Job ID = 1293022 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,640,309 reads read : 5,640,309 reads written : 5,640,309 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:01:16 5640309 reads; of these: 5640309 (100.00%) were unpaired; of these: 917743 (16.27%) aligned 0 times 4068572 (72.13%) aligned exactly 1 time 653994 (11.60%) aligned >1 times 83.73% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 585745 / 4722566 = 0.1240 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 @ Sun, 02 Jun 2019 21:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.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 @ Sun, 02 Jun 2019 21:26:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:26:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.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 @ Sun, 02 Jun 2019 21:26:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:26:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.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 @ Sun, 02 Jun 2019 21:26:22: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:26:22: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:26:30: 1000000 INFO @ Sun, 02 Jun 2019 21:26:31: 1000000 INFO @ Sun, 02 Jun 2019 21:26:34: 1000000 INFO @ Sun, 02 Jun 2019 21:26:38: 2000000 INFO @ Sun, 02 Jun 2019 21:26:41: 2000000 INFO @ Sun, 02 Jun 2019 21:26:45: 2000000 INFO @ Sun, 02 Jun 2019 21:26:46: 3000000 INFO @ Sun, 02 Jun 2019 21:26:49: 3000000 INFO @ Sun, 02 Jun 2019 21:26:54: 4000000 INFO @ Sun, 02 Jun 2019 21:26:55: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:26:55: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:26:55: #1 total tags in treatment: 4136821 INFO @ Sun, 02 Jun 2019 21:26:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:26:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:26:55: #1 tags after filtering in treatment: 4136821 INFO @ Sun, 02 Jun 2019 21:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:26:55: #1 finished! INFO @ Sun, 02 Jun 2019 21:26:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:26:56: 3000000 INFO @ Sun, 02 Jun 2019 21:26:56: #2 number of paired peaks: 1668 INFO @ Sun, 02 Jun 2019 21:26:56: start model_add_line... INFO @ Sun, 02 Jun 2019 21:26:56: start X-correlation... INFO @ Sun, 02 Jun 2019 21:26:56: end of X-cor INFO @ Sun, 02 Jun 2019 21:26:56: #2 finished! INFO @ Sun, 02 Jun 2019 21:26:56: #2 predicted fragment length is 194 bps INFO @ Sun, 02 Jun 2019 21:26:56: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 02 Jun 2019 21:26:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.20_model.r INFO @ Sun, 02 Jun 2019 21:26:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:26:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:26:58: 4000000 INFO @ Sun, 02 Jun 2019 21:26:59: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:26:59: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:26:59: #1 total tags in treatment: 4136821 INFO @ Sun, 02 Jun 2019 21:26:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:26:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:26:59: #1 tags after filtering in treatment: 4136821 INFO @ Sun, 02 Jun 2019 21:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:26:59: #1 finished! INFO @ Sun, 02 Jun 2019 21:26:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:26:59: #2 number of paired peaks: 1668 INFO @ Sun, 02 Jun 2019 21:26:59: start model_add_line... INFO @ Sun, 02 Jun 2019 21:26:59: start X-correlation... INFO @ Sun, 02 Jun 2019 21:26:59: end of X-cor INFO @ Sun, 02 Jun 2019 21:26:59: #2 finished! INFO @ Sun, 02 Jun 2019 21:26:59: #2 predicted fragment length is 194 bps INFO @ Sun, 02 Jun 2019 21:26:59: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 02 Jun 2019 21:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.10_model.r INFO @ Sun, 02 Jun 2019 21:26:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:27:06: 4000000 INFO @ Sun, 02 Jun 2019 21:27:07: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:27:07: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:27:07: #1 total tags in treatment: 4136821 INFO @ Sun, 02 Jun 2019 21:27:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:27:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 21:27:07: #1 tags after filtering in treatment: 4136821 INFO @ Sun, 02 Jun 2019 21:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:27:07: #1 finished! INFO @ Sun, 02 Jun 2019 21:27:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:27:08: #2 number of paired peaks: 1668 INFO @ Sun, 02 Jun 2019 21:27:08: start model_add_line... INFO @ Sun, 02 Jun 2019 21:27:08: start X-correlation... INFO @ Sun, 02 Jun 2019 21:27:08: end of X-cor INFO @ Sun, 02 Jun 2019 21:27:08: #2 finished! INFO @ Sun, 02 Jun 2019 21:27:08: #2 predicted fragment length is 194 bps INFO @ Sun, 02 Jun 2019 21:27:08: #2 alternative fragment length(s) may be 194 bps INFO @ Sun, 02 Jun 2019 21:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.05_model.r INFO @ Sun, 02 Jun 2019 21:27:08: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:27:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:27:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.20_summits.bed INFO @ Sun, 02 Jun 2019 21:27:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (497 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.10_summits.bed INFO @ Sun, 02 Jun 2019 21:27:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (938 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:27:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020791/SRX5020791.05_summits.bed INFO @ Sun, 02 Jun 2019 21:27:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1540 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。