Job ID = 2236678 sra ファイルのダウンロード中... Completed: 3238902K bytes transferred in 32 seconds (806203K 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 37807 0 37807 0 0 50475 0 --:--:-- --:--:-- --:--:-- 67876 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 7829986 spots for /home/okishinya/chipatlas/results/ce10/SRX012298/SRR029217.sra Written 7829986 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: 00:01:24 7829986 reads; of these: 7829986 (100.00%) were unpaired; of these: 2245544 (28.68%) aligned 0 times 4161905 (53.15%) aligned exactly 1 time 1422537 (18.17%) aligned >1 times 71.32% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1637859 / 5584442 = 0.2933 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 @ Thu, 30 Apr 2015 10:56:27: # Command line: callpeak -t SRX012298.bam -f BAM -g ce -n SRX012298.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX012298.20 # format = BAM # ChIP-seq file = ['SRX012298.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 10:56:27: # Command line: callpeak -t SRX012298.bam -f BAM -g ce -n SRX012298.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX012298.10 # format = BAM # ChIP-seq file = ['SRX012298.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 10:56:27: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:56:27: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:56:27: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:56:27: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:56:27: # Command line: callpeak -t SRX012298.bam -f BAM -g ce -n SRX012298.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX012298.05 # format = BAM # ChIP-seq file = ['SRX012298.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 10:56:27: #1 read tag files... INFO @ Thu, 30 Apr 2015 10:56:27: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 10:56:32: 1000000 INFO @ Thu, 30 Apr 2015 10:56:33: 1000000 INFO @ Thu, 30 Apr 2015 10:56:33: 1000000 INFO @ Thu, 30 Apr 2015 10:56:38: 2000000 INFO @ Thu, 30 Apr 2015 10:56:39: 2000000 INFO @ Thu, 30 Apr 2015 10:56:39: 2000000 INFO @ Thu, 30 Apr 2015 10:56:43: 3000000 INFO @ Thu, 30 Apr 2015 10:56:45: 3000000 INFO @ Thu, 30 Apr 2015 10:56:45: 3000000 INFO @ Thu, 30 Apr 2015 10:56:48: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:56:48: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:56:48: #1 total tags in treatment: 3946583 INFO @ Thu, 30 Apr 2015 10:56:48: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:56:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:56:49: #1 tags after filtering in treatment: 3946156 INFO @ Thu, 30 Apr 2015 10:56:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:56:49: #1 finished! INFO @ Thu, 30 Apr 2015 10:56:49: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:56:50: #2 number of paired peaks: 819 WARNING @ Thu, 30 Apr 2015 10:56:50: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Thu, 30 Apr 2015 10:56:50: start model_add_line... INFO @ Thu, 30 Apr 2015 10:56:51: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:56:51: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:56:51: #1 total tags in treatment: 3946583 INFO @ Thu, 30 Apr 2015 10:56:51: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:56:51: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 10:56:51: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 10:56:51: #1 total tags in treatment: 3946583 INFO @ Thu, 30 Apr 2015 10:56:51: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 10:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 10:56:51: #1 tags after filtering in treatment: 3946156 INFO @ Thu, 30 Apr 2015 10:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:56:51: #1 finished! INFO @ Thu, 30 Apr 2015 10:56:51: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:56:51: #1 tags after filtering in treatment: 3946156 INFO @ Thu, 30 Apr 2015 10:56:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 10:56:51: #1 finished! INFO @ Thu, 30 Apr 2015 10:56:51: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 10:56:52: #2 number of paired peaks: 819 WARNING @ Thu, 30 Apr 2015 10:56:52: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Thu, 30 Apr 2015 10:56:52: start model_add_line... INFO @ Thu, 30 Apr 2015 10:56:52: #2 number of paired peaks: 819 WARNING @ Thu, 30 Apr 2015 10:56:52: Fewer paired peaks (819) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 819 pairs to build model! INFO @ Thu, 30 Apr 2015 10:56:52: start model_add_line... INFO @ Thu, 30 Apr 2015 10:56:53: start X-correlation... INFO @ Thu, 30 Apr 2015 10:56:53: end of X-cor INFO @ Thu, 30 Apr 2015 10:56:53: #2 finished! INFO @ Thu, 30 Apr 2015 10:56:53: #2 predicted fragment length is 58 bps INFO @ Thu, 30 Apr 2015 10:56:53: #2 alternative fragment length(s) may be 2,58,76,97,119,139,573,597 bps INFO @ Thu, 30 Apr 2015 10:56:53: #2.2 Generate R script for model : SRX012298.20_model.r WARNING @ Thu, 30 Apr 2015 10:56:53: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:56:53: #2 You may need to consider one of the other alternative d(s): 2,58,76,97,119,139,573,597 WARNING @ Thu, 30 Apr 2015 10:56:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 10:56:53: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:56:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:56:55: start X-correlation... INFO @ Thu, 30 Apr 2015 10:56:56: end of X-cor INFO @ Thu, 30 Apr 2015 10:56:56: #2 finished! INFO @ Thu, 30 Apr 2015 10:56:56: #2 predicted fragment length is 58 bps INFO @ Thu, 30 Apr 2015 10:56:56: #2 alternative fragment length(s) may be 2,58,76,97,119,139,573,597 bps INFO @ Thu, 30 Apr 2015 10:56:56: #2.2 Generate R script for model : SRX012298.05_model.r WARNING @ Thu, 30 Apr 2015 10:56:56: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:56:56: #2 You may need to consider one of the other alternative d(s): 2,58,76,97,119,139,573,597 WARNING @ Thu, 30 Apr 2015 10:56:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 10:56:56: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:56:56: start X-correlation... INFO @ Thu, 30 Apr 2015 10:56:56: end of X-cor INFO @ Thu, 30 Apr 2015 10:56:56: #2 finished! INFO @ Thu, 30 Apr 2015 10:56:56: #2 predicted fragment length is 58 bps INFO @ Thu, 30 Apr 2015 10:56:56: #2 alternative fragment length(s) may be 2,58,76,97,119,139,573,597 bps INFO @ Thu, 30 Apr 2015 10:56:56: #2.2 Generate R script for model : SRX012298.10_model.r WARNING @ Thu, 30 Apr 2015 10:56:56: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 30 Apr 2015 10:56:56: #2 You may need to consider one of the other alternative d(s): 2,58,76,97,119,139,573,597 WARNING @ Thu, 30 Apr 2015 10:56:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 30 Apr 2015 10:56:56: #3 Call peaks... INFO @ Thu, 30 Apr 2015 10:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 10:57:17: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:57:18: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:57:18: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 10:57:33: #4 Write output xls file... SRX012298.20_peaks.xls INFO @ Thu, 30 Apr 2015 10:57:33: #4 Write peak in narrowPeak format file... SRX012298.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:57:33: #4 Write summits bed file... SRX012298.20_summits.bed INFO @ Thu, 30 Apr 2015 10:57:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:57:34: #4 Write output xls file... SRX012298.05_peaks.xls INFO @ Thu, 30 Apr 2015 10:57:34: #4 Write peak in narrowPeak format file... SRX012298.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:57:34: #4 Write summits bed file... SRX012298.05_summits.bed INFO @ Thu, 30 Apr 2015 10:57:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 10:57:34: #4 Write output xls file... SRX012298.10_peaks.xls INFO @ Thu, 30 Apr 2015 10:57:34: #4 Write peak in narrowPeak format file... SRX012298.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 10:57:34: #4 Write summits bed file... SRX012298.10_summits.bed INFO @ Thu, 30 Apr 2015 10:57:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。