Job ID = 2002134 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,614,586 reads read : 22,614,586 reads written : 22,614,586 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: 00:04:36 22614586 reads; of these: 22614586 (100.00%) were unpaired; of these: 550980 (2.44%) aligned 0 times 19977526 (88.34%) aligned exactly 1 time 2086080 (9.22%) aligned >1 times 97.56% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10419443 / 22063606 = 0.4722 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 10:17:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.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 @ Fri, 05 Jul 2019 10:17:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:17:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.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 @ Fri, 05 Jul 2019 10:17:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:17:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.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 @ Fri, 05 Jul 2019 10:17:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:17:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:18:04: 1000000 INFO @ Fri, 05 Jul 2019 10:18:04: 1000000 INFO @ Fri, 05 Jul 2019 10:18:04: 1000000 INFO @ Fri, 05 Jul 2019 10:18:12: 2000000 INFO @ Fri, 05 Jul 2019 10:18:13: 2000000 INFO @ Fri, 05 Jul 2019 10:18:13: 2000000 INFO @ Fri, 05 Jul 2019 10:18:19: 3000000 INFO @ Fri, 05 Jul 2019 10:18:22: 3000000 INFO @ Fri, 05 Jul 2019 10:18:22: 3000000 INFO @ Fri, 05 Jul 2019 10:18:27: 4000000 INFO @ Fri, 05 Jul 2019 10:18:30: 4000000 INFO @ Fri, 05 Jul 2019 10:18:32: 4000000 INFO @ Fri, 05 Jul 2019 10:18:34: 5000000 INFO @ Fri, 05 Jul 2019 10:18:39: 5000000 INFO @ Fri, 05 Jul 2019 10:18:40: 5000000 INFO @ Fri, 05 Jul 2019 10:18:42: 6000000 INFO @ Fri, 05 Jul 2019 10:18:48: 6000000 INFO @ Fri, 05 Jul 2019 10:18:49: 6000000 INFO @ Fri, 05 Jul 2019 10:18:50: 7000000 INFO @ Fri, 05 Jul 2019 10:18:57: 7000000 INFO @ Fri, 05 Jul 2019 10:18:57: 8000000 INFO @ Fri, 05 Jul 2019 10:18:58: 7000000 INFO @ Fri, 05 Jul 2019 10:19:05: 9000000 INFO @ Fri, 05 Jul 2019 10:19:06: 8000000 INFO @ Fri, 05 Jul 2019 10:19:07: 8000000 INFO @ Fri, 05 Jul 2019 10:19:12: 10000000 INFO @ Fri, 05 Jul 2019 10:19:14: 9000000 INFO @ Fri, 05 Jul 2019 10:19:16: 9000000 INFO @ Fri, 05 Jul 2019 10:19:20: 11000000 INFO @ Fri, 05 Jul 2019 10:19:23: 10000000 INFO @ Fri, 05 Jul 2019 10:19:24: 10000000 INFO @ Fri, 05 Jul 2019 10:19:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:19:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:19:24: #1 total tags in treatment: 11644163 INFO @ Fri, 05 Jul 2019 10:19:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:19:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:19:25: #1 tags after filtering in treatment: 11643896 INFO @ Fri, 05 Jul 2019 10:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:19:25: #1 finished! INFO @ Fri, 05 Jul 2019 10:19:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:19:28: #2 number of paired peaks: 40331 INFO @ Fri, 05 Jul 2019 10:19:28: start model_add_line... INFO @ Fri, 05 Jul 2019 10:19:28: start X-correlation... INFO @ Fri, 05 Jul 2019 10:19:28: end of X-cor INFO @ Fri, 05 Jul 2019 10:19:28: #2 finished! INFO @ Fri, 05 Jul 2019 10:19:28: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:19:28: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 10:19:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.20_model.r INFO @ Fri, 05 Jul 2019 10:19:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:19:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:19:31: 11000000 INFO @ Fri, 05 Jul 2019 10:19:32: 11000000 INFO @ Fri, 05 Jul 2019 10:19:36: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:19:36: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:19:36: #1 total tags in treatment: 11644163 INFO @ Fri, 05 Jul 2019 10:19:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:19:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:19:37: #1 tags after filtering in treatment: 11643896 INFO @ Fri, 05 Jul 2019 10:19:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:19:37: #1 finished! INFO @ Fri, 05 Jul 2019 10:19:37: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:19:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:19:38: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:19:38: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:19:38: #1 total tags in treatment: 11644163 INFO @ Fri, 05 Jul 2019 10:19:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:19:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 10:19:38: #1 tags after filtering in treatment: 11643896 INFO @ Fri, 05 Jul 2019 10:19:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:19:38: #1 finished! INFO @ Fri, 05 Jul 2019 10:19:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:19:40: #2 number of paired peaks: 40331 INFO @ Fri, 05 Jul 2019 10:19:40: start model_add_line... INFO @ Fri, 05 Jul 2019 10:19:40: start X-correlation... INFO @ Fri, 05 Jul 2019 10:19:40: end of X-cor INFO @ Fri, 05 Jul 2019 10:19:40: #2 finished! INFO @ Fri, 05 Jul 2019 10:19:40: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:19:40: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 10:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.05_model.r INFO @ Fri, 05 Jul 2019 10:19:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:19:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:19:41: #2 number of paired peaks: 40331 INFO @ Fri, 05 Jul 2019 10:19:41: start model_add_line... INFO @ Fri, 05 Jul 2019 10:19:41: start X-correlation... INFO @ Fri, 05 Jul 2019 10:19:41: end of X-cor INFO @ Fri, 05 Jul 2019 10:19:41: #2 finished! INFO @ Fri, 05 Jul 2019 10:19:41: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 10:19:41: #2 alternative fragment length(s) may be 4,135 bps INFO @ Fri, 05 Jul 2019 10:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.10_model.r INFO @ Fri, 05 Jul 2019 10:19:42: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:20:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:20:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:20:17: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:20:23: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:20:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:20:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.20_summits.bed INFO @ Fri, 05 Jul 2019 10:20:23: Done! pass1 - making usageList (81 chroms): 10 millis pass2 - checking and writing primary data (24530 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:20:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:20:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.05_summits.bed INFO @ Fri, 05 Jul 2019 10:20:36: Done! INFO @ Fri, 05 Jul 2019 10:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:20:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102035/ERX102035.10_summits.bed INFO @ Fri, 05 Jul 2019 10:20:37: Done! pass1 - making usageList (130 chroms): 12 millis pass2 - checking and writing primary data (40878 records, 4 fields): 59 millis pass1 - making usageList (111 chroms): 11 millis pass2 - checking and writing primary data (33566 records, 4 fields): 46 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。