Job ID = 10845187 sra ファイルのダウンロード中... Completed: 82255K bytes transferred in 8 seconds (78371K 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 1893558 spots for /home/okishinya/chipatlas/results/dm3/SRX2642403/SRR5345743.sra Written 1893558 spots for /home/okishinya/chipatlas/results/dm3/SRX2642403/SRR5345743.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: 00:01:02 1893558 reads; of these: 1893558 (100.00%) were unpaired; of these: 151438 (8.00%) aligned 0 times 1354202 (71.52%) aligned exactly 1 time 387918 (20.49%) aligned >1 times 92.00% overall alignment rate Time searching: 00:01:02 Overall time: 00:01:02 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] 16615 / 1742120 = 0.0095 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 @ Wed, 04 Jul 2018 09:28:20: # Command line: callpeak -t SRX2642403.bam -f BAM -g dm -n SRX2642403.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2642403.05 # format = BAM # ChIP-seq file = ['SRX2642403.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 @ Wed, 04 Jul 2018 09:28:20: # Command line: callpeak -t SRX2642403.bam -f BAM -g dm -n SRX2642403.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2642403.10 # format = BAM # ChIP-seq file = ['SRX2642403.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 @ Wed, 04 Jul 2018 09:28:20: # Command line: callpeak -t SRX2642403.bam -f BAM -g dm -n SRX2642403.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2642403.20 # format = BAM # ChIP-seq file = ['SRX2642403.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 @ Wed, 04 Jul 2018 09:28:20: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:20: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:20: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:20: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:20: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:20: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:29: 1000000 INFO @ Wed, 04 Jul 2018 09:28:29: 1000000 INFO @ Wed, 04 Jul 2018 09:28:29: 1000000 INFO @ Wed, 04 Jul 2018 09:28:35: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:28:35: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:28:35: #1 total tags in treatment: 1725505 INFO @ Wed, 04 Jul 2018 09:28:35: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:35: #1 tags after filtering in treatment: 1725505 INFO @ Wed, 04 Jul 2018 09:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:35: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:35: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:36: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:28:36: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:28:36: #1 total tags in treatment: 1725505 INFO @ Wed, 04 Jul 2018 09:28:36: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:36: #1 tags after filtering in treatment: 1725505 INFO @ Wed, 04 Jul 2018 09:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:36: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:36: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:28:36: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:36: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:36: #1 total tags in treatment: 1725505 INFO @ Wed, 04 Jul 2018 09:28:36: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:28:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:28:36: #1 tags after filtering in treatment: 1725505 INFO @ Wed, 04 Jul 2018 09:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:28:36: #1 finished! INFO @ Wed, 04 Jul 2018 09:28:36: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:28:36: #2 number of paired peaks: 189 WARNING @ Wed, 04 Jul 2018 09:28:36: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Wed, 04 Jul 2018 09:28:36: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:36: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:36: #2 number of paired peaks: 189 WARNING @ Wed, 04 Jul 2018 09:28:36: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Wed, 04 Jul 2018 09:28:36: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:36: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:36: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:36: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:36: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:36: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:36: #2 predicted fragment length is 99 bps INFO @ Wed, 04 Jul 2018 09:28:36: #2 predicted fragment length is 99 bps INFO @ Wed, 04 Jul 2018 09:28:36: #2 alternative fragment length(s) may be 99,298 bps INFO @ Wed, 04 Jul 2018 09:28:36: #2 alternative fragment length(s) may be 99,298 bps INFO @ Wed, 04 Jul 2018 09:28:36: #2.2 Generate R script for model : SRX2642403.10_model.r INFO @ Wed, 04 Jul 2018 09:28:36: #2.2 Generate R script for model : SRX2642403.05_model.r WARNING @ Wed, 04 Jul 2018 09:28:36: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:36: #2 You may need to consider one of the other alternative d(s): 99,298 WARNING @ Wed, 04 Jul 2018 09:28:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:36: #3 Call peaks... WARNING @ Wed, 04 Jul 2018 09:28:36: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:36: #2 You may need to consider one of the other alternative d(s): 99,298 WARNING @ Wed, 04 Jul 2018 09:28:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:36: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:28:36: #2 number of paired peaks: 189 WARNING @ Wed, 04 Jul 2018 09:28:36: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Wed, 04 Jul 2018 09:28:36: start model_add_line... INFO @ Wed, 04 Jul 2018 09:28:36: start X-correlation... INFO @ Wed, 04 Jul 2018 09:28:36: end of X-cor INFO @ Wed, 04 Jul 2018 09:28:36: #2 finished! INFO @ Wed, 04 Jul 2018 09:28:36: #2 predicted fragment length is 99 bps INFO @ Wed, 04 Jul 2018 09:28:36: #2 alternative fragment length(s) may be 99,298 bps INFO @ Wed, 04 Jul 2018 09:28:36: #2.2 Generate R script for model : SRX2642403.20_model.r WARNING @ Wed, 04 Jul 2018 09:28:36: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:28:36: #2 You may need to consider one of the other alternative d(s): 99,298 WARNING @ Wed, 04 Jul 2018 09:28:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:28:36: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:28:40: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:28:40: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:28:40: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write output xls file... SRX2642403.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write output xls file... SRX2642403.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write peak in narrowPeak format file... SRX2642403.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write peak in narrowPeak format file... SRX2642403.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write summits bed file... SRX2642403.20_summits.bed INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write summits bed file... SRX2642403.10_summits.bed INFO @ Wed, 04 Jul 2018 09:28:42: Done! INFO @ Wed, 04 Jul 2018 09:28:42: Done! INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write output xls file... SRX2642403.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write peak in narrowPeak format file... SRX2642403.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:28:42: #4 Write summits bed file... SRX2642403.05_summits.bed INFO @ Wed, 04 Jul 2018 09:28:42: Done! pass1 - making usageList (2 chroms)pass1 - making usageList (4 chroms)pass1 - making usageList (2 chroms): 30 millis : 30 millis : 29 millis pass2 - checking and writing primary data (61 records, 4 fields): 63 millis pass2 - checking and writing primary data (114 records, 4 fields): 63 millis pass2 - checking and writing primary data (27 records, 4 fields): 71 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。