Job ID = 9037568 sra ファイルのダウンロード中... Completed: 159632K bytes transferred in 5 seconds (259496K 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 --:--:-- 0:00:06 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 12695 0 12695 0 0 1627 0 --:--:-- 0:00:07 --:--:-- 9119 100 33142 0 33142 0 0 3766 0 --:--:-- 0:00:08 --:--:-- 13878 100 44861 0 44861 0 0 4913 0 --:--:-- 0:00:09 --:--:-- 16499 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 5798129 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876299/SRR1802402.sra Written 5798129 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: 00:00:40 5798129 reads; of these: 5798129 (100.00%) were unpaired; of these: 2292272 (39.53%) aligned 0 times 2778799 (47.93%) aligned exactly 1 time 727058 (12.54%) aligned >1 times 60.47% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 3028780 / 3505857 = 0.8639 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 @ Sun, 04 Jun 2017 04:54:31: # Command line: callpeak -t SRX876299.bam -f BAM -g 12100000 -n SRX876299.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876299.05 # format = BAM # ChIP-seq file = ['SRX876299.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 04:54:31: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:31: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:32: # Command line: callpeak -t SRX876299.bam -f BAM -g 12100000 -n SRX876299.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876299.10 # format = BAM # ChIP-seq file = ['SRX876299.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 04:54:32: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:32: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:32: # Command line: callpeak -t SRX876299.bam -f BAM -g 12100000 -n SRX876299.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876299.20 # format = BAM # ChIP-seq file = ['SRX876299.bam'] # control file = None # effective genome size = 1.21e+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 @ Sun, 04 Jun 2017 04:54:32: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:54:32: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:54:34: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:34: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:34: #1 total tags in treatment: 477077 INFO @ Sun, 04 Jun 2017 04:54:34: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 04:54:34: #1 tags after filtering in treatment: 476751 INFO @ Sun, 04 Jun 2017 04:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:34: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:34: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:34: #2 number of paired peaks: 298 WARNING @ Sun, 04 Jun 2017 04:54:34: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sun, 04 Jun 2017 04:54:34: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:35: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:35: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:35: #1 total tags in treatment: 477077 INFO @ Sun, 04 Jun 2017 04:54:35: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 04:54:35: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:54:35: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:54:35: #1 total tags in treatment: 477077 INFO @ Sun, 04 Jun 2017 04:54:35: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:54:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 04:54:35: #1 tags after filtering in treatment: 476751 INFO @ Sun, 04 Jun 2017 04:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:35: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:35: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:35: #1 tags after filtering in treatment: 476751 INFO @ Sun, 04 Jun 2017 04:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:54:35: #1 finished! INFO @ Sun, 04 Jun 2017 04:54:35: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:54:35: #2 number of paired peaks: 298 WARNING @ Sun, 04 Jun 2017 04:54:35: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sun, 04 Jun 2017 04:54:35: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:35: #2 number of paired peaks: 298 WARNING @ Sun, 04 Jun 2017 04:54:35: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Sun, 04 Jun 2017 04:54:35: start model_add_line... INFO @ Sun, 04 Jun 2017 04:54:36: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:36: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:36: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:36: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 04:54:36: #2 alternative fragment length(s) may be 2,37,132,171,201,226,252,275,294,343,377,391,411,426,472,498,526,555,591 bps INFO @ Sun, 04 Jun 2017 04:54:36: #2.2 Generate R script for model : SRX876299.05_model.r WARNING @ Sun, 04 Jun 2017 04:54:36: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:36: #2 You may need to consider one of the other alternative d(s): 2,37,132,171,201,226,252,275,294,343,377,391,411,426,472,498,526,555,591 WARNING @ Sun, 04 Jun 2017 04:54:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 04:54:36: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:54:36: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:36: start X-correlation... INFO @ Sun, 04 Jun 2017 04:54:36: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:36: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:36: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 04:54:36: #2 alternative fragment length(s) may be 2,37,132,171,201,226,252,275,294,343,377,391,411,426,472,498,526,555,591 bps INFO @ Sun, 04 Jun 2017 04:54:36: #2.2 Generate R script for model : SRX876299.20_model.r INFO @ Sun, 04 Jun 2017 04:54:36: end of X-cor INFO @ Sun, 04 Jun 2017 04:54:36: #2 finished! INFO @ Sun, 04 Jun 2017 04:54:36: #2 predicted fragment length is 37 bps INFO @ Sun, 04 Jun 2017 04:54:36: #2 alternative fragment length(s) may be 2,37,132,171,201,226,252,275,294,343,377,391,411,426,472,498,526,555,591 bps INFO @ Sun, 04 Jun 2017 04:54:36: #2.2 Generate R script for model : SRX876299.10_model.r WARNING @ Sun, 04 Jun 2017 04:54:36: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:36: #2 You may need to consider one of the other alternative d(s): 2,37,132,171,201,226,252,275,294,343,377,391,411,426,472,498,526,555,591 WARNING @ Sun, 04 Jun 2017 04:54:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 04:54:36: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:36: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Jun 2017 04:54:36: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 04:54:36: #2 You may need to consider one of the other alternative d(s): 2,37,132,171,201,226,252,275,294,343,377,391,411,426,472,498,526,555,591 WARNING @ Sun, 04 Jun 2017 04:54:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 04:54:36: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:54:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:54:40: #4 Write output xls file... SRX876299.05_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:40: #4 Write peak in narrowPeak format file... SRX876299.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:40: #4 Write summits bed file... SRX876299.05_summits.bed INFO @ Sun, 04 Jun 2017 04:54:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:54:41: #4 Write output xls file... SRX876299.20_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:41: #4 Write peak in narrowPeak format file... SRX876299.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:41: #4 Write summits bed file... SRX876299.20_summits.bed INFO @ Sun, 04 Jun 2017 04:54:41: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:54:41: #4 Write output xls file... SRX876299.10_peaks.xls INFO @ Sun, 04 Jun 2017 04:54:41: #4 Write peak in narrowPeak format file... SRX876299.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:54:41: #4 Write summits bed file... SRX876299.10_summits.bed INFO @ Sun, 04 Jun 2017 04:54:41: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (25 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。