Job ID = 1294319 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,550,936 reads read : 12,550,936 reads written : 12,550,936 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: 00:06:04 12550936 reads; of these: 12550936 (100.00%) were unpaired; of these: 296555 (2.36%) aligned 0 times 8474057 (67.52%) aligned exactly 1 time 3780324 (30.12%) aligned >1 times 97.64% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1075868 / 12254381 = 0.0878 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 06:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.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 06:31:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:31:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.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 06:31:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:31:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.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 06:31:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:31:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:31:28: 1000000 INFO @ Mon, 03 Jun 2019 06:31:29: 1000000 INFO @ Mon, 03 Jun 2019 06:31:30: 1000000 INFO @ Mon, 03 Jun 2019 06:31:36: 2000000 INFO @ Mon, 03 Jun 2019 06:31:37: 2000000 INFO @ Mon, 03 Jun 2019 06:31:40: 2000000 INFO @ Mon, 03 Jun 2019 06:31:44: 3000000 INFO @ Mon, 03 Jun 2019 06:31:45: 3000000 INFO @ Mon, 03 Jun 2019 06:31:50: 3000000 INFO @ Mon, 03 Jun 2019 06:31:52: 4000000 INFO @ Mon, 03 Jun 2019 06:31:53: 4000000 INFO @ Mon, 03 Jun 2019 06:31:59: 5000000 INFO @ Mon, 03 Jun 2019 06:31:59: 4000000 INFO @ Mon, 03 Jun 2019 06:32:02: 5000000 INFO @ Mon, 03 Jun 2019 06:32:07: 6000000 INFO @ Mon, 03 Jun 2019 06:32:09: 5000000 INFO @ Mon, 03 Jun 2019 06:32:10: 6000000 INFO @ Mon, 03 Jun 2019 06:32:14: 7000000 INFO @ Mon, 03 Jun 2019 06:32:18: 7000000 INFO @ Mon, 03 Jun 2019 06:32:18: 6000000 INFO @ Mon, 03 Jun 2019 06:32:22: 8000000 INFO @ Mon, 03 Jun 2019 06:32:26: 8000000 INFO @ Mon, 03 Jun 2019 06:32:27: 7000000 INFO @ Mon, 03 Jun 2019 06:32:30: 9000000 INFO @ Mon, 03 Jun 2019 06:32:34: 9000000 INFO @ Mon, 03 Jun 2019 06:32:36: 8000000 INFO @ Mon, 03 Jun 2019 06:32:37: 10000000 INFO @ Mon, 03 Jun 2019 06:32:42: 10000000 INFO @ Mon, 03 Jun 2019 06:32:45: 11000000 INFO @ Mon, 03 Jun 2019 06:32:45: 9000000 INFO @ Mon, 03 Jun 2019 06:32:46: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:32:46: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:32:46: #1 total tags in treatment: 11178513 INFO @ Mon, 03 Jun 2019 06:32:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:32:46: #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 06:32:47: #1 tags after filtering in treatment: 11178513 INFO @ Mon, 03 Jun 2019 06:32:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:32:47: #1 finished! INFO @ Mon, 03 Jun 2019 06:32:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:32:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:32:48: #2 number of paired peaks: 919 WARNING @ Mon, 03 Jun 2019 06:32:48: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Mon, 03 Jun 2019 06:32:48: start model_add_line... INFO @ Mon, 03 Jun 2019 06:32:48: start X-correlation... INFO @ Mon, 03 Jun 2019 06:32:48: end of X-cor INFO @ Mon, 03 Jun 2019 06:32:48: #2 finished! INFO @ Mon, 03 Jun 2019 06:32:48: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 06:32:48: #2 alternative fragment length(s) may be 3,68 bps INFO @ Mon, 03 Jun 2019 06:32:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.05_model.r WARNING @ Mon, 03 Jun 2019 06:32:48: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:32:48: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Mon, 03 Jun 2019 06:32:48: #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 06:32:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:32:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:32:51: 11000000 INFO @ Mon, 03 Jun 2019 06:32:52: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:32:52: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:32:52: #1 total tags in treatment: 11178513 INFO @ Mon, 03 Jun 2019 06:32:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:32:52: #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 06:32:52: #1 tags after filtering in treatment: 11178513 INFO @ Mon, 03 Jun 2019 06:32:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:32:52: #1 finished! INFO @ Mon, 03 Jun 2019 06:32:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:32:53: #2 number of paired peaks: 919 WARNING @ Mon, 03 Jun 2019 06:32:53: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Mon, 03 Jun 2019 06:32:53: start model_add_line... INFO @ Mon, 03 Jun 2019 06:32:54: start X-correlation... INFO @ Mon, 03 Jun 2019 06:32:54: end of X-cor INFO @ Mon, 03 Jun 2019 06:32:54: #2 finished! INFO @ Mon, 03 Jun 2019 06:32:54: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 06:32:54: #2 alternative fragment length(s) may be 3,68 bps INFO @ Mon, 03 Jun 2019 06:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.10_model.r WARNING @ Mon, 03 Jun 2019 06:32:54: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:32:54: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Mon, 03 Jun 2019 06:32:54: #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 06:32:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:32:54: 10000000 INFO @ Mon, 03 Jun 2019 06:33:03: 11000000 INFO @ Mon, 03 Jun 2019 06:33:05: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:33:05: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:33:05: #1 total tags in treatment: 11178513 INFO @ Mon, 03 Jun 2019 06:33:05: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:33:05: #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 06:33:05: #1 tags after filtering in treatment: 11178513 INFO @ Mon, 03 Jun 2019 06:33:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:33:05: #1 finished! INFO @ Mon, 03 Jun 2019 06:33:05: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:33:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:33:06: #2 number of paired peaks: 919 WARNING @ Mon, 03 Jun 2019 06:33:06: Fewer paired peaks (919) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 919 pairs to build model! INFO @ Mon, 03 Jun 2019 06:33:06: start model_add_line... INFO @ Mon, 03 Jun 2019 06:33:06: start X-correlation... INFO @ Mon, 03 Jun 2019 06:33:06: end of X-cor INFO @ Mon, 03 Jun 2019 06:33:06: #2 finished! INFO @ Mon, 03 Jun 2019 06:33:06: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 06:33:06: #2 alternative fragment length(s) may be 3,68 bps INFO @ Mon, 03 Jun 2019 06:33:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.20_model.r WARNING @ Mon, 03 Jun 2019 06:33:06: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:33:06: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Mon, 03 Jun 2019 06:33:06: #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 06:33:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:33:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:33:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:33:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:33:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:33:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:33:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.05_summits.bed INFO @ Mon, 03 Jun 2019 06:33:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2912 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:33:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:33:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:33:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:33:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.10_summits.bed INFO @ Mon, 03 Jun 2019 06:33:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1450 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:33:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:33:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:33:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422645/SRX2422645.20_summits.bed INFO @ Mon, 03 Jun 2019 06:33:53: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (687 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。