Job ID = 2640690 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,730,768 reads read : 11,461,536 reads written : 5,730,768 reads 0-length : 5,730,768 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: 00:03:40 5730768 reads; of these: 5730768 (100.00%) were unpaired; of these: 642015 (11.20%) aligned 0 times 4253618 (74.22%) aligned exactly 1 time 835135 (14.57%) aligned >1 times 88.80% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 187371 / 5088753 = 0.0368 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.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 18:20:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:20:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:20:55: 1000000 INFO @ Sat, 24 Aug 2019 18:21:01: 2000000 INFO @ Sat, 24 Aug 2019 18:21:08: 3000000 INFO @ Sat, 24 Aug 2019 18:21:14: 4000000 INFO @ Sat, 24 Aug 2019 18:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.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 18:21:17: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:21:17: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:21:20: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:21:20: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:21:20: #1 total tags in treatment: 4901382 INFO @ Sat, 24 Aug 2019 18:21:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:21:20: #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 18:21:20: #1 tags after filtering in treatment: 4901066 INFO @ Sat, 24 Aug 2019 18:21:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:21:20: #1 finished! INFO @ Sat, 24 Aug 2019 18:21:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:21:23: #2 number of paired peaks: 56102 INFO @ Sat, 24 Aug 2019 18:21:23: start model_add_line... INFO @ Sat, 24 Aug 2019 18:21:23: start X-correlation... INFO @ Sat, 24 Aug 2019 18:21:23: end of X-cor INFO @ Sat, 24 Aug 2019 18:21:23: #2 finished! INFO @ Sat, 24 Aug 2019 18:21:23: #2 predicted fragment length is 190 bps INFO @ Sat, 24 Aug 2019 18:21:23: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 24 Aug 2019 18:21:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.05_model.r INFO @ Sat, 24 Aug 2019 18:21:23: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:21:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:21:24: 1000000 INFO @ Sat, 24 Aug 2019 18:21:31: 2000000 INFO @ Sat, 24 Aug 2019 18:21:38: 3000000 INFO @ Sat, 24 Aug 2019 18:21:39: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:21:45: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:21:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:21:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.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 18:21:47: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:21:47: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:21:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.05_summits.bed INFO @ Sat, 24 Aug 2019 18:21:48: Done! pass1 - making usageList (83 chroms): 6 millis pass2 - checking and writing primary data (17183 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:21:51: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:21:51: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:21:51: #1 total tags in treatment: 4901382 INFO @ Sat, 24 Aug 2019 18:21:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:21:51: #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 18:21:51: #1 tags after filtering in treatment: 4901066 INFO @ Sat, 24 Aug 2019 18:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:21:51: #1 finished! INFO @ Sat, 24 Aug 2019 18:21:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:21:54: #2 number of paired peaks: 56102 INFO @ Sat, 24 Aug 2019 18:21:54: start model_add_line... INFO @ Sat, 24 Aug 2019 18:21:54: start X-correlation... INFO @ Sat, 24 Aug 2019 18:21:54: end of X-cor INFO @ Sat, 24 Aug 2019 18:21:54: #2 finished! INFO @ Sat, 24 Aug 2019 18:21:54: #2 predicted fragment length is 190 bps INFO @ Sat, 24 Aug 2019 18:21:54: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 24 Aug 2019 18:21:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.10_model.r INFO @ Sat, 24 Aug 2019 18:21:54: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:21:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:21:54: 1000000 INFO @ Sat, 24 Aug 2019 18:22:01: 2000000 INFO @ Sat, 24 Aug 2019 18:22:07: 3000000 INFO @ Sat, 24 Aug 2019 18:22:10: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:22:13: 4000000 INFO @ Sat, 24 Aug 2019 18:22:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:22:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:22:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.10_summits.bed INFO @ Sat, 24 Aug 2019 18:22:18: Done! pass1 - making usageList (58 chroms): 3 millis pass2 - checking and writing primary data (9783 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:22:19: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:22:19: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:22:19: #1 total tags in treatment: 4901382 INFO @ Sat, 24 Aug 2019 18:22:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:22:19: #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 18:22:19: #1 tags after filtering in treatment: 4901066 INFO @ Sat, 24 Aug 2019 18:22:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:22:19: #1 finished! INFO @ Sat, 24 Aug 2019 18:22:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:22:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:22:22: #2 number of paired peaks: 56102 INFO @ Sat, 24 Aug 2019 18:22:22: start model_add_line... INFO @ Sat, 24 Aug 2019 18:22:22: start X-correlation... INFO @ Sat, 24 Aug 2019 18:22:22: end of X-cor INFO @ Sat, 24 Aug 2019 18:22:22: #2 finished! INFO @ Sat, 24 Aug 2019 18:22:22: #2 predicted fragment length is 190 bps INFO @ Sat, 24 Aug 2019 18:22:22: #2 alternative fragment length(s) may be 190 bps INFO @ Sat, 24 Aug 2019 18:22:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.20_model.r INFO @ Sat, 24 Aug 2019 18:22:22: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:22:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:22:38: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:22:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:22:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:22:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375049/SRX5375049.20_summits.bed INFO @ Sat, 24 Aug 2019 18:22:46: Done! pass1 - making usageList (36 chroms): 3 millis pass2 - checking and writing primary data (3897 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。