:37: 11000000 INFO @ Tue, 21 Apr 2015 13:12:38: 12000000 INFO @ Tue, 21 Apr 2015 13:12:38: 12000000 INFO @ Tue, 21 Apr 2015 13:12:45: 13000000 INFO @ Tue, 21 Apr 2015 13:12:45: 12000000 INFO @ Tue, 21 Apr 2015 13:12:45: 13000000 INFO @ Tue, 21 Apr 2015 13:12:52: 14000000 INFO @ Tue, 21 Apr 2015 13:12:52: 14000000 INFO @ Tue, 21 Apr 2015 13:12:53: 13000000 INFO @ Tue, 21 Apr 2015 13:12:59: 15000000 INFO @ Tue, 21 Apr 2015 13:12:59: 15000000 INFO @ Tue, 21 Apr 2015 13:13:01: 14000000 INFO @ Tue, 21 Apr 2015 13:13:06: 16000000 INFO @ Tue, 21 Apr 2015 13:13:06: 16000000 INFO @ Tue, 21 Apr 2015 13:13:08: 15000000 INFO @ Tue, 21 Apr 2015 13:13:13: 17000000 INFO @ Tue, 21 Apr 2015 13:13:13: 17000000 INFO @ Tue, 21 Apr 2015 13:13:16: 16000000 INFO @ Tue, 21 Apr 2015 13:13:20: 18000000 INFO @ Tue, 21 Apr 2015 13:13:20: 18000000 INFO @ Tue, 21 Apr 2015 13:13:24: 17000000 INFO @ Tue, 21 Apr 2015 13:13:27: 19000000 INFO @ Tue, 21 Apr 2015 13:13:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:27: #1 total tags in treatment: 19003569 INFO @ Tue, 21 Apr 2015 13:13:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:27: #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 13:13:27: 19000000 INFO @ Tue, 21 Apr 2015 13:13:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:27: #1 total tags in treatment: 19003569 INFO @ Tue, 21 Apr 2015 13:13:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:27: #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 13:13:30: #1 tags after filtering in treatment: 19000283 INFO @ Tue, 21 Apr 2015 13:13:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:30: 18000000 INFO @ Tue, 21 Apr 2015 13:13:31: #1 tags after filtering in treatment: 19000283 INFO @ Tue, 21 Apr 2015 13:13:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:31: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:33: #2 number of paired peaks: 269 WARNING @ Tue, 21 Apr 2015 13:13:33: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Tue, 21 Apr 2015 13:13:33: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:35: #2 number of paired peaks: 269 WARNING @ Tue, 21 Apr 2015 13:13:35: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Tue, 21 Apr 2015 13:13:35: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:36: 19000000 INFO @ Tue, 21 Apr 2015 13:13:36: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:36: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:36: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:36: #2 predicted fragment length is 33 bps INFO @ Tue, 21 Apr 2015 13:13:36: #2 alternative fragment length(s) may be 33 bps INFO @ Tue, 21 Apr 2015 13:13:36: #2.2 Generate R script for model : SRX032115.05_model.r WARNING @ Tue, 21 Apr 2015 13:13:36: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:13:36: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Tue, 21 Apr 2015 13:13:36: #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 13:13:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:36: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:13:36: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:13:36: #1 total tags in treatment: 19003569 INFO @ Tue, 21 Apr 2015 13:13:36: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:13:36: #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 13:13:38: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:38: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:38: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:38: #2 predicted fragment length is 33 bps INFO @ Tue, 21 Apr 2015 13:13:38: #2 alternative fragment length(s) may be 33 bps INFO @ Tue, 21 Apr 2015 13:13:38: #2.2 Generate R script for model : SRX032115.10_model.r WARNING @ Tue, 21 Apr 2015 13:13:38: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:13:38: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Tue, 21 Apr 2015 13:13:38: #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 13:13:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:13:40: #1 tags after filtering in treatment: 19000283 INFO @ Tue, 21 Apr 2015 13:13:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:13:40: #1 finished! INFO @ Tue, 21 Apr 2015 13:13:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:13:43: #2 number of paired peaks: 269 WARNING @ Tue, 21 Apr 2015 13:13:43: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Tue, 21 Apr 2015 13:13:43: start model_add_line... INFO @ Tue, 21 Apr 2015 13:13:46: start X-correlation... INFO @ Tue, 21 Apr 2015 13:13:46: end of X-cor INFO @ Tue, 21 Apr 2015 13:13:46: #2 finished! INFO @ Tue, 21 Apr 2015 13:13:46: #2 predicted fragment length is 33 bps INFO @ Tue, 21 Apr 2015 13:13:46: #2 alternative fragment length(s) may be 33 bps INFO @ Tue, 21 Apr 2015 13:13:46: #2.2 Generate R script for model : SRX032115.20_model.r WARNING @ Tue, 21 Apr 2015 13:13:46: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:13:46: #2 You may need to consider one of the other alternative d(s): 33 WARNING @ Tue, 21 Apr 2015 13:13:46: #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 13:13:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:15:08: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:15: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:15:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:16:15: #4 Write output xls file... SRX032115.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:16: #4 Write peak in narrowPeak format file... SRX032115.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:16: #4 Write summits bed file... SRX032115.10_summits.bed INFO @ Tue, 21 Apr 2015 13:16:16: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1797 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:16:24: #4 Write output xls file... SRX032115.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:24: #4 Write peak in narrowPeak format file... SRX032115.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:24: #4 Write summits bed file... SRX032115.05_summits.bed INFO @ Tue, 21 Apr 2015 13:16:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2090 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:16:27: #4 Write output xls file... SRX032115.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:16:27: #4 Write peak in narrowPeak format file... SRX032115.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:16:27: #4 Write summits bed file... SRX032115.20_summits.bed INFO @ Tue, 21 Apr 2015 13:16:27: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1165 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。