Job ID = 11171344 sra ファイルのダウンロード中... Completed: 245429K bytes transferred in 8 seconds (244254K 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 6205781 spots for /home/okishinya/chipatlas/results/dm3/SRX3511954/SRR6418939.sra Written 6205781 spots for /home/okishinya/chipatlas/results/dm3/SRX3511954/SRR6418939.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: 00:00:01 Multiseed full-index search: 00:03:41 6205781 reads; of these: 6205781 (100.00%) were unpaired; of these: 524115 (8.45%) aligned 0 times 4077596 (65.71%) aligned exactly 1 time 1604070 (25.85%) aligned >1 times 91.55% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 565816 / 5681666 = 0.0996 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 @ Sat, 08 Sep 2018 13:54:16: # Command line: callpeak -t SRX3511954.bam -f BAM -g dm -n SRX3511954.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511954.10 # format = BAM # ChIP-seq file = ['SRX3511954.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 @ Sat, 08 Sep 2018 13:54:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:54:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:54:16: # Command line: callpeak -t SRX3511954.bam -f BAM -g dm -n SRX3511954.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511954.05 # format = BAM # ChIP-seq file = ['SRX3511954.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 @ Sat, 08 Sep 2018 13:54:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:54:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:54:16: # Command line: callpeak -t SRX3511954.bam -f BAM -g dm -n SRX3511954.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511954.20 # format = BAM # ChIP-seq file = ['SRX3511954.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 @ Sat, 08 Sep 2018 13:54:16: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:54:16: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:54:24: 1000000 INFO @ Sat, 08 Sep 2018 13:54:24: 1000000 INFO @ Sat, 08 Sep 2018 13:54:24: 1000000 INFO @ Sat, 08 Sep 2018 13:54:31: 2000000 INFO @ Sat, 08 Sep 2018 13:54:31: 2000000 INFO @ Sat, 08 Sep 2018 13:54:32: 2000000 INFO @ Sat, 08 Sep 2018 13:54:38: 3000000 INFO @ Sat, 08 Sep 2018 13:54:39: 3000000 INFO @ Sat, 08 Sep 2018 13:54:39: 3000000 INFO @ Sat, 08 Sep 2018 13:54:46: 4000000 INFO @ Sat, 08 Sep 2018 13:54:46: 4000000 INFO @ Sat, 08 Sep 2018 13:54:48: 4000000 INFO @ Sat, 08 Sep 2018 13:54:53: 5000000 INFO @ Sat, 08 Sep 2018 13:54:54: 5000000 INFO @ Sat, 08 Sep 2018 13:54:54: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:54:54: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:54:54: #1 total tags in treatment: 5115850 INFO @ Sat, 08 Sep 2018 13:54:54: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:54:54: #1 tags after filtering in treatment: 5115850 INFO @ Sat, 08 Sep 2018 13:54:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:54: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:54: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:55: #2 number of paired peaks: 112 WARNING @ Sat, 08 Sep 2018 13:54:55: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:55: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:55: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:55: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:55: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:55: #2 predicted fragment length is 118 bps INFO @ Sat, 08 Sep 2018 13:54:55: #2 alternative fragment length(s) may be 2,87,118,140,248,287,308,396,419,445,470,494 bps INFO @ Sat, 08 Sep 2018 13:54:55: #2.2 Generate R script for model : SRX3511954.05_model.r INFO @ Sat, 08 Sep 2018 13:54:55: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:54:55: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:54:55: #1 total tags in treatment: 5115850 INFO @ Sat, 08 Sep 2018 13:54:55: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) WARNING @ Sat, 08 Sep 2018 13:54:55: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:55: #2 You may need to consider one of the other alternative d(s): 2,87,118,140,248,287,308,396,419,445,470,494 WARNING @ Sat, 08 Sep 2018 13:54:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:54:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:55: #1 tags after filtering in treatment: 5115850 INFO @ Sat, 08 Sep 2018 13:54:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:55: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:55: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:55: #2 number of paired peaks: 112 WARNING @ Sat, 08 Sep 2018 13:54:55: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:55: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:55: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:55: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:55: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:55: #2 predicted fragment length is 118 bps INFO @ Sat, 08 Sep 2018 13:54:55: #2 alternative fragment length(s) may be 2,87,118,140,248,287,308,396,419,445,470,494 bps INFO @ Sat, 08 Sep 2018 13:54:55: #2.2 Generate R script for model : SRX3511954.20_model.r WARNING @ Sat, 08 Sep 2018 13:54:55: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:55: #2 You may need to consider one of the other alternative d(s): 2,87,118,140,248,287,308,396,419,445,470,494 WARNING @ Sat, 08 Sep 2018 13:54:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:54:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:56: 5000000 INFO @ Sat, 08 Sep 2018 13:54:56: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:54:56: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:54:56: #1 total tags in treatment: 5115850 INFO @ Sat, 08 Sep 2018 13:54:56: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:54:57: #1 tags after filtering in treatment: 5115850 INFO @ Sat, 08 Sep 2018 13:54:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:57: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:57: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:57: #2 number of paired peaks: 112 WARNING @ Sat, 08 Sep 2018 13:54:57: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:57: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:57: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:57: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:57: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:57: #2 predicted fragment length is 118 bps INFO @ Sat, 08 Sep 2018 13:54:57: #2 alternative fragment length(s) may be 2,87,118,140,248,287,308,396,419,445,470,494 bps INFO @ Sat, 08 Sep 2018 13:54:57: #2.2 Generate R script for model : SRX3511954.10_model.r WARNING @ Sat, 08 Sep 2018 13:54:57: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:57: #2 You may need to consider one of the other alternative d(s): 2,87,118,140,248,287,308,396,419,445,470,494 WARNING @ Sat, 08 Sep 2018 13:54:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:54:57: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:55:07: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:09: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:55:14: #4 Write output xls file... SRX3511954.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:14: #4 Write peak in narrowPeak format file... SRX3511954.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:14: #4 Write summits bed file... SRX3511954.05_summits.bed INFO @ Sat, 08 Sep 2018 13:55:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:55:15: #4 Write output xls file... SRX3511954.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:15: #4 Write peak in narrowPeak format file... SRX3511954.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:15: #4 Write summits bed file... SRX3511954.20_summits.bed INFO @ Sat, 08 Sep 2018 13:55:15: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:55:16: #4 Write output xls file... SRX3511954.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:55:16: #4 Write peak in narrowPeak format file... SRX3511954.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:55:16: #4 Write summits bed file... SRX3511954.10_summits.bed INFO @ Sat, 08 Sep 2018 13:55:16: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (69 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。