Job ID = 2589150 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,704,498 reads read : 2,704,498 reads written : 2,704,498 spots read : 3,974,972 reads read : 3,974,972 reads written : 3,974,972 spots read : 3,392,023 reads read : 3,392,023 reads written : 3,392,023 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107352.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107353.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107354.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: 00:00:51 10071493 reads; of these: 10071493 (100.00%) were unpaired; of these: 9723740 (96.55%) aligned 0 times 301691 (3.00%) aligned exactly 1 time 46062 (0.46%) aligned >1 times 3.45% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 5932 / 347753 = 0.0171 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 17:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.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 17:03:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.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 17:03:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.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 17:03:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:28: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:03:28: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:03:28: #1 total tags in treatment: 341821 INFO @ Mon, 12 Aug 2019 17:03:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:28: #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 17:03:28: #1 tags after filtering in treatment: 341821 INFO @ Mon, 12 Aug 2019 17:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:28: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:28: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 17:03:28: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 17:03:28: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:28: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:28: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:28: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:28: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 17:03:28: #2 alternative fragment length(s) may be 53,121,179,192,268,554,592 bps INFO @ Mon, 12 Aug 2019 17:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.05_model.r WARNING @ Mon, 12 Aug 2019 17:03:28: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:03:28: #2 You may need to consider one of the other alternative d(s): 53,121,179,192,268,554,592 WARNING @ Mon, 12 Aug 2019 17:03:28: #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 17:03:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:28: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:03:28: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:03:28: #1 total tags in treatment: 341821 INFO @ Mon, 12 Aug 2019 17:03:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:28: #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 17:03:28: #1 tags after filtering in treatment: 341821 INFO @ Mon, 12 Aug 2019 17:03:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:28: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:28: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 17:03:28: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 17:03:28: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:28: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:28: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:28: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:28: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 17:03:28: #2 alternative fragment length(s) may be 53,121,179,192,268,554,592 bps INFO @ Mon, 12 Aug 2019 17:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.10_model.r WARNING @ Mon, 12 Aug 2019 17:03:28: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:03:28: #2 You may need to consider one of the other alternative d(s): 53,121,179,192,268,554,592 WARNING @ Mon, 12 Aug 2019 17:03:28: #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 17:03:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:29: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:03:29: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:03:29: #1 total tags in treatment: 341821 INFO @ Mon, 12 Aug 2019 17:03:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:29: #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 17:03:29: #1 tags after filtering in treatment: 341821 INFO @ Mon, 12 Aug 2019 17:03:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:29: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:29: #2 number of paired peaks: 263 WARNING @ Mon, 12 Aug 2019 17:03:29: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Mon, 12 Aug 2019 17:03:29: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:29: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:29: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:29: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:29: #2 predicted fragment length is 53 bps INFO @ Mon, 12 Aug 2019 17:03:29: #2 alternative fragment length(s) may be 53,121,179,192,268,554,592 bps INFO @ Mon, 12 Aug 2019 17:03:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.20_model.r WARNING @ Mon, 12 Aug 2019 17:03:29: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:03:29: #2 You may need to consider one of the other alternative d(s): 53,121,179,192,268,554,592 WARNING @ Mon, 12 Aug 2019 17:03:29: #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 17:03:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:03:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 17:03:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.05_summits.bed INFO @ Mon, 12 Aug 2019 17:03:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.10_summits.bed INFO @ Mon, 12 Aug 2019 17:03:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (10 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:03:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 17:03:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043879/SRX043879.20_summits.bed INFO @ Mon, 12 Aug 2019 17:03:30: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling