Job ID = 2640586 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,296,455 reads read : 8,592,910 reads written : 4,296,455 reads 0-length : 4,296,455 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:21 4296455 reads; of these: 4296455 (100.00%) were unpaired; of these: 340912 (7.93%) aligned 0 times 3339128 (77.72%) aligned exactly 1 time 616415 (14.35%) aligned >1 times 92.07% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 62773 / 3955543 = 0.0159 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:58:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:58:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:59:04: 1000000 INFO @ Sat, 24 Aug 2019 17:59:15: 2000000 INFO @ Sat, 24 Aug 2019 17:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:59:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:59:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:59:26: 3000000 INFO @ Sat, 24 Aug 2019 17:59:31: 1000000 INFO @ Sat, 24 Aug 2019 17:59:36: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:59:36: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:59:36: #1 total tags in treatment: 3892770 INFO @ Sat, 24 Aug 2019 17:59:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:59:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:59:37: #1 tags after filtering in treatment: 3892452 INFO @ Sat, 24 Aug 2019 17:59:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:59:37: #1 finished! INFO @ Sat, 24 Aug 2019 17:59:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:59:39: #2 number of paired peaks: 55778 INFO @ Sat, 24 Aug 2019 17:59:39: start model_add_line... INFO @ Sat, 24 Aug 2019 17:59:39: start X-correlation... INFO @ Sat, 24 Aug 2019 17:59:39: end of X-cor INFO @ Sat, 24 Aug 2019 17:59:39: #2 finished! INFO @ Sat, 24 Aug 2019 17:59:39: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 17:59:39: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 17:59:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.05_model.r INFO @ Sat, 24 Aug 2019 17:59:39: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:59:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:59:39: 2000000 INFO @ Sat, 24 Aug 2019 17:59:48: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 17:59:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:59:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:59:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:59:56: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:59:56: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:59:56: #1 total tags in treatment: 3892770 INFO @ Sat, 24 Aug 2019 17:59:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:59:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 17:59:56: #1 tags after filtering in treatment: 3892452 INFO @ Sat, 24 Aug 2019 17:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:59:56: #1 finished! INFO @ Sat, 24 Aug 2019 17:59:56: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:59:59: #2 number of paired peaks: 55778 INFO @ Sat, 24 Aug 2019 17:59:59: start model_add_line... INFO @ Sat, 24 Aug 2019 17:59:59: start X-correlation... INFO @ Sat, 24 Aug 2019 17:59:59: end of X-cor INFO @ Sat, 24 Aug 2019 17:59:59: #2 finished! INFO @ Sat, 24 Aug 2019 17:59:59: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 17:59:59: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 17:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.10_model.r INFO @ Sat, 24 Aug 2019 17:59:59: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:59:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:00:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:00:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.05_summits.bed INFO @ Sat, 24 Aug 2019 18:00:00: Done! pass1 - making usageList (70 chroms): 6 millis pass2 - checking and writing primary data (13998 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:00:04: 1000000 INFO @ Sat, 24 Aug 2019 18:00:12: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:00:16: 2000000 INFO @ Sat, 24 Aug 2019 18:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:00:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.10_summits.bed INFO @ Sat, 24 Aug 2019 18:00:19: Done! pass1 - making usageList (40 chroms): 4 millis pass2 - checking and writing primary data (5426 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:00:28: 3000000 INFO @ Sat, 24 Aug 2019 18:00:38: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:00:38: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:00:38: #1 total tags in treatment: 3892770 INFO @ Sat, 24 Aug 2019 18:00:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:00:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:00:38: #1 tags after filtering in treatment: 3892452 INFO @ Sat, 24 Aug 2019 18:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:00:38: #1 finished! INFO @ Sat, 24 Aug 2019 18:00:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:00:41: #2 number of paired peaks: 55778 INFO @ Sat, 24 Aug 2019 18:00:41: start model_add_line... INFO @ Sat, 24 Aug 2019 18:00:41: start X-correlation... INFO @ Sat, 24 Aug 2019 18:00:41: end of X-cor INFO @ Sat, 24 Aug 2019 18:00:41: #2 finished! INFO @ Sat, 24 Aug 2019 18:00:41: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 18:00:41: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 18:00:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.20_model.r INFO @ Sat, 24 Aug 2019 18:00:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:00:54: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:01:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:01:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:01:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375024/SRX5375024.20_summits.bed INFO @ Sat, 24 Aug 2019 18:01:00: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (931 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。