Job ID = 2161289 sra ファイルのダウンロード中... Completed: 284808K bytes transferred in 5 seconds (416888K 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 4007 0 4007 0 0 7686 0 --:--:-- --:--:-- --:--:-- 12105 100 34337 0 34337 0 0 48288 0 --:--:-- --:--:-- --:--:-- 66032 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 12516454 spots for /home/okishinya/chipatlas/results/dm3/SRX016155/SRR034717.sra Written 12516454 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: 00:03:56 12516454 reads; of these: 12516454 (100.00%) were unpaired; of these: 672280 (5.37%) aligned 0 times 9075002 (72.50%) aligned exactly 1 time 2769172 (22.12%) aligned >1 times 94.63% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 1323228 / 11844174 = 0.1117 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 12:19:52: # Command line: callpeak -t SRX016155.bam -f BAM -g dm -n SRX016155.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016155.05 # format = BAM # ChIP-seq file = ['SRX016155.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 12:19:52: # Command line: callpeak -t SRX016155.bam -f BAM -g dm -n SRX016155.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016155.10 # format = BAM # ChIP-seq file = ['SRX016155.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 12:19:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:19:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:19:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:19:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:19:52: # Command line: callpeak -t SRX016155.bam -f BAM -g dm -n SRX016155.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016155.20 # format = BAM # ChIP-seq file = ['SRX016155.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 12:19:52: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:19:52: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:19:58: 1000000 INFO @ Tue, 21 Apr 2015 12:19:58: 1000000 INFO @ Tue, 21 Apr 2015 12:19:58: 1000000 INFO @ Tue, 21 Apr 2015 12:20:04: 2000000 INFO @ Tue, 21 Apr 2015 12:20:05: 2000000 INFO @ Tue, 21 Apr 2015 12:20:05: 2000000 INFO @ Tue, 21 Apr 2015 12:20:10: 3000000 INFO @ Tue, 21 Apr 2015 12:20:11: 3000000 INFO @ Tue, 21 Apr 2015 12:20:11: 3000000 INFO @ Tue, 21 Apr 2015 12:20:16: 4000000 INFO @ Tue, 21 Apr 2015 12:20:18: 4000000 INFO @ Tue, 21 Apr 2015 12:20:18: 4000000 INFO @ Tue, 21 Apr 2015 12:20:22: 5000000 INFO @ Tue, 21 Apr 2015 12:20:24: 5000000 INFO @ Tue, 21 Apr 2015 12:20:24: 5000000 INFO @ Tue, 21 Apr 2015 12:20:28: 6000000 INFO @ Tue, 21 Apr 2015 12:20:30: 6000000 INFO @ Tue, 21 Apr 2015 12:20:30: 6000000 INFO @ Tue, 21 Apr 2015 12:20:34: 7000000 INFO @ Tue, 21 Apr 2015 12:20:37: 7000000 INFO @ Tue, 21 Apr 2015 12:20:37: 7000000 INFO @ Tue, 21 Apr 2015 12:20:40: 8000000 INFO @ Tue, 21 Apr 2015 12:20:43: 8000000 INFO @ Tue, 21 Apr 2015 12:20:43: 8000000 INFO @ Tue, 21 Apr 2015 12:20:46: 9000000 INFO @ Tue, 21 Apr 2015 12:20:50: 9000000 INFO @ Tue, 21 Apr 2015 12:20:50: 9000000 INFO @ Tue, 21 Apr 2015 12:20:52: 10000000 INFO @ Tue, 21 Apr 2015 12:20:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:20:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:20:55: #1 total tags in treatment: 10520946 INFO @ Tue, 21 Apr 2015 12:20:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:20:55: #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 12:20:56: 10000000 INFO @ Tue, 21 Apr 2015 12:20:56: 10000000 INFO @ Tue, 21 Apr 2015 12:20:57: #1 tags after filtering in treatment: 10519637 INFO @ Tue, 21 Apr 2015 12:20:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:20:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:20:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:20:59: #2 number of paired peaks: 225 WARNING @ Tue, 21 Apr 2015 12:20:59: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 21 Apr 2015 12:20:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:21:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:21:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:21:00: #1 total tags in treatment: 10520946 INFO @ Tue, 21 Apr 2015 12:21:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:21:00: #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 12:21:00: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:21:00: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:21:00: #1 total tags in treatment: 10520946 INFO @ Tue, 21 Apr 2015 12:21:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:21:00: #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 12:21:01: start X-correlation... INFO @ Tue, 21 Apr 2015 12:21:01: end of X-cor INFO @ Tue, 21 Apr 2015 12:21:01: #2 finished! INFO @ Tue, 21 Apr 2015 12:21:01: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 12:21:01: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 12:21:01: #2.2 Generate R script for model : SRX016155.20_model.r WARNING @ Tue, 21 Apr 2015 12:21:01: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:21:01: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 12:21:01: #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 12:21:01: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:21:02: #1 tags after filtering in treatment: 10519637 INFO @ Tue, 21 Apr 2015 12:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:21:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:21:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:21:02: #1 tags after filtering in treatment: 10519637 INFO @ Tue, 21 Apr 2015 12:21:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:21:02: #1 finished! INFO @ Tue, 21 Apr 2015 12:21:02: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:21:03: #2 number of paired peaks: 225 WARNING @ Tue, 21 Apr 2015 12:21:03: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 21 Apr 2015 12:21:03: start model_add_line... INFO @ Tue, 21 Apr 2015 12:21:04: #2 number of paired peaks: 225 WARNING @ Tue, 21 Apr 2015 12:21:04: Fewer paired peaks (225) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 225 pairs to build model! INFO @ Tue, 21 Apr 2015 12:21:04: start model_add_line... INFO @ Tue, 21 Apr 2015 12:21:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:21:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:21:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:21:05: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 12:21:05: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 12:21:05: #2.2 Generate R script for model : SRX016155.10_model.r WARNING @ Tue, 21 Apr 2015 12:21:05: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:21:05: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 12:21:05: #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 12:21:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:21:06: start X-correlation... INFO @ Tue, 21 Apr 2015 12:21:06: end of X-cor INFO @ Tue, 21 Apr 2015 12:21:06: #2 finished! INFO @ Tue, 21 Apr 2015 12:21:06: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 12:21:06: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 12:21:06: #2.2 Generate R script for model : SRX016155.05_model.r WARNING @ Tue, 21 Apr 2015 12:21:06: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:21:06: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 12:21:06: #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 12:21:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:21:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:22:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:22:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:22:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:22:40: #4 Write output xls file... SRX016155.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:22:40: #4 Write peak in narrowPeak format file... SRX016155.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:22:40: #4 Write summits bed file... SRX016155.05_summits.bed INFO @ Tue, 21 Apr 2015 12:22:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (936 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:22:40: #4 Write output xls file... SRX016155.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:22:40: #4 Write peak in narrowPeak format file... SRX016155.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:22:40: #4 Write summits bed file... SRX016155.20_summits.bed INFO @ Tue, 21 Apr 2015 12:22:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:22:46: #4 Write output xls file... SRX016155.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:22:46: #4 Write peak in narrowPeak format file... SRX016155.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:22:46: #4 Write summits bed file... SRX016155.10_summits.bed INFO @ Tue, 21 Apr 2015 12:22:46: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (627 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。