Job ID = 10714587 sra ファイルのダウンロード中... Completed: 86452K bytes transferred in 7 seconds (88807K bits/sec), in 1 file. 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... Read 4877417 spots for /home/okishinya/chipatlas/results/dm3/SRX4053367/SRR7132346.sra Written 4877417 spots for /home/okishinya/chipatlas/results/dm3/SRX4053367/SRR7132346.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:02:39 4877417 reads; of these: 4877417 (100.00%) were unpaired; of these: 769382 (15.77%) aligned 0 times 2112844 (43.32%) aligned exactly 1 time 1995191 (40.91%) aligned >1 times 84.23% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 1235664 / 4108035 = 0.3008 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, 03 Jun 2018 13:41:24: # Command line: callpeak -t SRX4053367.bam -f BAM -g dm -n SRX4053367.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053367.20 # format = BAM # ChIP-seq file = ['SRX4053367.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 # Paired-End mode is off INFO @ Sun, 03 Jun 2018 13:41:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:41:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:41:24: # Command line: callpeak -t SRX4053367.bam -f BAM -g dm -n SRX4053367.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053367.05 # format = BAM # ChIP-seq file = ['SRX4053367.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 # Paired-End mode is off INFO @ Sun, 03 Jun 2018 13:41:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:41:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:41:24: # Command line: callpeak -t SRX4053367.bam -f BAM -g dm -n SRX4053367.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053367.10 # format = BAM # ChIP-seq file = ['SRX4053367.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 # Paired-End mode is off INFO @ Sun, 03 Jun 2018 13:41:24: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:41:24: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:41:31: 1000000 INFO @ Sun, 03 Jun 2018 13:41:31: 1000000 INFO @ Sun, 03 Jun 2018 13:41:31: 1000000 INFO @ Sun, 03 Jun 2018 13:41:38: 2000000 INFO @ Sun, 03 Jun 2018 13:41:38: 2000000 INFO @ Sun, 03 Jun 2018 13:41:38: 2000000 INFO @ Sun, 03 Jun 2018 13:41:44: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:41:44: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:41:44: #1 total tags in treatment: 2872371 INFO @ Sun, 03 Jun 2018 13:41:44: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:41:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:41:44: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:41:44: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:41:44: #1 total tags in treatment: 2872371 INFO @ Sun, 03 Jun 2018 13:41:44: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:41:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:41:44: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:41:44: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:41:44: #1 total tags in treatment: 2872371 INFO @ Sun, 03 Jun 2018 13:41:44: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:41:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:41:44: #1 tags after filtering in treatment: 2872371 INFO @ Sun, 03 Jun 2018 13:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:41:44: #1 finished! INFO @ Sun, 03 Jun 2018 13:41:44: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:41:44: #1 tags after filtering in treatment: 2872371 INFO @ Sun, 03 Jun 2018 13:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:41:44: #1 finished! INFO @ Sun, 03 Jun 2018 13:41:44: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:41:44: #1 tags after filtering in treatment: 2872371 INFO @ Sun, 03 Jun 2018 13:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:41:44: #1 finished! INFO @ Sun, 03 Jun 2018 13:41:44: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:41:44: #2 number of paired peaks: 908 WARNING @ Sun, 03 Jun 2018 13:41:44: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Sun, 03 Jun 2018 13:41:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:41:44: #2 number of paired peaks: 908 WARNING @ Sun, 03 Jun 2018 13:41:44: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Sun, 03 Jun 2018 13:41:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:41:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:41:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:41:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:41:44: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:41:44: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:41:44: #2.2 Generate R script for model : SRX4053367.20_model.r WARNING @ Sun, 03 Jun 2018 13:41:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:41:44: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:41:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:41:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:41:44: #2 number of paired peaks: 908 WARNING @ Sun, 03 Jun 2018 13:41:44: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Sun, 03 Jun 2018 13:41:44: start model_add_line... INFO @ Sun, 03 Jun 2018 13:41:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:41:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:41:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:41:44: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:41:44: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:41:44: #2.2 Generate R script for model : SRX4053367.05_model.r WARNING @ Sun, 03 Jun 2018 13:41:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:41:44: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:41:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:41:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:41:44: start X-correlation... INFO @ Sun, 03 Jun 2018 13:41:44: end of X-cor INFO @ Sun, 03 Jun 2018 13:41:44: #2 finished! INFO @ Sun, 03 Jun 2018 13:41:44: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:41:44: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:41:44: #2.2 Generate R script for model : SRX4053367.10_model.r WARNING @ Sun, 03 Jun 2018 13:41:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:41:44: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:41:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:41:44: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:41:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:41:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:41:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:41:51: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write output xls file... SRX4053367.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write peak in narrowPeak format file... SRX4053367.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write summits bed file... SRX4053367.20_summits.bed INFO @ Sun, 03 Jun 2018 13:41:55: Done! INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write output xls file... SRX4053367.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write peak in narrowPeak format file... SRX4053367.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write summits bed file... SRX4053367.05_summits.bed pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (809 records, 4 fields): 3 millis INFO @ Sun, 03 Jun 2018 13:41:55: Done! CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1709 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write output xls file... SRX4053367.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write peak in narrowPeak format file... SRX4053367.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:41:55: #4 Write summits bed file... SRX4053367.10_summits.bed INFO @ Sun, 03 Jun 2018 13:41:55: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1257 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。