Job ID = 4178267 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,061,539 reads read : 15,061,539 reads written : 15,061,539 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: 00:02:35 15061539 reads; of these: 15061539 (100.00%) were unpaired; of these: 7033821 (46.70%) aligned 0 times 6412807 (42.58%) aligned exactly 1 time 1614911 (10.72%) aligned >1 times 53.30% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 1370800 / 8027718 = 0.1708 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.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 @ Thu, 05 Dec 2019 12:29:01: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:01: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:10: 1000000 INFO @ Thu, 05 Dec 2019 12:29:19: 2000000 INFO @ Thu, 05 Dec 2019 12:29:28: 3000000 INFO @ Thu, 05 Dec 2019 12:29:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.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 @ Thu, 05 Dec 2019 12:29:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:37: 4000000 INFO @ Thu, 05 Dec 2019 12:29:38: 1000000 INFO @ Thu, 05 Dec 2019 12:29:47: 5000000 INFO @ Thu, 05 Dec 2019 12:29:47: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:29:56: 3000000 INFO @ Thu, 05 Dec 2019 12:29:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.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 @ Thu, 05 Dec 2019 12:29:58: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:29:58: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:29:59: 6000000 INFO @ Thu, 05 Dec 2019 12:30:06: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:30:06: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:30:06: #1 total tags in treatment: 6656918 INFO @ Thu, 05 Dec 2019 12:30:06: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:07: #1 tags after filtering in treatment: 6656918 INFO @ Thu, 05 Dec 2019 12:30:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:07: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:07: #2 number of paired peaks: 1980 INFO @ Thu, 05 Dec 2019 12:30:07: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:07: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:07: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:07: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:07: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:30:07: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.05_model.r INFO @ Thu, 05 Dec 2019 12:30:07: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:08: 4000000 INFO @ Thu, 05 Dec 2019 12:30:10: 1000000 INFO @ Thu, 05 Dec 2019 12:30:19: 5000000 INFO @ Thu, 05 Dec 2019 12:30:19: 2000000 INFO @ Thu, 05 Dec 2019 12:30:30: 3000000 INFO @ Thu, 05 Dec 2019 12:30:30: 6000000 INFO @ Thu, 05 Dec 2019 12:30:33: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:30:38: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:30:38: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:30:38: #1 total tags in treatment: 6656918 INFO @ Thu, 05 Dec 2019 12:30:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:30:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:30:38: #1 tags after filtering in treatment: 6656918 INFO @ Thu, 05 Dec 2019 12:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:30:38: #1 finished! INFO @ Thu, 05 Dec 2019 12:30:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:30:39: #2 number of paired peaks: 1980 INFO @ Thu, 05 Dec 2019 12:30:39: start model_add_line... INFO @ Thu, 05 Dec 2019 12:30:39: start X-correlation... INFO @ Thu, 05 Dec 2019 12:30:39: end of X-cor INFO @ Thu, 05 Dec 2019 12:30:39: #2 finished! INFO @ Thu, 05 Dec 2019 12:30:39: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:30:39: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.10_model.r INFO @ Thu, 05 Dec 2019 12:30:39: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:30:41: 4000000 INFO @ Thu, 05 Dec 2019 12:30:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:30:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.05_summits.bed INFO @ Thu, 05 Dec 2019 12:30:46: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (5507 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:30:51: 5000000 INFO @ Thu, 05 Dec 2019 12:31:01: 6000000 INFO @ Thu, 05 Dec 2019 12:31:01: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:07: #1 tag size is determined as 49 bps INFO @ Thu, 05 Dec 2019 12:31:07: #1 tag size = 49 INFO @ Thu, 05 Dec 2019 12:31:07: #1 total tags in treatment: 6656918 INFO @ Thu, 05 Dec 2019 12:31:07: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:31:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:31:07: #1 tags after filtering in treatment: 6656918 INFO @ Thu, 05 Dec 2019 12:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:31:07: #1 finished! INFO @ Thu, 05 Dec 2019 12:31:07: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:31:08: #2 number of paired peaks: 1980 INFO @ Thu, 05 Dec 2019 12:31:08: start model_add_line... INFO @ Thu, 05 Dec 2019 12:31:08: start X-correlation... INFO @ Thu, 05 Dec 2019 12:31:08: end of X-cor INFO @ Thu, 05 Dec 2019 12:31:08: #2 finished! INFO @ Thu, 05 Dec 2019 12:31:08: #2 predicted fragment length is 153 bps INFO @ Thu, 05 Dec 2019 12:31:08: #2 alternative fragment length(s) may be 153 bps INFO @ Thu, 05 Dec 2019 12:31:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.20_model.r INFO @ Thu, 05 Dec 2019 12:31:08: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:31:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:31:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.10_summits.bed INFO @ Thu, 05 Dec 2019 12:31:12: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2975 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:31:31: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107866/SRX4107866.20_summits.bed INFO @ Thu, 05 Dec 2019 12:31:41: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1125 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。