Job ID = 2001713 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,731,640 reads read : 21,731,640 reads written : 21,731,640 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:03 21731640 reads; of these: 21731640 (100.00%) were unpaired; of these: 576108 (2.65%) aligned 0 times 16118812 (74.17%) aligned exactly 1 time 5036720 (23.18%) aligned >1 times 97.35% overall alignment rate Time searching: 00:08:04 Overall time: 00:08:04 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] 1257486 / 21155532 = 0.0594 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 09:49:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.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 09:49:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:49:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.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 09:49:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:49:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:49:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.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 09:49:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:49:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:49:27: 1000000 INFO @ Fri, 05 Jul 2019 09:49:28: 1000000 INFO @ Fri, 05 Jul 2019 09:49:29: 1000000 INFO @ Fri, 05 Jul 2019 09:49:38: 2000000 INFO @ Fri, 05 Jul 2019 09:49:38: 2000000 INFO @ Fri, 05 Jul 2019 09:49:39: 2000000 INFO @ Fri, 05 Jul 2019 09:49:47: 3000000 INFO @ Fri, 05 Jul 2019 09:49:48: 3000000 INFO @ Fri, 05 Jul 2019 09:49:49: 3000000 INFO @ Fri, 05 Jul 2019 09:49:55: 4000000 INFO @ Fri, 05 Jul 2019 09:49:57: 4000000 INFO @ Fri, 05 Jul 2019 09:49:59: 4000000 INFO @ Fri, 05 Jul 2019 09:50:05: 5000000 INFO @ Fri, 05 Jul 2019 09:50:07: 5000000 INFO @ Fri, 05 Jul 2019 09:50:08: 5000000 INFO @ Fri, 05 Jul 2019 09:50:13: 6000000 INFO @ Fri, 05 Jul 2019 09:50:17: 6000000 INFO @ Fri, 05 Jul 2019 09:50:18: 6000000 INFO @ Fri, 05 Jul 2019 09:50:22: 7000000 INFO @ Fri, 05 Jul 2019 09:50:27: 7000000 INFO @ Fri, 05 Jul 2019 09:50:27: 7000000 INFO @ Fri, 05 Jul 2019 09:50:31: 8000000 INFO @ Fri, 05 Jul 2019 09:50:37: 8000000 INFO @ Fri, 05 Jul 2019 09:50:37: 8000000 INFO @ Fri, 05 Jul 2019 09:50:40: 9000000 INFO @ Fri, 05 Jul 2019 09:50:47: 9000000 INFO @ Fri, 05 Jul 2019 09:50:47: 9000000 INFO @ Fri, 05 Jul 2019 09:50:48: 10000000 INFO @ Fri, 05 Jul 2019 09:50:56: 10000000 INFO @ Fri, 05 Jul 2019 09:50:56: 10000000 INFO @ Fri, 05 Jul 2019 09:50:57: 11000000 INFO @ Fri, 05 Jul 2019 09:51:06: 11000000 INFO @ Fri, 05 Jul 2019 09:51:06: 11000000 INFO @ Fri, 05 Jul 2019 09:51:06: 12000000 INFO @ Fri, 05 Jul 2019 09:51:15: 13000000 INFO @ Fri, 05 Jul 2019 09:51:15: 12000000 INFO @ Fri, 05 Jul 2019 09:51:15: 12000000 INFO @ Fri, 05 Jul 2019 09:51:24: 14000000 INFO @ Fri, 05 Jul 2019 09:51:25: 13000000 INFO @ Fri, 05 Jul 2019 09:51:25: 13000000 INFO @ Fri, 05 Jul 2019 09:51:33: 15000000 INFO @ Fri, 05 Jul 2019 09:51:35: 14000000 INFO @ Fri, 05 Jul 2019 09:51:36: 14000000 INFO @ Fri, 05 Jul 2019 09:51:42: 16000000 INFO @ Fri, 05 Jul 2019 09:51:45: 15000000 INFO @ Fri, 05 Jul 2019 09:51:46: 15000000 INFO @ Fri, 05 Jul 2019 09:51:51: 17000000 INFO @ Fri, 05 Jul 2019 09:51:55: 16000000 INFO @ Fri, 05 Jul 2019 09:51:56: 16000000 INFO @ Fri, 05 Jul 2019 09:52:00: 18000000 INFO @ Fri, 05 Jul 2019 09:52:05: 17000000 INFO @ Fri, 05 Jul 2019 09:52:06: 17000000 INFO @ Fri, 05 Jul 2019 09:52:09: 19000000 INFO @ Fri, 05 Jul 2019 09:52:15: 18000000 INFO @ Fri, 05 Jul 2019 09:52:16: 18000000 INFO @ Fri, 05 Jul 2019 09:52:18: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:52:18: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:52:18: #1 total tags in treatment: 19898046 INFO @ Fri, 05 Jul 2019 09:52:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:52:18: #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 09:52:18: #1 tags after filtering in treatment: 19897867 INFO @ Fri, 05 Jul 2019 09:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:52:18: #1 finished! INFO @ Fri, 05 Jul 2019 09:52:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:52:23: #2 number of paired peaks: 62736 INFO @ Fri, 05 Jul 2019 09:52:23: start model_add_line... INFO @ Fri, 05 Jul 2019 09:52:23: start X-correlation... INFO @ Fri, 05 Jul 2019 09:52:23: end of X-cor INFO @ Fri, 05 Jul 2019 09:52:23: #2 finished! INFO @ Fri, 05 Jul 2019 09:52:23: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 09:52:23: #2 alternative fragment length(s) may be 4,130,494 bps INFO @ Fri, 05 Jul 2019 09:52:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.20_model.r INFO @ Fri, 05 Jul 2019 09:52:23: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:52:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:52:25: 19000000 INFO @ Fri, 05 Jul 2019 09:52:26: 19000000 INFO @ Fri, 05 Jul 2019 09:52:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:52:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:52:34: #1 total tags in treatment: 19898046 INFO @ Fri, 05 Jul 2019 09:52:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:52:34: #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 09:52:35: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:52:35: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:52:35: #1 total tags in treatment: 19898046 INFO @ Fri, 05 Jul 2019 09:52:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:52:35: #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 09:52:35: #1 tags after filtering in treatment: 19897867 INFO @ Fri, 05 Jul 2019 09:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:52:35: #1 finished! INFO @ Fri, 05 Jul 2019 09:52:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:52:35: #1 tags after filtering in treatment: 19897867 INFO @ Fri, 05 Jul 2019 09:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:52:35: #1 finished! INFO @ Fri, 05 Jul 2019 09:52:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:52:40: #2 number of paired peaks: 62736 INFO @ Fri, 05 Jul 2019 09:52:40: start model_add_line... INFO @ Fri, 05 Jul 2019 09:52:40: start X-correlation... INFO @ Fri, 05 Jul 2019 09:52:40: end of X-cor INFO @ Fri, 05 Jul 2019 09:52:40: #2 finished! INFO @ Fri, 05 Jul 2019 09:52:40: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 09:52:40: #2 alternative fragment length(s) may be 4,130,494 bps INFO @ Fri, 05 Jul 2019 09:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.10_model.r INFO @ Fri, 05 Jul 2019 09:52:40: #2 number of paired peaks: 62736 INFO @ Fri, 05 Jul 2019 09:52:40: start model_add_line... INFO @ Fri, 05 Jul 2019 09:52:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:52:40: start X-correlation... INFO @ Fri, 05 Jul 2019 09:52:40: end of X-cor INFO @ Fri, 05 Jul 2019 09:52:40: #2 finished! INFO @ Fri, 05 Jul 2019 09:52:40: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 09:52:40: #2 alternative fragment length(s) may be 4,130,494 bps INFO @ Fri, 05 Jul 2019 09:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.05_model.r INFO @ Fri, 05 Jul 2019 09:52:40: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:53:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:53:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:53:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:53:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:53:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:53:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.20_summits.bed INFO @ Fri, 05 Jul 2019 09:53:59: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 09:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:54:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:54:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.10_summits.bed INFO @ Fri, 05 Jul 2019 09:54:16: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (908 records, 4 fields): 6 millis INFO @ Fri, 05 Jul 2019 09:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.05_peaks.xls INFO @ Fri, 05 Jul 2019 09:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102020/ERX102020.05_summits.bed INFO @ Fri, 05 Jul 2019 09:54:17: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (4128 records, 4 fields): 11 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。