Job ID = 2640559 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,240,453 reads read : 16,480,906 reads written : 8,240,453 reads 0-length : 8,240,453 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: 00:07:30 8240453 reads; of these: 8240453 (100.00%) were unpaired; of these: 390931 (4.74%) aligned 0 times 5890072 (71.48%) aligned exactly 1 time 1959450 (23.78%) aligned >1 times 95.26% overall alignment rate Time searching: 00:07:33 Overall time: 00:07:33 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] 340187 / 7849522 = 0.0433 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 17:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.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 17:46:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:46:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:46:36: 1000000 INFO @ Sat, 24 Aug 2019 17:46:45: 2000000 INFO @ Sat, 24 Aug 2019 17:46:53: 3000000 INFO @ Sat, 24 Aug 2019 17:46:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.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 17:46:57: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:46:57: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:47:01: 4000000 INFO @ Sat, 24 Aug 2019 17:47:06: 1000000 INFO @ Sat, 24 Aug 2019 17:47:10: 5000000 INFO @ Sat, 24 Aug 2019 17:47:20: 2000000 INFO @ Sat, 24 Aug 2019 17:47:24: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 17:47:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.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 17:47:28: #1 read tag files... INFO @ Sat, 24 Aug 2019 17:47:28: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 17:47:29: 3000000 INFO @ Sat, 24 Aug 2019 17:47:31: 7000000 INFO @ Sat, 24 Aug 2019 17:47:36: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:47:36: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:47:36: #1 total tags in treatment: 7509335 INFO @ Sat, 24 Aug 2019 17:47:36: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:47:36: #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 17:47:36: #1 tags after filtering in treatment: 7509071 INFO @ Sat, 24 Aug 2019 17:47:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:47:36: #1 finished! INFO @ Sat, 24 Aug 2019 17:47:36: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:47:36: 1000000 INFO @ Sat, 24 Aug 2019 17:47:36: 4000000 INFO @ Sat, 24 Aug 2019 17:47:38: #2 number of paired peaks: 32326 INFO @ Sat, 24 Aug 2019 17:47:38: start model_add_line... INFO @ Sat, 24 Aug 2019 17:47:38: start X-correlation... INFO @ Sat, 24 Aug 2019 17:47:38: end of X-cor INFO @ Sat, 24 Aug 2019 17:47:38: #2 finished! INFO @ Sat, 24 Aug 2019 17:47:38: #2 predicted fragment length is 190 bps INFO @ Sat, 24 Aug 2019 17:47:38: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 24 Aug 2019 17:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.05_model.r INFO @ Sat, 24 Aug 2019 17:47:38: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:47:43: 5000000 INFO @ Sat, 24 Aug 2019 17:47:43: 2000000 INFO @ Sat, 24 Aug 2019 17:47:50: 6000000 INFO @ Sat, 24 Aug 2019 17:47:51: 3000000 INFO @ Sat, 24 Aug 2019 17:47:57: 7000000 INFO @ Sat, 24 Aug 2019 17:48:00: 4000000 INFO @ Sat, 24 Aug 2019 17:48:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:48:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:48:00: #1 total tags in treatment: 7509335 INFO @ Sat, 24 Aug 2019 17:48:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:48:00: #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 17:48:01: #1 tags after filtering in treatment: 7509071 INFO @ Sat, 24 Aug 2019 17:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:48:01: #1 finished! INFO @ Sat, 24 Aug 2019 17:48:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:48:02: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:48:03: #2 number of paired peaks: 32326 INFO @ Sat, 24 Aug 2019 17:48:03: start model_add_line... INFO @ Sat, 24 Aug 2019 17:48:03: start X-correlation... INFO @ Sat, 24 Aug 2019 17:48:03: end of X-cor INFO @ Sat, 24 Aug 2019 17:48:03: #2 finished! INFO @ Sat, 24 Aug 2019 17:48:03: #2 predicted fragment length is 190 bps INFO @ Sat, 24 Aug 2019 17:48:03: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 24 Aug 2019 17:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.10_model.r INFO @ Sat, 24 Aug 2019 17:48:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:48:08: 5000000 INFO @ Sat, 24 Aug 2019 17:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.05_peaks.xls INFO @ Sat, 24 Aug 2019 17:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.05_summits.bed INFO @ Sat, 24 Aug 2019 17:48:14: Done! pass1 - making usageList (40 chroms): 3 millis pass2 - checking and writing primary data (1304 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:48:16: 6000000 INFO @ Sat, 24 Aug 2019 17:48:24: 7000000 INFO @ Sat, 24 Aug 2019 17:48:27: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:48:29: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 17:48:29: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 17:48:29: #1 total tags in treatment: 7509335 INFO @ Sat, 24 Aug 2019 17:48:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 17:48:29: #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 17:48:29: #1 tags after filtering in treatment: 7509071 INFO @ Sat, 24 Aug 2019 17:48:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 17:48:29: #1 finished! INFO @ Sat, 24 Aug 2019 17:48:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 17:48:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 17:48:31: #2 number of paired peaks: 32326 INFO @ Sat, 24 Aug 2019 17:48:31: start model_add_line... INFO @ Sat, 24 Aug 2019 17:48:31: start X-correlation... INFO @ Sat, 24 Aug 2019 17:48:31: end of X-cor INFO @ Sat, 24 Aug 2019 17:48:31: #2 finished! INFO @ Sat, 24 Aug 2019 17:48:31: #2 predicted fragment length is 190 bps INFO @ Sat, 24 Aug 2019 17:48:31: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 24 Aug 2019 17:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.20_model.r INFO @ Sat, 24 Aug 2019 17:48:31: #3 Call peaks... INFO @ Sat, 24 Aug 2019 17:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 17:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.10_peaks.xls INFO @ Sat, 24 Aug 2019 17:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.10_summits.bed INFO @ Sat, 24 Aug 2019 17:48:39: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (309 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 17:48:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 17:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.20_peaks.xls INFO @ Sat, 24 Aug 2019 17:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 17:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375010/SRX5375010.20_summits.bed INFO @ Sat, 24 Aug 2019 17:49:07: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (115 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。