Job ID = 11293702 sra ファイルのダウンロード中... Completed: 219458K bytes transferred in 14 seconds (122999K 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 5831465 spots for /home/okishinya/chipatlas/results/dm3/SRX4375863/SRR7506517.sra Written 5831465 spots for /home/okishinya/chipatlas/results/dm3/SRX4375863/SRR7506517.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: 00:02:11 5831465 reads; of these: 5831465 (100.00%) were unpaired; of these: 1219046 (20.90%) aligned 0 times 3292715 (56.46%) aligned exactly 1 time 1319704 (22.63%) aligned >1 times 79.10% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 1616720 / 4612419 = 0.3505 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 Nov 2018 17:51:20: # Command line: callpeak -t SRX4375863.bam -f BAM -g dm -n SRX4375863.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375863.20 # format = BAM # ChIP-seq file = ['SRX4375863.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, 04 Nov 2018 17:51:20: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:20: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:20: # Command line: callpeak -t SRX4375863.bam -f BAM -g dm -n SRX4375863.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375863.05 # format = BAM # ChIP-seq file = ['SRX4375863.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, 04 Nov 2018 17:51:20: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:20: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:20: # Command line: callpeak -t SRX4375863.bam -f BAM -g dm -n SRX4375863.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375863.10 # format = BAM # ChIP-seq file = ['SRX4375863.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, 04 Nov 2018 17:51:20: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:51:20: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:51:27: 1000000 INFO @ Sun, 04 Nov 2018 17:51:27: 1000000 INFO @ Sun, 04 Nov 2018 17:51:28: 1000000 INFO @ Sun, 04 Nov 2018 17:51:34: 2000000 INFO @ Sun, 04 Nov 2018 17:51:34: 2000000 INFO @ Sun, 04 Nov 2018 17:51:35: 2000000 INFO @ Sun, 04 Nov 2018 17:51:41: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:51:41: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:51:41: #1 total tags in treatment: 2995699 INFO @ Sun, 04 Nov 2018 17:51:41: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:51:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:51:41: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:51:41: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:51:41: #1 total tags in treatment: 2995699 INFO @ Sun, 04 Nov 2018 17:51:41: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:51:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:51:41: #1 tags after filtering in treatment: 2995699 INFO @ Sun, 04 Nov 2018 17:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:51:41: #1 finished! INFO @ Sun, 04 Nov 2018 17:51:41: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:51:41: #1 tags after filtering in treatment: 2995699 INFO @ Sun, 04 Nov 2018 17:51:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:51:41: #1 finished! INFO @ Sun, 04 Nov 2018 17:51:41: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:51:42: #2 number of paired peaks: 936 WARNING @ Sun, 04 Nov 2018 17:51:42: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sun, 04 Nov 2018 17:51:42: start model_add_line... INFO @ Sun, 04 Nov 2018 17:51:42: #2 number of paired peaks: 936 WARNING @ Sun, 04 Nov 2018 17:51:42: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sun, 04 Nov 2018 17:51:42: start model_add_line... INFO @ Sun, 04 Nov 2018 17:51:42: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:51:42: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:51:42: #1 total tags in treatment: 2995699 INFO @ Sun, 04 Nov 2018 17:51:42: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:51:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:51:42: start X-correlation... INFO @ Sun, 04 Nov 2018 17:51:42: start X-correlation... INFO @ Sun, 04 Nov 2018 17:51:42: end of X-cor INFO @ Sun, 04 Nov 2018 17:51:42: #2 finished! INFO @ Sun, 04 Nov 2018 17:51:42: #2 predicted fragment length is 57 bps INFO @ Sun, 04 Nov 2018 17:51:42: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 04 Nov 2018 17:51:42: #2.2 Generate R script for model : SRX4375863.20_model.r INFO @ Sun, 04 Nov 2018 17:51:42: end of X-cor INFO @ Sun, 04 Nov 2018 17:51:42: #2 finished! INFO @ Sun, 04 Nov 2018 17:51:42: #2 predicted fragment length is 57 bps INFO @ Sun, 04 Nov 2018 17:51:42: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 04 Nov 2018 17:51:42: #2.2 Generate R script for model : SRX4375863.05_model.r WARNING @ Sun, 04 Nov 2018 17:51:42: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:51:42: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 04 Nov 2018 17:51:42: #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 Nov 2018 17:51:42: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:51:42: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 04 Nov 2018 17:51:42: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:51:42: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 04 Nov 2018 17:51:42: #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 Nov 2018 17:51:42: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:51:42: #1 tags after filtering in treatment: 2995699 INFO @ Sun, 04 Nov 2018 17:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:51:42: #1 finished! INFO @ Sun, 04 Nov 2018 17:51:42: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:51:42: #2 number of paired peaks: 936 WARNING @ Sun, 04 Nov 2018 17:51:42: Fewer paired peaks (936) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 936 pairs to build model! INFO @ Sun, 04 Nov 2018 17:51:42: start model_add_line... INFO @ Sun, 04 Nov 2018 17:51:42: start X-correlation... INFO @ Sun, 04 Nov 2018 17:51:42: end of X-cor INFO @ Sun, 04 Nov 2018 17:51:42: #2 finished! INFO @ Sun, 04 Nov 2018 17:51:42: #2 predicted fragment length is 57 bps INFO @ Sun, 04 Nov 2018 17:51:42: #2 alternative fragment length(s) may be 57 bps INFO @ Sun, 04 Nov 2018 17:51:42: #2.2 Generate R script for model : SRX4375863.10_model.r WARNING @ Sun, 04 Nov 2018 17:51:42: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:51:42: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Sun, 04 Nov 2018 17:51:42: #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 Nov 2018 17:51:42: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:51:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:51:49: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:51:53: #4 Write output xls file... SRX4375863.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:53: #4 Write peak in narrowPeak format file... SRX4375863.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:53: #4 Write summits bed file... SRX4375863.20_summits.bed INFO @ Sun, 04 Nov 2018 17:51:53: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (679 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:51:54: #4 Write output xls file... SRX4375863.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:54: #4 Write peak in narrowPeak format file... SRX4375863.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:54: #4 Write summits bed file... SRX4375863.10_summits.bed INFO @ Sun, 04 Nov 2018 17:51:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:51:54: #4 Write output xls file... SRX4375863.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:51:54: #4 Write peak in narrowPeak format file... SRX4375863.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:51:54: #4 Write summits bed file... SRX4375863.05_summits.bed INFO @ Sun, 04 Nov 2018 17:51:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1327 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。