Job ID = 2640683 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,929,136 reads read : 11,858,272 reads written : 5,929,136 reads 0-length : 5,929,136 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:07 5929136 reads; of these: 5929136 (100.00%) were unpaired; of these: 652886 (11.01%) aligned 0 times 3839279 (64.75%) aligned exactly 1 time 1436971 (24.24%) aligned >1 times 88.99% overall alignment rate Time searching: 00:05:08 Overall time: 00:05:08 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] 196757 / 5276250 = 0.0373 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:18:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.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 18:18:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:18:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:18:08: 1000000 INFO @ Sat, 24 Aug 2019 18:18:16: 2000000 INFO @ Sat, 24 Aug 2019 18:18:23: 3000000 INFO @ Sat, 24 Aug 2019 18:18:29: 4000000 INFO @ Sat, 24 Aug 2019 18:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.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 18:18:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:18:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:18:37: 5000000 INFO @ Sat, 24 Aug 2019 18:18:37: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:18:37: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:18:37: #1 total tags in treatment: 5079493 INFO @ Sat, 24 Aug 2019 18:18:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:18:37: #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 18:18:37: #1 tags after filtering in treatment: 5079214 INFO @ Sat, 24 Aug 2019 18:18:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:18:37: #1 finished! INFO @ Sat, 24 Aug 2019 18:18:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:18:38: 1000000 INFO @ Sat, 24 Aug 2019 18:18:39: #2 number of paired peaks: 12756 INFO @ Sat, 24 Aug 2019 18:18:39: start model_add_line... INFO @ Sat, 24 Aug 2019 18:18:39: start X-correlation... INFO @ Sat, 24 Aug 2019 18:18:39: end of X-cor INFO @ Sat, 24 Aug 2019 18:18:39: #2 finished! INFO @ Sat, 24 Aug 2019 18:18:39: #2 predicted fragment length is 148 bps INFO @ Sat, 24 Aug 2019 18:18:39: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 24 Aug 2019 18:18:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.05_model.r INFO @ Sat, 24 Aug 2019 18:18:39: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:18:44: 2000000 INFO @ Sat, 24 Aug 2019 18:18:51: 3000000 INFO @ Sat, 24 Aug 2019 18:18:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:18:57: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.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 18:19:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:19:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.05_summits.bed INFO @ Sat, 24 Aug 2019 18:19:04: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (1792 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:19:04: 5000000 INFO @ Sat, 24 Aug 2019 18:19:04: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:19:04: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:19:04: #1 total tags in treatment: 5079493 INFO @ Sat, 24 Aug 2019 18:19:04: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:19:04: #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 18:19:05: #1 tags after filtering in treatment: 5079214 INFO @ Sat, 24 Aug 2019 18:19:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:19:05: #1 finished! INFO @ Sat, 24 Aug 2019 18:19:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:19:06: #2 number of paired peaks: 12756 INFO @ Sat, 24 Aug 2019 18:19:06: start model_add_line... INFO @ Sat, 24 Aug 2019 18:19:06: start X-correlation... INFO @ Sat, 24 Aug 2019 18:19:06: end of X-cor INFO @ Sat, 24 Aug 2019 18:19:06: #2 finished! INFO @ Sat, 24 Aug 2019 18:19:06: #2 predicted fragment length is 148 bps INFO @ Sat, 24 Aug 2019 18:19:06: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 24 Aug 2019 18:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.10_model.r INFO @ Sat, 24 Aug 2019 18:19:06: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:19:08: 1000000 INFO @ Sat, 24 Aug 2019 18:19:16: 2000000 INFO @ Sat, 24 Aug 2019 18:19:22: 3000000 INFO @ Sat, 24 Aug 2019 18:19:23: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:19:29: 4000000 INFO @ Sat, 24 Aug 2019 18:19:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:19:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:19:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.10_summits.bed INFO @ Sat, 24 Aug 2019 18:19:31: Done! pass1 - making usageList (28 chroms): 2 millis pass2 - checking and writing primary data (867 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:19:36: 5000000 INFO @ Sat, 24 Aug 2019 18:19:37: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:19:37: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:19:37: #1 total tags in treatment: 5079493 INFO @ Sat, 24 Aug 2019 18:19:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:19:37: #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 18:19:37: #1 tags after filtering in treatment: 5079214 INFO @ Sat, 24 Aug 2019 18:19:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:19:37: #1 finished! INFO @ Sat, 24 Aug 2019 18:19:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:19:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:19:39: #2 number of paired peaks: 12756 INFO @ Sat, 24 Aug 2019 18:19:39: start model_add_line... INFO @ Sat, 24 Aug 2019 18:19:39: start X-correlation... INFO @ Sat, 24 Aug 2019 18:19:39: end of X-cor INFO @ Sat, 24 Aug 2019 18:19:39: #2 finished! INFO @ Sat, 24 Aug 2019 18:19:39: #2 predicted fragment length is 148 bps INFO @ Sat, 24 Aug 2019 18:19:39: #2 alternative fragment length(s) may be 148 bps INFO @ Sat, 24 Aug 2019 18:19:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.20_model.r INFO @ Sat, 24 Aug 2019 18:19:39: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:19:55: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375045/SRX5375045.20_summits.bed INFO @ Sat, 24 Aug 2019 18:20:03: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (348 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。