Job ID = 2640685 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,480,680 reads read : 14,961,360 reads written : 7,480,680 reads 0-length : 7,480,680 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:19 7480680 reads; of these: 7480680 (100.00%) were unpaired; of these: 526375 (7.04%) aligned 0 times 5845164 (78.14%) aligned exactly 1 time 1109141 (14.83%) aligned >1 times 92.96% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 312099 / 6954305 = 0.0449 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:19:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.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 18:19:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:19:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:19:31: 1000000 INFO @ Sat, 24 Aug 2019 18:19:37: 2000000 INFO @ Sat, 24 Aug 2019 18:19:44: 3000000 INFO @ Sat, 24 Aug 2019 18:19:50: 4000000 INFO @ Sat, 24 Aug 2019 18:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.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 18:19:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:19:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:19:57: 5000000 INFO @ Sat, 24 Aug 2019 18:20:00: 1000000 INFO @ Sat, 24 Aug 2019 18:20:04: 6000000 INFO @ Sat, 24 Aug 2019 18:20:07: 2000000 INFO @ Sat, 24 Aug 2019 18:20:08: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:20:08: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:20:08: #1 total tags in treatment: 6642206 INFO @ Sat, 24 Aug 2019 18:20:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:20:08: #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 18:20:09: #1 tags after filtering in treatment: 6641903 INFO @ Sat, 24 Aug 2019 18:20:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:20:09: #1 finished! INFO @ Sat, 24 Aug 2019 18:20:09: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:20:11: #2 number of paired peaks: 58651 INFO @ Sat, 24 Aug 2019 18:20:11: start model_add_line... INFO @ Sat, 24 Aug 2019 18:20:11: start X-correlation... INFO @ Sat, 24 Aug 2019 18:20:12: end of X-cor INFO @ Sat, 24 Aug 2019 18:20:12: #2 finished! INFO @ Sat, 24 Aug 2019 18:20:12: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 18:20:12: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 18:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.05_model.r INFO @ Sat, 24 Aug 2019 18:20:12: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:20:15: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:20:22: 4000000 INFO @ Sat, 24 Aug 2019 18:20:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.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 18:20:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:20:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:20:35: 5000000 INFO @ Sat, 24 Aug 2019 18:20:36: 1000000 INFO @ Sat, 24 Aug 2019 18:20:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:20:44: 6000000 INFO @ Sat, 24 Aug 2019 18:20:46: 2000000 INFO @ Sat, 24 Aug 2019 18:20:50: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:20:50: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:20:50: #1 total tags in treatment: 6642206 INFO @ Sat, 24 Aug 2019 18:20:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:20:50: #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 18:20:50: #1 tags after filtering in treatment: 6641903 INFO @ Sat, 24 Aug 2019 18:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:20:50: #1 finished! INFO @ Sat, 24 Aug 2019 18:20:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:20:54: 3000000 INFO @ Sat, 24 Aug 2019 18:20:54: #2 number of paired peaks: 58651 INFO @ Sat, 24 Aug 2019 18:20:54: start model_add_line... INFO @ Sat, 24 Aug 2019 18:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:20:54: start X-correlation... INFO @ Sat, 24 Aug 2019 18:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.05_summits.bed INFO @ Sat, 24 Aug 2019 18:20:55: Done! INFO @ Sat, 24 Aug 2019 18:20:55: end of X-cor INFO @ Sat, 24 Aug 2019 18:20:55: #2 finished! INFO @ Sat, 24 Aug 2019 18:20:55: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 18:20:55: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 18:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.10_model.r INFO @ Sat, 24 Aug 2019 18:20:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:20:55: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (94 chroms): 9 millis pass2 - checking and writing primary data (23373 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:21:03: 4000000 INFO @ Sat, 24 Aug 2019 18:21:11: 5000000 INFO @ Sat, 24 Aug 2019 18:21:19: 6000000 INFO @ Sat, 24 Aug 2019 18:21:20: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:21:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:21:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:21:25: #1 total tags in treatment: 6642206 INFO @ Sat, 24 Aug 2019 18:21:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:21:25: #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 18:21:25: #1 tags after filtering in treatment: 6641903 INFO @ Sat, 24 Aug 2019 18:21:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:21:25: #1 finished! INFO @ Sat, 24 Aug 2019 18:21:25: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:21:28: #2 number of paired peaks: 58651 INFO @ Sat, 24 Aug 2019 18:21:28: start model_add_line... INFO @ Sat, 24 Aug 2019 18:21:28: start X-correlation... INFO @ Sat, 24 Aug 2019 18:21:29: end of X-cor INFO @ Sat, 24 Aug 2019 18:21:29: #2 finished! INFO @ Sat, 24 Aug 2019 18:21:29: #2 predicted fragment length is 180 bps INFO @ Sat, 24 Aug 2019 18:21:29: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 24 Aug 2019 18:21:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.20_model.r INFO @ Sat, 24 Aug 2019 18:21:29: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:21:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.10_summits.bed INFO @ Sat, 24 Aug 2019 18:21:32: Done! pass1 - making usageList (69 chroms): 6 millis pass2 - checking and writing primary data (13534 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:21:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375046/SRX5375046.20_summits.bed INFO @ Sat, 24 Aug 2019 18:22:01: Done! pass1 - making usageList (42 chroms): 4 millis pass2 - checking and writing primary data (5641 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。