Job ID = 2161374 sra ファイルのダウンロード中... Completed: 211773K bytes transferred in 5 seconds (340355K 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 44420 0 44420 0 0 46822 0 --:--:-- --:--:-- --:--:-- 58678 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 9053691 spots for /home/okishinya/chipatlas/results/dm3/SRX025463/SRR063856.sra Written 9053691 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: 00:02:36 9053691 reads; of these: 9053691 (100.00%) were unpaired; of these: 307452 (3.40%) aligned 0 times 6858009 (75.75%) aligned exactly 1 time 1888230 (20.86%) aligned >1 times 96.60% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 626961 / 8746239 = 0.0717 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 12:33:09: # Command line: callpeak -t SRX025463.bam -f BAM -g dm -n SRX025463.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX025463.20 # format = BAM # ChIP-seq file = ['SRX025463.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 12:33:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:33:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:33:09: # Command line: callpeak -t SRX025463.bam -f BAM -g dm -n SRX025463.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX025463.10 # format = BAM # ChIP-seq file = ['SRX025463.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 12:33:09: # Command line: callpeak -t SRX025463.bam -f BAM -g dm -n SRX025463.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX025463.05 # format = BAM # ChIP-seq file = ['SRX025463.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 12:33:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:33:09: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:33:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:33:09: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:33:15: 1000000 INFO @ Tue, 21 Apr 2015 12:33:15: 1000000 INFO @ Tue, 21 Apr 2015 12:33:15: 1000000 INFO @ Tue, 21 Apr 2015 12:33:21: 2000000 INFO @ Tue, 21 Apr 2015 12:33:21: 2000000 INFO @ Tue, 21 Apr 2015 12:33:22: 2000000 INFO @ Tue, 21 Apr 2015 12:33:27: 3000000 INFO @ Tue, 21 Apr 2015 12:33:27: 3000000 INFO @ Tue, 21 Apr 2015 12:33:28: 3000000 INFO @ Tue, 21 Apr 2015 12:33:32: 4000000 INFO @ Tue, 21 Apr 2015 12:33:33: 4000000 INFO @ Tue, 21 Apr 2015 12:33:34: 4000000 INFO @ Tue, 21 Apr 2015 12:33:38: 5000000 INFO @ Tue, 21 Apr 2015 12:33:39: 5000000 INFO @ Tue, 21 Apr 2015 12:33:41: 5000000 INFO @ Tue, 21 Apr 2015 12:33:43: 6000000 INFO @ Tue, 21 Apr 2015 12:33:45: 6000000 INFO @ Tue, 21 Apr 2015 12:33:47: 6000000 INFO @ Tue, 21 Apr 2015 12:33:49: 7000000 INFO @ Tue, 21 Apr 2015 12:33:51: 7000000 INFO @ Tue, 21 Apr 2015 12:33:53: 7000000 INFO @ Tue, 21 Apr 2015 12:33:54: 8000000 INFO @ Tue, 21 Apr 2015 12:33:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:33:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:33:55: #1 total tags in treatment: 8119278 INFO @ Tue, 21 Apr 2015 12:33:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:33:55: #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 12:33:57: #1 tags after filtering in treatment: 8119021 INFO @ Tue, 21 Apr 2015 12:33:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:57: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:57: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:33:57: 8000000 INFO @ Tue, 21 Apr 2015 12:33:58: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:33:58: 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 12:33:58: start model_add_line... INFO @ Tue, 21 Apr 2015 12:33:58: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:33:58: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:33:58: #1 total tags in treatment: 8119278 INFO @ Tue, 21 Apr 2015 12:33:58: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:33:58: #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 12:33:59: 8000000 INFO @ Tue, 21 Apr 2015 12:33:59: start X-correlation... INFO @ Tue, 21 Apr 2015 12:33:59: end of X-cor INFO @ Tue, 21 Apr 2015 12:33:59: #2 finished! INFO @ Tue, 21 Apr 2015 12:33:59: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:33:59: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:33:59: #2.2 Generate R script for model : SRX025463.05_model.r WARNING @ Tue, 21 Apr 2015 12:33:59: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:33:59: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:33:59: #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 12:33:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:33:59: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:33:59: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:33:59: #1 total tags in treatment: 8119278 INFO @ Tue, 21 Apr 2015 12:33:59: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:33:59: #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 12:33:59: #1 tags after filtering in treatment: 8119021 INFO @ Tue, 21 Apr 2015 12:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:33:59: #1 finished! INFO @ Tue, 21 Apr 2015 12:33:59: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:34:01: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:34:01: 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 12:34:01: start model_add_line... INFO @ Tue, 21 Apr 2015 12:34:01: #1 tags after filtering in treatment: 8119021 INFO @ Tue, 21 Apr 2015 12:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:34:01: #1 finished! INFO @ Tue, 21 Apr 2015 12:34:01: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:34:01: start X-correlation... INFO @ Tue, 21 Apr 2015 12:34:02: end of X-cor INFO @ Tue, 21 Apr 2015 12:34:02: #2 finished! INFO @ Tue, 21 Apr 2015 12:34:02: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:34:02: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:34:02: #2.2 Generate R script for model : SRX025463.10_model.r WARNING @ Tue, 21 Apr 2015 12:34:02: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:34:02: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:34:02: #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 12:34:02: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:34:02: #2 number of paired peaks: 144 WARNING @ Tue, 21 Apr 2015 12:34:02: 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 12:34:02: start model_add_line... INFO @ Tue, 21 Apr 2015 12:34:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:34:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:34:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:34:03: #2 predicted fragment length is 38 bps INFO @ Tue, 21 Apr 2015 12:34:03: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 21 Apr 2015 12:34:03: #2.2 Generate R script for model : SRX025463.20_model.r WARNING @ Tue, 21 Apr 2015 12:34:03: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:34:03: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 21 Apr 2015 12:34:03: #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 12:34:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:34:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:34:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:34:47: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:34:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:35:18: #4 Write output xls file... SRX025463.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:35:18: #4 Write peak in narrowPeak format file... SRX025463.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:35:18: #4 Write summits bed file... SRX025463.05_summits.bed INFO @ Tue, 21 Apr 2015 12:35:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:35:20: #4 Write output xls file... SRX025463.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:35:20: #4 Write peak in narrowPeak format file... SRX025463.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:35:20: #4 Write summits bed file... SRX025463.20_summits.bed INFO @ Tue, 21 Apr 2015 12:35:20: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:35:20: #4 Write output xls file... SRX025463.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:35:20: #4 Write peak in narrowPeak format file... SRX025463.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:35:20: #4 Write summits bed file... SRX025463.10_summits.bed INFO @ Tue, 21 Apr 2015 12:35:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (472 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。