Job ID = 1294026 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,913,372 reads read : 7,826,744 reads written : 3,913,372 reads 0-length : 3,913,372 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: No such file or directory 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: 00:07:20 3913372 reads; of these: 3913372 (100.00%) were unpaired; of these: 987243 (25.23%) aligned 0 times 1603191 (40.97%) aligned exactly 1 time 1322938 (33.81%) aligned >1 times 74.77% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 134916 / 2926129 = 0.0461 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 @ Mon, 03 Jun 2019 04:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.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 @ Mon, 03 Jun 2019 04:24:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:24:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.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 @ Mon, 03 Jun 2019 04:24:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:24:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:24:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.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 @ Mon, 03 Jun 2019 04:24:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:24:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:24:12: 1000000 INFO @ Mon, 03 Jun 2019 04:24:17: 1000000 INFO @ Mon, 03 Jun 2019 04:24:17: 1000000 INFO @ Mon, 03 Jun 2019 04:24:23: 2000000 INFO @ Mon, 03 Jun 2019 04:24:32: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:24:32: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:24:32: #1 total tags in treatment: 2791213 INFO @ Mon, 03 Jun 2019 04:24:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:24:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:24:32: #1 tags after filtering in treatment: 2791213 INFO @ Mon, 03 Jun 2019 04:24:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:24:32: #1 finished! INFO @ Mon, 03 Jun 2019 04:24:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:24:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:24:33: #2 number of paired peaks: 744 WARNING @ Mon, 03 Jun 2019 04:24:33: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Mon, 03 Jun 2019 04:24:33: start model_add_line... INFO @ Mon, 03 Jun 2019 04:24:33: start X-correlation... INFO @ Mon, 03 Jun 2019 04:24:33: end of X-cor INFO @ Mon, 03 Jun 2019 04:24:33: #2 finished! INFO @ Mon, 03 Jun 2019 04:24:33: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 04:24:33: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 04:24:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.10_model.r WARNING @ Mon, 03 Jun 2019 04:24:33: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:24:33: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Mon, 03 Jun 2019 04:24:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:24:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:24:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:24:33: 2000000 INFO @ Mon, 03 Jun 2019 04:24:33: 2000000 INFO @ Mon, 03 Jun 2019 04:24:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.10_summits.bed INFO @ Mon, 03 Jun 2019 04:24:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (665 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:24:46: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:24:46: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:24:46: #1 total tags in treatment: 2791213 INFO @ Mon, 03 Jun 2019 04:24:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:24:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:24:46: #1 tag size is determined as 151 bps INFO @ Mon, 03 Jun 2019 04:24:46: #1 tag size = 151 INFO @ Mon, 03 Jun 2019 04:24:46: #1 total tags in treatment: 2791213 INFO @ Mon, 03 Jun 2019 04:24:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:24:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:24:46: #1 tags after filtering in treatment: 2791213 INFO @ Mon, 03 Jun 2019 04:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:24:46: #1 finished! INFO @ Mon, 03 Jun 2019 04:24:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:24:46: #1 tags after filtering in treatment: 2791213 INFO @ Mon, 03 Jun 2019 04:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:24:46: #1 finished! INFO @ Mon, 03 Jun 2019 04:24:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:24:47: #2 number of paired peaks: 744 WARNING @ Mon, 03 Jun 2019 04:24:47: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Mon, 03 Jun 2019 04:24:47: start model_add_line... INFO @ Mon, 03 Jun 2019 04:24:47: start X-correlation... INFO @ Mon, 03 Jun 2019 04:24:47: #2 number of paired peaks: 744 WARNING @ Mon, 03 Jun 2019 04:24:47: Fewer paired peaks (744) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 744 pairs to build model! INFO @ Mon, 03 Jun 2019 04:24:47: start model_add_line... INFO @ Mon, 03 Jun 2019 04:24:47: end of X-cor INFO @ Mon, 03 Jun 2019 04:24:47: #2 finished! INFO @ Mon, 03 Jun 2019 04:24:47: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 04:24:47: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 04:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.20_model.r WARNING @ Mon, 03 Jun 2019 04:24:47: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:24:47: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Mon, 03 Jun 2019 04:24:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:24:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:24:47: start X-correlation... INFO @ Mon, 03 Jun 2019 04:24:47: end of X-cor INFO @ Mon, 03 Jun 2019 04:24:47: #2 finished! INFO @ Mon, 03 Jun 2019 04:24:47: #2 predicted fragment length is 137 bps INFO @ Mon, 03 Jun 2019 04:24:47: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 03 Jun 2019 04:24:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.05_model.r WARNING @ Mon, 03 Jun 2019 04:24:47: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 04:24:47: #2 You may need to consider one of the other alternative d(s): 137 WARNING @ Mon, 03 Jun 2019 04:24:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 04:24:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:24:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:24:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:24:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.20_summits.bed INFO @ Mon, 03 Jun 2019 04:25:00: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (272 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:25:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:25:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:25:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1760702/SRX1760702.05_summits.bed INFO @ Mon, 03 Jun 2019 04:25:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1585 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。