Job ID = 2590974 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,221,201 reads read : 6,442,402 reads written : 3,221,201 reads 0-length : 3,221,201 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: 00:06:17 3221201 reads; of these: 3221201 (100.00%) were unpaired; of these: 481404 (14.94%) aligned 0 times 1433151 (44.49%) aligned exactly 1 time 1306646 (40.56%) aligned >1 times 85.06% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 186906 / 2739797 = 0.0682 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 00:16:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.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 00:16:40: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:16:40: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.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 00:16:41: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:16:41: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:16:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.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 00:16:42: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:16:42: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:17:00: 1000000 INFO @ Tue, 13 Aug 2019 00:17:01: 1000000 INFO @ Tue, 13 Aug 2019 00:17:02: 1000000 INFO @ Tue, 13 Aug 2019 00:17:24: 2000000 INFO @ Tue, 13 Aug 2019 00:17:25: 2000000 INFO @ Tue, 13 Aug 2019 00:17:25: 2000000 INFO @ Tue, 13 Aug 2019 00:17:37: #1 tag size is determined as 151 bps INFO @ Tue, 13 Aug 2019 00:17:37: #1 tag size = 151 INFO @ Tue, 13 Aug 2019 00:17:37: #1 total tags in treatment: 2552891 INFO @ Tue, 13 Aug 2019 00:17:37: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:17:37: #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 00:17:37: #1 tags after filtering in treatment: 2552891 INFO @ Tue, 13 Aug 2019 00:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:17:37: #1 finished! INFO @ Tue, 13 Aug 2019 00:17:37: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:17:38: #2 number of paired peaks: 561 WARNING @ Tue, 13 Aug 2019 00:17:38: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Tue, 13 Aug 2019 00:17:38: start model_add_line... INFO @ Tue, 13 Aug 2019 00:17:38: start X-correlation... INFO @ Tue, 13 Aug 2019 00:17:38: end of X-cor INFO @ Tue, 13 Aug 2019 00:17:38: #2 finished! INFO @ Tue, 13 Aug 2019 00:17:38: #2 predicted fragment length is 135 bps INFO @ Tue, 13 Aug 2019 00:17:38: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 13 Aug 2019 00:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.05_model.r WARNING @ Tue, 13 Aug 2019 00:17:38: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:17:38: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Tue, 13 Aug 2019 00:17:38: #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 00:17:38: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:17:38: #1 tag size is determined as 151 bps INFO @ Tue, 13 Aug 2019 00:17:38: #1 tag size = 151 INFO @ Tue, 13 Aug 2019 00:17:38: #1 total tags in treatment: 2552891 INFO @ Tue, 13 Aug 2019 00:17:38: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:17:38: #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 00:17:38: #1 tags after filtering in treatment: 2552891 INFO @ Tue, 13 Aug 2019 00:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:17:38: #1 finished! INFO @ Tue, 13 Aug 2019 00:17:38: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:17:38: #2 number of paired peaks: 561 WARNING @ Tue, 13 Aug 2019 00:17:38: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Tue, 13 Aug 2019 00:17:38: start model_add_line... INFO @ Tue, 13 Aug 2019 00:17:38: start X-correlation... INFO @ Tue, 13 Aug 2019 00:17:38: end of X-cor INFO @ Tue, 13 Aug 2019 00:17:38: #2 finished! INFO @ Tue, 13 Aug 2019 00:17:38: #2 predicted fragment length is 135 bps INFO @ Tue, 13 Aug 2019 00:17:38: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 13 Aug 2019 00:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.20_model.r WARNING @ Tue, 13 Aug 2019 00:17:38: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:17:38: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Tue, 13 Aug 2019 00:17:38: #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 00:17:38: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:17:38: #1 tag size is determined as 151 bps INFO @ Tue, 13 Aug 2019 00:17:38: #1 tag size = 151 INFO @ Tue, 13 Aug 2019 00:17:38: #1 total tags in treatment: 2552891 INFO @ Tue, 13 Aug 2019 00:17:38: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:17:38: #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 00:17:38: #1 tags after filtering in treatment: 2552891 INFO @ Tue, 13 Aug 2019 00:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:17:38: #1 finished! INFO @ Tue, 13 Aug 2019 00:17:38: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:17:39: #2 number of paired peaks: 561 WARNING @ Tue, 13 Aug 2019 00:17:39: Fewer paired peaks (561) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 561 pairs to build model! INFO @ Tue, 13 Aug 2019 00:17:39: start model_add_line... INFO @ Tue, 13 Aug 2019 00:17:39: start X-correlation... INFO @ Tue, 13 Aug 2019 00:17:39: end of X-cor INFO @ Tue, 13 Aug 2019 00:17:39: #2 finished! INFO @ Tue, 13 Aug 2019 00:17:39: #2 predicted fragment length is 135 bps INFO @ Tue, 13 Aug 2019 00:17:39: #2 alternative fragment length(s) may be 135 bps INFO @ Tue, 13 Aug 2019 00:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.10_model.r WARNING @ Tue, 13 Aug 2019 00:17:39: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:17:39: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Tue, 13 Aug 2019 00:17:39: #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 00:17:39: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:17:46: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:17:46: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:17:47: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:17:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:17:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:17:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.05_summits.bed INFO @ Tue, 13 Aug 2019 00:17:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1367 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:17:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:17:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:17:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.20_summits.bed INFO @ Tue, 13 Aug 2019 00:17:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:17:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:17:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:17:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5931378/SRX5931378.10_summits.bed INFO @ Tue, 13 Aug 2019 00:17:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (536 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。