Job ID = 2163347 sra ファイルのダウンロード中... Completed: 98482K bytes transferred in 4 seconds (179366K 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 8380 0 8380 0 0 15216 0 --:--:-- --:--:-- --:--:-- 23277 100 34931 0 34931 0 0 47194 0 --:--:-- --:--:-- --:--:-- 63510 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 4950487 spots for /home/okishinya/chipatlas/results/dm3/SRX124477/SRR423933.sra Written 4950487 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: 00:01:27 4950487 reads; of these: 4950487 (100.00%) were unpaired; of these: 226989 (4.59%) aligned 0 times 3498819 (70.68%) aligned exactly 1 time 1224679 (24.74%) aligned >1 times 95.41% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 164083 / 4723498 = 0.0347 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 16:00:37: # Command line: callpeak -t SRX124477.bam -f BAM -g dm -n SRX124477.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX124477.20 # format = BAM # ChIP-seq file = ['SRX124477.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 16:00:37: # Command line: callpeak -t SRX124477.bam -f BAM -g dm -n SRX124477.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX124477.10 # format = BAM # ChIP-seq file = ['SRX124477.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 16:00:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:00:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:00:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:00:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:00:37: # Command line: callpeak -t SRX124477.bam -f BAM -g dm -n SRX124477.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX124477.05 # format = BAM # ChIP-seq file = ['SRX124477.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 16:00:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 16:00:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 16:00:42: 1000000 INFO @ Tue, 21 Apr 2015 16:00:42: 1000000 INFO @ Tue, 21 Apr 2015 16:00:42: 1000000 INFO @ Tue, 21 Apr 2015 16:00:47: 2000000 INFO @ Tue, 21 Apr 2015 16:00:47: 2000000 INFO @ Tue, 21 Apr 2015 16:00:47: 2000000 INFO @ Tue, 21 Apr 2015 16:00:52: 3000000 INFO @ Tue, 21 Apr 2015 16:00:52: 3000000 INFO @ Tue, 21 Apr 2015 16:00:52: 3000000 INFO @ Tue, 21 Apr 2015 16:00:57: 4000000 INFO @ Tue, 21 Apr 2015 16:00:57: 4000000 INFO @ Tue, 21 Apr 2015 16:00:57: 4000000 INFO @ Tue, 21 Apr 2015 16:01:00: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 16:01:00: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 16:01:00: #1 total tags in treatment: 4559415 INFO @ Tue, 21 Apr 2015 16:01:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:01:00: #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 16:01:00: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 16:01:00: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 16:01:00: #1 total tags in treatment: 4559415 INFO @ Tue, 21 Apr 2015 16:01:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:01:00: #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 16:01:00: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 16:01:00: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 16:01:00: #1 total tags in treatment: 4559415 INFO @ Tue, 21 Apr 2015 16:01:00: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 16:01:00: #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 16:01:01: #1 tags after filtering in treatment: 4559315 INFO @ Tue, 21 Apr 2015 16:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 16:01:01: #1 finished! INFO @ Tue, 21 Apr 2015 16:01:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:01:01: #1 tags after filtering in treatment: 4559315 INFO @ Tue, 21 Apr 2015 16:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 16:01:01: #1 finished! INFO @ Tue, 21 Apr 2015 16:01:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:01:01: #1 tags after filtering in treatment: 4559315 INFO @ Tue, 21 Apr 2015 16:01:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 16:01:01: #1 finished! INFO @ Tue, 21 Apr 2015 16:01:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 16:01:01: #2 number of paired peaks: 189 WARNING @ Tue, 21 Apr 2015 16:01:01: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 21 Apr 2015 16:01:01: start model_add_line... INFO @ Tue, 21 Apr 2015 16:01:01: #2 number of paired peaks: 189 WARNING @ Tue, 21 Apr 2015 16:01:01: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 21 Apr 2015 16:01:01: start model_add_line... INFO @ Tue, 21 Apr 2015 16:01:02: #2 number of paired peaks: 189 WARNING @ Tue, 21 Apr 2015 16:01:02: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Tue, 21 Apr 2015 16:01:02: start model_add_line... INFO @ Tue, 21 Apr 2015 16:01:02: start X-correlation... INFO @ Tue, 21 Apr 2015 16:01:02: end of X-cor INFO @ Tue, 21 Apr 2015 16:01:02: #2 finished! INFO @ Tue, 21 Apr 2015 16:01:02: #2 predicted fragment length is 31 bps INFO @ Tue, 21 Apr 2015 16:01:02: #2 alternative fragment length(s) may be 31 bps INFO @ Tue, 21 Apr 2015 16:01:02: #2.2 Generate R script for model : SRX124477.05_model.r WARNING @ Tue, 21 Apr 2015 16:01:02: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 16:01:02: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Tue, 21 Apr 2015 16:01:02: #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 16:01:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:01:02: start X-correlation... INFO @ Tue, 21 Apr 2015 16:01:02: end of X-cor INFO @ Tue, 21 Apr 2015 16:01:02: #2 finished! INFO @ Tue, 21 Apr 2015 16:01:02: #2 predicted fragment length is 31 bps INFO @ Tue, 21 Apr 2015 16:01:02: #2 alternative fragment length(s) may be 31 bps INFO @ Tue, 21 Apr 2015 16:01:02: #2.2 Generate R script for model : SRX124477.10_model.r WARNING @ Tue, 21 Apr 2015 16:01:02: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 16:01:02: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Tue, 21 Apr 2015 16:01:02: #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 16:01:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:01:02: start X-correlation... INFO @ Tue, 21 Apr 2015 16:01:02: end of X-cor INFO @ Tue, 21 Apr 2015 16:01:02: #2 finished! INFO @ Tue, 21 Apr 2015 16:01:02: #2 predicted fragment length is 31 bps INFO @ Tue, 21 Apr 2015 16:01:02: #2 alternative fragment length(s) may be 31 bps INFO @ Tue, 21 Apr 2015 16:01:02: #2.2 Generate R script for model : SRX124477.20_model.r WARNING @ Tue, 21 Apr 2015 16:01:02: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 16:01:02: #2 You may need to consider one of the other alternative d(s): 31 WARNING @ Tue, 21 Apr 2015 16:01:02: #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 16:01:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 16:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 16:01:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:01:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:01:29: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 16:01:46: #4 Write output xls file... SRX124477.20_peaks.xls INFO @ Tue, 21 Apr 2015 16:01:46: #4 Write peak in narrowPeak format file... SRX124477.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:01:46: #4 Write summits bed file... SRX124477.20_summits.bed INFO @ Tue, 21 Apr 2015 16:01:46: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 16:01:47: #4 Write output xls file... SRX124477.10_peaks.xls INFO @ Tue, 21 Apr 2015 16:01:47: #4 Write peak in narrowPeak format file... SRX124477.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:01:47: #4 Write summits bed file... SRX124477.10_summits.bed INFO @ Tue, 21 Apr 2015 16:01:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 16:01:49: #4 Write output xls file... SRX124477.05_peaks.xls INFO @ Tue, 21 Apr 2015 16:01:49: #4 Write peak in narrowPeak format file... SRX124477.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 16:01:49: #4 Write summits bed file... SRX124477.05_summits.bed INFO @ Tue, 21 Apr 2015 16:01:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1056 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。