Job ID = 2640688 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,537,023 reads read : 13,074,046 reads written : 6,537,023 reads 0-length : 6,537,023 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: 00:04:53 6537023 reads; of these: 6537023 (100.00%) were unpaired; of these: 430752 (6.59%) aligned 0 times 4929625 (75.41%) aligned exactly 1 time 1176646 (18.00%) aligned >1 times 93.41% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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] 208510 / 6106271 = 0.0341 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.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 18:21:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:21:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:21:12: 1000000 INFO @ Sat, 24 Aug 2019 18:21:19: 2000000 INFO @ Sat, 24 Aug 2019 18:21:27: 3000000 INFO @ Sat, 24 Aug 2019 18:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.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 18:21:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:21:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:21:34: 4000000 INFO @ Sat, 24 Aug 2019 18:21:41: 1000000 INFO @ Sat, 24 Aug 2019 18:21:41: 5000000 INFO @ Sat, 24 Aug 2019 18:21:48: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:21:48: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:21:48: #1 total tags in treatment: 5897761 INFO @ Sat, 24 Aug 2019 18:21:48: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:21:48: #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 18:21:48: #1 tags after filtering in treatment: 5897457 INFO @ Sat, 24 Aug 2019 18:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:21:48: #1 finished! INFO @ Sat, 24 Aug 2019 18:21:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:21:48: 2000000 INFO @ Sat, 24 Aug 2019 18:21:51: #2 number of paired peaks: 54465 INFO @ Sat, 24 Aug 2019 18:21:51: start model_add_line... INFO @ Sat, 24 Aug 2019 18:21:51: start X-correlation... INFO @ Sat, 24 Aug 2019 18:21:51: end of X-cor INFO @ Sat, 24 Aug 2019 18:21:51: #2 finished! INFO @ Sat, 24 Aug 2019 18:21:51: #2 predicted fragment length is 183 bps INFO @ Sat, 24 Aug 2019 18:21:51: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 24 Aug 2019 18:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.05_model.r INFO @ Sat, 24 Aug 2019 18:21:51: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:21:55: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:22:02: 4000000 INFO @ Sat, 24 Aug 2019 18:22:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.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 18:22:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:22:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:22:09: 5000000 INFO @ Sat, 24 Aug 2019 18:22:10: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:22:14: 1000000 INFO @ Sat, 24 Aug 2019 18:22:16: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:22:16: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:22:16: #1 total tags in treatment: 5897761 INFO @ Sat, 24 Aug 2019 18:22:16: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:22:16: #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 18:22:16: #1 tags after filtering in treatment: 5897457 INFO @ Sat, 24 Aug 2019 18:22:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:22:16: #1 finished! INFO @ Sat, 24 Aug 2019 18:22:16: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:22:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:22:19: #2 number of paired peaks: 54465 INFO @ Sat, 24 Aug 2019 18:22:19: start model_add_line... INFO @ Sat, 24 Aug 2019 18:22:19: start X-correlation... INFO @ Sat, 24 Aug 2019 18:22:19: end of X-cor INFO @ Sat, 24 Aug 2019 18:22:19: #2 finished! INFO @ Sat, 24 Aug 2019 18:22:19: #2 predicted fragment length is 183 bps INFO @ Sat, 24 Aug 2019 18:22:19: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 24 Aug 2019 18:22:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.10_model.r INFO @ Sat, 24 Aug 2019 18:22:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:22:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:22:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:22:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:22:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.05_summits.bed INFO @ Sat, 24 Aug 2019 18:22:20: Done! pass1 - making usageList (81 chroms): 7 millis pass2 - checking and writing primary data (16441 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:22:24: 2000000 INFO @ Sat, 24 Aug 2019 18:22:34: 3000000 INFO @ Sat, 24 Aug 2019 18:22:37: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:22:43: 4000000 INFO @ Sat, 24 Aug 2019 18:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.10_summits.bed INFO @ Sat, 24 Aug 2019 18:22:47: Done! pass1 - making usageList (56 chroms): 5 millis pass2 - checking and writing primary data (8642 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:22:53: 5000000 INFO @ Sat, 24 Aug 2019 18:23:01: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:23:01: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:23:01: #1 total tags in treatment: 5897761 INFO @ Sat, 24 Aug 2019 18:23:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:23:01: #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 18:23:02: #1 tags after filtering in treatment: 5897457 INFO @ Sat, 24 Aug 2019 18:23:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:23:02: #1 finished! INFO @ Sat, 24 Aug 2019 18:23:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:23:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:23:04: #2 number of paired peaks: 54465 INFO @ Sat, 24 Aug 2019 18:23:04: start model_add_line... INFO @ Sat, 24 Aug 2019 18:23:04: start X-correlation... INFO @ Sat, 24 Aug 2019 18:23:04: end of X-cor INFO @ Sat, 24 Aug 2019 18:23:04: #2 finished! INFO @ Sat, 24 Aug 2019 18:23:04: #2 predicted fragment length is 183 bps INFO @ Sat, 24 Aug 2019 18:23:04: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 24 Aug 2019 18:23:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.20_model.r INFO @ Sat, 24 Aug 2019 18:23:04: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:23:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:23:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:23:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:23:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:23:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375048/SRX5375048.20_summits.bed INFO @ Sat, 24 Aug 2019 18:23:33: Done! pass1 - making usageList (34 chroms): 2 millis pass2 - checking and writing primary data (2835 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。