Job ID = 2589942 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,394,702 reads read : 42,789,404 reads written : 21,394,702 reads 0-length : 21,394,702 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: 00:03:39 21394702 reads; of these: 21394702 (100.00%) were unpaired; of these: 17044831 (79.67%) aligned 0 times 3706256 (17.32%) aligned exactly 1 time 643615 (3.01%) aligned >1 times 20.33% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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] 3887473 / 4349871 = 0.8937 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 19:03:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.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 19:03:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.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 19:03:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.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 19:03:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:03:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:03:31: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:03:31: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:03:31: #1 total tags in treatment: 462398 INFO @ Mon, 12 Aug 2019 19:03:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:31: #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 19:03:31: #1 tags after filtering in treatment: 462398 INFO @ Mon, 12 Aug 2019 19:03:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:31: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:31: #2 number of paired peaks: 891 WARNING @ Mon, 12 Aug 2019 19:03:31: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:31: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:31: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:31: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:31: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:31: #2 predicted fragment length is 72 bps INFO @ Mon, 12 Aug 2019 19:03:31: #2 alternative fragment length(s) may be 72,209,586 bps INFO @ Mon, 12 Aug 2019 19:03:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.05_model.r WARNING @ Mon, 12 Aug 2019 19:03:31: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:03:31: #2 You may need to consider one of the other alternative d(s): 72,209,586 WARNING @ Mon, 12 Aug 2019 19:03:31: #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 19:03:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:03:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:03:33: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:03:33: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:03:33: #1 total tags in treatment: 462398 INFO @ Mon, 12 Aug 2019 19:03:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:33: #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 19:03:33: #1 tags after filtering in treatment: 462398 INFO @ Mon, 12 Aug 2019 19:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:33: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:33: #1 tag size is determined as 74 bps INFO @ Mon, 12 Aug 2019 19:03:33: #1 tag size = 74 INFO @ Mon, 12 Aug 2019 19:03:33: #1 total tags in treatment: 462398 INFO @ Mon, 12 Aug 2019 19:03:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:03:33: #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 19:03:33: #1 tags after filtering in treatment: 462398 INFO @ Mon, 12 Aug 2019 19:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:03:33: #1 finished! INFO @ Mon, 12 Aug 2019 19:03:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:03:33: #2 number of paired peaks: 891 WARNING @ Mon, 12 Aug 2019 19:03:33: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:33: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:33: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:33: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:33: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:33: #2 predicted fragment length is 72 bps INFO @ Mon, 12 Aug 2019 19:03:33: #2 alternative fragment length(s) may be 72,209,586 bps INFO @ Mon, 12 Aug 2019 19:03:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.20_model.r WARNING @ Mon, 12 Aug 2019 19:03:33: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:03:33: #2 You may need to consider one of the other alternative d(s): 72,209,586 WARNING @ Mon, 12 Aug 2019 19:03:33: #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 19:03:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:03:33: #2 number of paired peaks: 891 WARNING @ Mon, 12 Aug 2019 19:03:33: Fewer paired peaks (891) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 891 pairs to build model! INFO @ Mon, 12 Aug 2019 19:03:33: start model_add_line... INFO @ Mon, 12 Aug 2019 19:03:33: start X-correlation... INFO @ Mon, 12 Aug 2019 19:03:33: end of X-cor INFO @ Mon, 12 Aug 2019 19:03:33: #2 finished! INFO @ Mon, 12 Aug 2019 19:03:33: #2 predicted fragment length is 72 bps INFO @ Mon, 12 Aug 2019 19:03:33: #2 alternative fragment length(s) may be 72,209,586 bps INFO @ Mon, 12 Aug 2019 19:03:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.10_model.r WARNING @ Mon, 12 Aug 2019 19:03:33: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:03:33: #2 You may need to consider one of the other alternative d(s): 72,209,586 WARNING @ Mon, 12 Aug 2019 19:03:33: #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 19:03:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:03:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:03:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:03:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.05_summits.bed INFO @ Mon, 12 Aug 2019 19:03:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 19:03:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:03:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.20_summits.bed INFO @ Mon, 12 Aug 2019 19:03:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3862417/SRX3862417.10_summits.bed INFO @ Mon, 12 Aug 2019 19:03:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。