Job ID = 2589917 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,098,925 reads read : 4,098,925 reads written : 4,098,925 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947561.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: 00:00:36 4098925 reads; of these: 4098925 (100.00%) were unpaired; of these: 831418 (20.28%) aligned 0 times 2881328 (70.29%) aligned exactly 1 time 386179 (9.42%) aligned >1 times 79.72% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 757915 / 3267507 = 0.2320 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 18:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.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 18:46:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.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 18:46:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.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 18:46:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:36: 1000000 INFO @ Mon, 12 Aug 2019 18:46:37: 1000000 INFO @ Mon, 12 Aug 2019 18:46:39: 1000000 INFO @ Mon, 12 Aug 2019 18:46:43: 2000000 INFO @ Mon, 12 Aug 2019 18:46:46: 2000000 INFO @ Mon, 12 Aug 2019 18:46:46: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:46:46: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:46:46: #1 total tags in treatment: 2509592 INFO @ Mon, 12 Aug 2019 18:46:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:46:46: #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 18:46:47: #1 tags after filtering in treatment: 2509592 INFO @ Mon, 12 Aug 2019 18:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:46:47: #1 finished! INFO @ Mon, 12 Aug 2019 18:46:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:46:47: #2 number of paired peaks: 3311 INFO @ Mon, 12 Aug 2019 18:46:47: start model_add_line... INFO @ Mon, 12 Aug 2019 18:46:47: start X-correlation... INFO @ Mon, 12 Aug 2019 18:46:47: end of X-cor INFO @ Mon, 12 Aug 2019 18:46:47: #2 finished! INFO @ Mon, 12 Aug 2019 18:46:47: #2 predicted fragment length is 164 bps INFO @ Mon, 12 Aug 2019 18:46:47: #2 alternative fragment length(s) may be 164 bps INFO @ Mon, 12 Aug 2019 18:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.10_model.r INFO @ Mon, 12 Aug 2019 18:46:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:46:48: 2000000 INFO @ Mon, 12 Aug 2019 18:46:51: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:46:51: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:46:51: #1 total tags in treatment: 2509592 INFO @ Mon, 12 Aug 2019 18:46:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:46:51: #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 18:46:51: #1 tags after filtering in treatment: 2509592 INFO @ Mon, 12 Aug 2019 18:46:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:46:51: #1 finished! INFO @ Mon, 12 Aug 2019 18:46:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:46:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:46:51: #2 number of paired peaks: 3311 INFO @ Mon, 12 Aug 2019 18:46:51: start model_add_line... INFO @ Mon, 12 Aug 2019 18:46:51: start X-correlation... INFO @ Mon, 12 Aug 2019 18:46:51: end of X-cor INFO @ Mon, 12 Aug 2019 18:46:51: #2 finished! INFO @ Mon, 12 Aug 2019 18:46:51: #2 predicted fragment length is 164 bps INFO @ Mon, 12 Aug 2019 18:46:51: #2 alternative fragment length(s) may be 164 bps INFO @ Mon, 12 Aug 2019 18:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.05_model.r INFO @ Mon, 12 Aug 2019 18:46:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:46:52: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:46:52: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:46:52: #1 total tags in treatment: 2509592 INFO @ Mon, 12 Aug 2019 18:46:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:46:52: #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 18:46:52: #1 tags after filtering in treatment: 2509592 INFO @ Mon, 12 Aug 2019 18:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:46:52: #1 finished! INFO @ Mon, 12 Aug 2019 18:46:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:46:52: #2 number of paired peaks: 3311 INFO @ Mon, 12 Aug 2019 18:46:52: start model_add_line... INFO @ Mon, 12 Aug 2019 18:46:52: start X-correlation... INFO @ Mon, 12 Aug 2019 18:46:52: end of X-cor INFO @ Mon, 12 Aug 2019 18:46:52: #2 finished! INFO @ Mon, 12 Aug 2019 18:46:52: #2 predicted fragment length is 164 bps INFO @ Mon, 12 Aug 2019 18:46:52: #2 alternative fragment length(s) may be 164 bps INFO @ Mon, 12 Aug 2019 18:46:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.20_model.r INFO @ Mon, 12 Aug 2019 18:46:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:46:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:46:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.10_summits.bed INFO @ Mon, 12 Aug 2019 18:47:00: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4207 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:47:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.05_summits.bed INFO @ Mon, 12 Aug 2019 18:47:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6265 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:47:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331324/SRX331324.20_summits.bed INFO @ Mon, 12 Aug 2019 18:47:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2326 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。