Job ID = 2640584 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,179,823 reads read : 10,359,646 reads written : 5,179,823 reads 0-length : 5,179,823 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: 00:04:55 5179823 reads; of these: 5179823 (100.00%) were unpaired; of these: 412375 (7.96%) aligned 0 times 3527635 (68.10%) aligned exactly 1 time 1239813 (23.94%) aligned >1 times 92.04% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 172227 / 4767448 = 0.0361 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.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 18:00:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:22: 1000000 INFO @ Sat, 24 Aug 2019 18:00:30: 2000000 INFO @ Sat, 24 Aug 2019 18:00:38: 3000000 INFO @ Sat, 24 Aug 2019 18:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.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 18:00:44: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:00:44: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:00:47: 4000000 INFO @ Sat, 24 Aug 2019 18:00:52: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:00:52: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:00:52: #1 total tags in treatment: 4595221 INFO @ Sat, 24 Aug 2019 18:00:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:00:52: #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 18:00:52: #1 tags after filtering in treatment: 4594931 INFO @ Sat, 24 Aug 2019 18:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:00:52: #1 finished! INFO @ Sat, 24 Aug 2019 18:00:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:00:54: 1000000 INFO @ Sat, 24 Aug 2019 18:00:55: #2 number of paired peaks: 34666 INFO @ Sat, 24 Aug 2019 18:00:55: start model_add_line... INFO @ Sat, 24 Aug 2019 18:00:55: start X-correlation... INFO @ Sat, 24 Aug 2019 18:00:56: end of X-cor INFO @ Sat, 24 Aug 2019 18:00:56: #2 finished! INFO @ Sat, 24 Aug 2019 18:00:56: #2 predicted fragment length is 221 bps INFO @ Sat, 24 Aug 2019 18:00:56: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 24 Aug 2019 18:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.05_model.r INFO @ Sat, 24 Aug 2019 18:00:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:01:03: 2000000 INFO @ Sat, 24 Aug 2019 18:01:10: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:01:13: 3000000 INFO @ Sat, 24 Aug 2019 18:01:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.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 18:01:14: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:01:14: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:01:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:01:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:01:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.05_summits.bed INFO @ Sat, 24 Aug 2019 18:01:18: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (485 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:01:22: 1000000 INFO @ Sat, 24 Aug 2019 18:01:23: 4000000 INFO @ Sat, 24 Aug 2019 18:01:29: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:01:29: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:01:29: #1 total tags in treatment: 4595221 INFO @ Sat, 24 Aug 2019 18:01:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:01:29: #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 18:01:29: #1 tags after filtering in treatment: 4594931 INFO @ Sat, 24 Aug 2019 18:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:01:29: #1 finished! INFO @ Sat, 24 Aug 2019 18:01:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:01:31: 2000000 INFO @ Sat, 24 Aug 2019 18:01:32: #2 number of paired peaks: 34666 INFO @ Sat, 24 Aug 2019 18:01:32: start model_add_line... INFO @ Sat, 24 Aug 2019 18:01:32: start X-correlation... INFO @ Sat, 24 Aug 2019 18:01:32: end of X-cor INFO @ Sat, 24 Aug 2019 18:01:32: #2 finished! INFO @ Sat, 24 Aug 2019 18:01:32: #2 predicted fragment length is 221 bps INFO @ Sat, 24 Aug 2019 18:01:32: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 24 Aug 2019 18:01:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.10_model.r INFO @ Sat, 24 Aug 2019 18:01:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:01:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:01:39: 3000000 INFO @ Sat, 24 Aug 2019 18:01:47: 4000000 INFO @ Sat, 24 Aug 2019 18:01:47: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:01:52: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:01:52: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:01:52: #1 total tags in treatment: 4595221 INFO @ Sat, 24 Aug 2019 18:01:52: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:01:52: #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 18:01:52: #1 tags after filtering in treatment: 4594931 INFO @ Sat, 24 Aug 2019 18:01:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:01:52: #1 finished! INFO @ Sat, 24 Aug 2019 18:01:52: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:01:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:01:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:01:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:01:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.10_summits.bed INFO @ Sat, 24 Aug 2019 18:01:55: Done! INFO @ Sat, 24 Aug 2019 18:01:55: #2 number of paired peaks: 34666 INFO @ Sat, 24 Aug 2019 18:01:55: start model_add_line... INFO @ Sat, 24 Aug 2019 18:01:55: start X-correlation... INFO @ Sat, 24 Aug 2019 18:01:55: end of X-cor INFO @ Sat, 24 Aug 2019 18:01:55: #2 finished! INFO @ Sat, 24 Aug 2019 18:01:55: #2 predicted fragment length is 221 bps INFO @ Sat, 24 Aug 2019 18:01:55: #2 alternative fragment length(s) may be 221 bps INFO @ Sat, 24 Aug 2019 18:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.20_model.r INFO @ Sat, 24 Aug 2019 18:01:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:01:55: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (197 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:02:10: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375023/SRX5375023.20_summits.bed INFO @ Sat, 24 Aug 2019 18:02:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (68 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。