Job ID = 2589740 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,689,890 reads read : 3,689,890 reads written : 3,689,890 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947347.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: 00:00:20 3689890 reads; of these: 3689890 (100.00%) were unpaired; of these: 2936064 (79.57%) aligned 0 times 620944 (16.83%) aligned exactly 1 time 132882 (3.60%) aligned >1 times 20.43% overall alignment rate Time searching: 00:00:20 Overall time: 00:00:20 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] 109137 / 753826 = 0.1448 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 18:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.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 18:21:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:21:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.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 18:21:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:21:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:21:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.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 18:21:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:21:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:21:34: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:21:34: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:21:34: #1 total tags in treatment: 644689 INFO @ Mon, 12 Aug 2019 18:21:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:21:34: #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 18:21:34: #1 tags after filtering in treatment: 644689 INFO @ Mon, 12 Aug 2019 18:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:21:34: #1 finished! INFO @ Mon, 12 Aug 2019 18:21:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:21:34: #2 number of paired peaks: 571 WARNING @ Mon, 12 Aug 2019 18:21:34: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 12 Aug 2019 18:21:34: start model_add_line... INFO @ Mon, 12 Aug 2019 18:21:34: start X-correlation... INFO @ Mon, 12 Aug 2019 18:21:34: end of X-cor INFO @ Mon, 12 Aug 2019 18:21:34: #2 finished! INFO @ Mon, 12 Aug 2019 18:21:34: #2 predicted fragment length is 108 bps INFO @ Mon, 12 Aug 2019 18:21:34: #2 alternative fragment length(s) may be 108,148,558 bps INFO @ Mon, 12 Aug 2019 18:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.05_model.r INFO @ Mon, 12 Aug 2019 18:21:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:21:35: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:21:35: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:21:35: #1 total tags in treatment: 644689 INFO @ Mon, 12 Aug 2019 18:21:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:21:35: #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 18:21:35: #1 tags after filtering in treatment: 644689 INFO @ Mon, 12 Aug 2019 18:21:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:21:35: #1 finished! INFO @ Mon, 12 Aug 2019 18:21:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:21:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:21:35: #2 number of paired peaks: 571 WARNING @ Mon, 12 Aug 2019 18:21:35: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 12 Aug 2019 18:21:35: start model_add_line... INFO @ Mon, 12 Aug 2019 18:21:35: start X-correlation... INFO @ Mon, 12 Aug 2019 18:21:35: end of X-cor INFO @ Mon, 12 Aug 2019 18:21:35: #2 finished! INFO @ Mon, 12 Aug 2019 18:21:35: #2 predicted fragment length is 108 bps INFO @ Mon, 12 Aug 2019 18:21:35: #2 alternative fragment length(s) may be 108,148,558 bps INFO @ Mon, 12 Aug 2019 18:21:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.10_model.r INFO @ Mon, 12 Aug 2019 18:21:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:21:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:21:36: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:21:36: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:21:36: #1 total tags in treatment: 644689 INFO @ Mon, 12 Aug 2019 18:21:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:21:36: #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 18:21:36: #1 tags after filtering in treatment: 644689 INFO @ Mon, 12 Aug 2019 18:21:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:21:36: #1 finished! INFO @ Mon, 12 Aug 2019 18:21:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:21:36: #2 number of paired peaks: 571 WARNING @ Mon, 12 Aug 2019 18:21:36: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Mon, 12 Aug 2019 18:21:36: start model_add_line... INFO @ Mon, 12 Aug 2019 18:21:36: start X-correlation... INFO @ Mon, 12 Aug 2019 18:21:36: end of X-cor INFO @ Mon, 12 Aug 2019 18:21:36: #2 finished! INFO @ Mon, 12 Aug 2019 18:21:36: #2 predicted fragment length is 108 bps INFO @ Mon, 12 Aug 2019 18:21:36: #2 alternative fragment length(s) may be 108,148,558 bps INFO @ Mon, 12 Aug 2019 18:21:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.20_model.r INFO @ Mon, 12 Aug 2019 18:21:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:21:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:21:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 12 Aug 2019 18:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:21:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.05_summits.bed INFO @ Mon, 12 Aug 2019 18:21:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:21:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:21:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.10_summits.bed INFO @ Mon, 12 Aug 2019 18:21:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 12 Aug 2019 18:21:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:21:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:21:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331116/SRX331116.20_summits.bed INFO @ Mon, 12 Aug 2019 18:21:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (19 records, 4 fields): 2 millis CompletedMACS2peakCalling