Job ID = 2162163 sra ファイルのダウンロード中... Completed: 159063K bytes transferred in 5 seconds (255497K 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 35456 0 35456 0 0 49605 0 --:--:-- --:--:-- --:--:-- 67793 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 8148551 spots for /home/okishinya/chipatlas/results/dm3/SRX050600/SRR139082.sra Written 8148551 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: 00:02:37 8148551 reads; of these: 8148551 (100.00%) were unpaired; of these: 358926 (4.40%) aligned 0 times 5601514 (68.74%) aligned exactly 1 time 2188111 (26.85%) aligned >1 times 95.60% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 707856 / 7789625 = 0.0909 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 13:36:04: # Command line: callpeak -t SRX050600.bam -f BAM -g dm -n SRX050600.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX050600.20 # format = BAM # ChIP-seq file = ['SRX050600.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 13:36:04: # Command line: callpeak -t SRX050600.bam -f BAM -g dm -n SRX050600.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX050600.05 # format = BAM # ChIP-seq file = ['SRX050600.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 13:36:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:36:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:36:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:36:04: # Command line: callpeak -t SRX050600.bam -f BAM -g dm -n SRX050600.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX050600.10 # format = BAM # ChIP-seq file = ['SRX050600.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 13:36:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:36:04: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:36:04: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:36:09: 1000000 INFO @ Tue, 21 Apr 2015 13:36:09: 1000000 INFO @ Tue, 21 Apr 2015 13:36:09: 1000000 INFO @ Tue, 21 Apr 2015 13:36:14: 2000000 INFO @ Tue, 21 Apr 2015 13:36:15: 2000000 INFO @ Tue, 21 Apr 2015 13:36:15: 2000000 INFO @ Tue, 21 Apr 2015 13:36:19: 3000000 INFO @ Tue, 21 Apr 2015 13:36:20: 3000000 INFO @ Tue, 21 Apr 2015 13:36:20: 3000000 INFO @ Tue, 21 Apr 2015 13:36:24: 4000000 INFO @ Tue, 21 Apr 2015 13:36:25: 4000000 INFO @ Tue, 21 Apr 2015 13:36:25: 4000000 INFO @ Tue, 21 Apr 2015 13:36:30: 5000000 INFO @ Tue, 21 Apr 2015 13:36:31: 5000000 INFO @ Tue, 21 Apr 2015 13:36:31: 5000000 INFO @ Tue, 21 Apr 2015 13:36:35: 6000000 INFO @ Tue, 21 Apr 2015 13:36:36: 6000000 INFO @ Tue, 21 Apr 2015 13:36:36: 6000000 INFO @ Tue, 21 Apr 2015 13:36:40: 7000000 INFO @ Tue, 21 Apr 2015 13:36:41: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:41: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:41: #1 total tags in treatment: 7081769 INFO @ Tue, 21 Apr 2015 13:36:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:41: #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 13:36:42: 7000000 INFO @ Tue, 21 Apr 2015 13:36:42: 7000000 INFO @ Tue, 21 Apr 2015 13:36:42: #1 tags after filtering in treatment: 7081580 INFO @ Tue, 21 Apr 2015 13:36:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:42: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:42: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:42: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:42: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:42: #1 total tags in treatment: 7081769 INFO @ Tue, 21 Apr 2015 13:36:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:42: #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 13:36:42: #1 tag size is determined as 30 bps INFO @ Tue, 21 Apr 2015 13:36:42: #1 tag size = 30 INFO @ Tue, 21 Apr 2015 13:36:42: #1 total tags in treatment: 7081769 INFO @ Tue, 21 Apr 2015 13:36:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:36:42: #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 13:36:43: #2 number of paired peaks: 288 WARNING @ Tue, 21 Apr 2015 13:36:43: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 21 Apr 2015 13:36:43: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:44: #1 tags after filtering in treatment: 7081580 INFO @ Tue, 21 Apr 2015 13:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:44: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:44: #1 tags after filtering in treatment: 7081580 INFO @ Tue, 21 Apr 2015 13:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:36:44: #1 finished! INFO @ Tue, 21 Apr 2015 13:36:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:36:45: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:45: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:45: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:45: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:36:45: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:36:45: #2.2 Generate R script for model : SRX050600.10_model.r WARNING @ Tue, 21 Apr 2015 13:36:45: #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 13:36:45: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:36:45: #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 13:36:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:36:45: #2 number of paired peaks: 288 WARNING @ Tue, 21 Apr 2015 13:36:45: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 21 Apr 2015 13:36:45: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:45: #2 number of paired peaks: 288 WARNING @ Tue, 21 Apr 2015 13:36:45: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 21 Apr 2015 13:36:45: start model_add_line... INFO @ Tue, 21 Apr 2015 13:36:46: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:46: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:46: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:46: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:36:46: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:36:46: start X-correlation... INFO @ Tue, 21 Apr 2015 13:36:46: #2.2 Generate R script for model : SRX050600.05_model.r INFO @ Tue, 21 Apr 2015 13:36:46: end of X-cor INFO @ Tue, 21 Apr 2015 13:36:46: #2 finished! INFO @ Tue, 21 Apr 2015 13:36:46: #2 predicted fragment length is 37 bps INFO @ Tue, 21 Apr 2015 13:36:46: #2 alternative fragment length(s) may be 37 bps INFO @ Tue, 21 Apr 2015 13:36:46: #2.2 Generate R script for model : SRX050600.20_model.r WARNING @ Tue, 21 Apr 2015 13:36:46: #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 13:36:46: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:36:46: #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 13:36:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:46: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 21 Apr 2015 13:36:46: #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 13:36:46: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Tue, 21 Apr 2015 13:36:46: #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 13:36:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:36:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:37:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:37:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:37:26: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write output xls file... SRX050600.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write peak in narrowPeak format file... SRX050600.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write summits bed file... SRX050600.05_summits.bed INFO @ Tue, 21 Apr 2015 13:37:55: Done! INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write output xls file... SRX050600.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write peak in narrowPeak format file... SRX050600.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write summits bed file... SRX050600.20_summits.bed INFO @ Tue, 21 Apr 2015 13:37:55: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1510 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write output xls file... SRX050600.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write peak in narrowPeak format file... SRX050600.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:37:55: #4 Write summits bed file... SRX050600.10_summits.bed INFO @ Tue, 21 Apr 2015 13:37:55: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1167 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。