Job ID = 2589667 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,399,019 reads read : 5,399,019 reads written : 5,399,019 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947267.sra.cache’: 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: 00:00:58 5399019 reads; of these: 5399019 (100.00%) were unpaired; of these: 373961 (6.93%) aligned 0 times 4239691 (78.53%) aligned exactly 1 time 785367 (14.55%) aligned >1 times 93.07% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 468336 / 5025058 = 0.0932 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, 12 Aug 2019 18:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 18:13:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 18:13:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 12 Aug 2019 18:13:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:13:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:14:05: 1000000 INFO @ Mon, 12 Aug 2019 18:14:06: 1000000 INFO @ Mon, 12 Aug 2019 18:14:08: 1000000 INFO @ Mon, 12 Aug 2019 18:14:12: 2000000 INFO @ Mon, 12 Aug 2019 18:14:14: 2000000 INFO @ Mon, 12 Aug 2019 18:14:16: 2000000 INFO @ Mon, 12 Aug 2019 18:14:18: 3000000 INFO @ Mon, 12 Aug 2019 18:14:22: 3000000 INFO @ Mon, 12 Aug 2019 18:14:24: 3000000 INFO @ Mon, 12 Aug 2019 18:14:25: 4000000 INFO @ Mon, 12 Aug 2019 18:14:29: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:29: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:29: #1 total tags in treatment: 4556722 INFO @ Mon, 12 Aug 2019 18:14:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:14:29: #1 tags after filtering in treatment: 4556722 INFO @ Mon, 12 Aug 2019 18:14:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:29: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:29: #2 number of paired peaks: 420 WARNING @ Mon, 12 Aug 2019 18:14:29: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:29: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:29: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:29: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:29: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:29: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:14:29: #2 alternative fragment length(s) may be 4,30,559 bps INFO @ Mon, 12 Aug 2019 18:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.10_model.r WARNING @ Mon, 12 Aug 2019 18:14:29: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:14:29: #2 You may need to consider one of the other alternative d(s): 4,30,559 WARNING @ Mon, 12 Aug 2019 18:14:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:14:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:30: 4000000 INFO @ Mon, 12 Aug 2019 18:14:33: 4000000 INFO @ Mon, 12 Aug 2019 18:14:34: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:34: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:34: #1 total tags in treatment: 4556722 INFO @ Mon, 12 Aug 2019 18:14:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:14:35: #1 tags after filtering in treatment: 4556722 INFO @ Mon, 12 Aug 2019 18:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:35: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:35: #2 number of paired peaks: 420 WARNING @ Mon, 12 Aug 2019 18:14:35: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:35: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:35: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:35: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:35: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:35: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:14:35: #2 alternative fragment length(s) may be 4,30,559 bps INFO @ Mon, 12 Aug 2019 18:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.05_model.r WARNING @ Mon, 12 Aug 2019 18:14:35: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:14:35: #2 You may need to consider one of the other alternative d(s): 4,30,559 WARNING @ Mon, 12 Aug 2019 18:14:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:14:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:37: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:14:37: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:14:37: #1 total tags in treatment: 4556722 INFO @ Mon, 12 Aug 2019 18:14:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:14:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:14:37: #1 tags after filtering in treatment: 4556722 INFO @ Mon, 12 Aug 2019 18:14:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:14:37: #1 finished! INFO @ Mon, 12 Aug 2019 18:14:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:14:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:14:37: #2 number of paired peaks: 420 WARNING @ Mon, 12 Aug 2019 18:14:37: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Mon, 12 Aug 2019 18:14:37: start model_add_line... INFO @ Mon, 12 Aug 2019 18:14:37: start X-correlation... INFO @ Mon, 12 Aug 2019 18:14:37: end of X-cor INFO @ Mon, 12 Aug 2019 18:14:37: #2 finished! INFO @ Mon, 12 Aug 2019 18:14:37: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:14:37: #2 alternative fragment length(s) may be 4,30,559 bps INFO @ Mon, 12 Aug 2019 18:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.20_model.r WARNING @ Mon, 12 Aug 2019 18:14:37: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:14:37: #2 You may need to consider one of the other alternative d(s): 4,30,559 WARNING @ Mon, 12 Aug 2019 18:14:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:14:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:14:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.10_summits.bed INFO @ Mon, 12 Aug 2019 18:14:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:14:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.05_summits.bed INFO @ Mon, 12 Aug 2019 18:14:55: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (418 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:14:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:14:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:14:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331045/SRX331045.20_summits.bed INFO @ Mon, 12 Aug 2019 18:14:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。