Job ID = 2591001 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,193,840 reads read : 36,193,840 reads written : 36,193,840 rm: cannot remove ‘[DSE]RR*’: 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: 00:09:33 36193840 reads; of these: 36193840 (100.00%) were unpaired; of these: 32750154 (90.49%) aligned 0 times 2370369 (6.55%) aligned exactly 1 time 1073317 (2.97%) aligned >1 times 9.51% overall alignment rate Time searching: 00:09:33 Overall time: 00:09:33 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] 2612793 / 3443686 = 0.7587 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 @ Tue, 13 Aug 2019 01:10:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.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 @ Tue, 13 Aug 2019 01:10:45: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:10:45: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:10:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.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 @ Tue, 13 Aug 2019 01:10:46: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:10:46: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:10:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.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 @ Tue, 13 Aug 2019 01:10:47: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:10:47: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:10:55: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:10:55: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:10:55: #1 total tags in treatment: 830893 INFO @ Tue, 13 Aug 2019 01:10:55: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:10:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:10:55: #1 tags after filtering in treatment: 830893 INFO @ Tue, 13 Aug 2019 01:10:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:10:55: #1 finished! INFO @ Tue, 13 Aug 2019 01:10:55: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:10:55: #2 number of paired peaks: 2979 INFO @ Tue, 13 Aug 2019 01:10:55: start model_add_line... INFO @ Tue, 13 Aug 2019 01:10:55: start X-correlation... INFO @ Tue, 13 Aug 2019 01:10:55: end of X-cor INFO @ Tue, 13 Aug 2019 01:10:55: #2 finished! INFO @ Tue, 13 Aug 2019 01:10:55: #2 predicted fragment length is 96 bps INFO @ Tue, 13 Aug 2019 01:10:55: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 13 Aug 2019 01:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.05_model.r WARNING @ Tue, 13 Aug 2019 01:10:55: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:10:55: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Tue, 13 Aug 2019 01:10:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:10:55: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:10:57: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:10:57: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:10:57: #1 total tags in treatment: 830893 INFO @ Tue, 13 Aug 2019 01:10:57: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:10:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:10:57: #1 tags after filtering in treatment: 830893 INFO @ Tue, 13 Aug 2019 01:10:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:10:57: #1 finished! INFO @ Tue, 13 Aug 2019 01:10:57: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:10:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:10:57: #2 number of paired peaks: 2979 INFO @ Tue, 13 Aug 2019 01:10:57: start model_add_line... INFO @ Tue, 13 Aug 2019 01:10:57: start X-correlation... INFO @ Tue, 13 Aug 2019 01:10:57: end of X-cor INFO @ Tue, 13 Aug 2019 01:10:57: #2 finished! INFO @ Tue, 13 Aug 2019 01:10:57: #2 predicted fragment length is 96 bps INFO @ Tue, 13 Aug 2019 01:10:57: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 13 Aug 2019 01:10:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.10_model.r WARNING @ Tue, 13 Aug 2019 01:10:57: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:10:57: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Tue, 13 Aug 2019 01:10:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:10:57: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:10:58: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 01:10:58: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 01:10:58: #1 total tags in treatment: 830893 INFO @ Tue, 13 Aug 2019 01:10:58: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:10:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:10:58: #1 tags after filtering in treatment: 830893 INFO @ Tue, 13 Aug 2019 01:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 01:10:58: #1 finished! INFO @ Tue, 13 Aug 2019 01:10:58: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:10:58: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:10:58: #2 number of paired peaks: 2979 INFO @ Tue, 13 Aug 2019 01:10:58: start model_add_line... INFO @ Tue, 13 Aug 2019 01:10:58: start X-correlation... INFO @ Tue, 13 Aug 2019 01:10:58: end of X-cor INFO @ Tue, 13 Aug 2019 01:10:58: #2 finished! INFO @ Tue, 13 Aug 2019 01:10:58: #2 predicted fragment length is 96 bps INFO @ Tue, 13 Aug 2019 01:10:58: #2 alternative fragment length(s) may be 96 bps INFO @ Tue, 13 Aug 2019 01:10:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.20_model.r WARNING @ Tue, 13 Aug 2019 01:10:58: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:10:58: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Tue, 13 Aug 2019 01:10:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:10:58: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:10:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.05_summits.bed INFO @ Tue, 13 Aug 2019 01:10:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2555 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:11:00: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:11:01: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:11:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:11:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:11:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.10_summits.bed INFO @ Tue, 13 Aug 2019 01:11:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (969 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 13 Aug 2019 01:11:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:11:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:11:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645107/SRX645107.20_summits.bed INFO @ Tue, 13 Aug 2019 01:11:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。