Job ID = 2001678 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,602,008 reads read : 23,602,008 reads written : 23,602,008 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:23 23602008 reads; of these: 23602008 (100.00%) were unpaired; of these: 504708 (2.14%) aligned 0 times 20300727 (86.01%) aligned exactly 1 time 2796573 (11.85%) aligned >1 times 97.86% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 9890370 / 23097300 = 0.4282 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 08:31:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.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 08:31:40: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:31:40: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.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 08:31:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:31:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:31:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.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 08:31:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:31:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:31:49: 1000000 INFO @ Fri, 05 Jul 2019 08:31:50: 1000000 INFO @ Fri, 05 Jul 2019 08:31:51: 1000000 INFO @ Fri, 05 Jul 2019 08:31:57: 2000000 INFO @ Fri, 05 Jul 2019 08:31:58: 2000000 INFO @ Fri, 05 Jul 2019 08:32:00: 2000000 INFO @ Fri, 05 Jul 2019 08:32:05: 3000000 INFO @ Fri, 05 Jul 2019 08:32:06: 3000000 INFO @ Fri, 05 Jul 2019 08:32:08: 3000000 INFO @ Fri, 05 Jul 2019 08:32:14: 4000000 INFO @ Fri, 05 Jul 2019 08:32:14: 4000000 INFO @ Fri, 05 Jul 2019 08:32:18: 4000000 INFO @ Fri, 05 Jul 2019 08:32:21: 5000000 INFO @ Fri, 05 Jul 2019 08:32:23: 5000000 INFO @ Fri, 05 Jul 2019 08:32:27: 5000000 INFO @ Fri, 05 Jul 2019 08:32:28: 6000000 INFO @ Fri, 05 Jul 2019 08:32:31: 6000000 INFO @ Fri, 05 Jul 2019 08:32:35: 6000000 INFO @ Fri, 05 Jul 2019 08:32:36: 7000000 INFO @ Fri, 05 Jul 2019 08:32:40: 7000000 INFO @ Fri, 05 Jul 2019 08:32:43: 8000000 INFO @ Fri, 05 Jul 2019 08:32:44: 7000000 INFO @ Fri, 05 Jul 2019 08:32:48: 8000000 INFO @ Fri, 05 Jul 2019 08:32:51: 9000000 INFO @ Fri, 05 Jul 2019 08:32:53: 8000000 INFO @ Fri, 05 Jul 2019 08:32:57: 9000000 INFO @ Fri, 05 Jul 2019 08:32:59: 10000000 INFO @ Fri, 05 Jul 2019 08:33:00: 9000000 INFO @ Fri, 05 Jul 2019 08:33:05: 10000000 INFO @ Fri, 05 Jul 2019 08:33:08: 11000000 INFO @ Fri, 05 Jul 2019 08:33:08: 10000000 INFO @ Fri, 05 Jul 2019 08:33:14: 11000000 INFO @ Fri, 05 Jul 2019 08:33:16: 11000000 INFO @ Fri, 05 Jul 2019 08:33:16: 12000000 INFO @ Fri, 05 Jul 2019 08:33:23: 12000000 INFO @ Fri, 05 Jul 2019 08:33:23: 12000000 INFO @ Fri, 05 Jul 2019 08:33:25: 13000000 INFO @ Fri, 05 Jul 2019 08:33:27: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:33:27: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:33:27: #1 total tags in treatment: 13206930 INFO @ Fri, 05 Jul 2019 08:33:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:33:27: #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 08:33:27: #1 tags after filtering in treatment: 13206682 INFO @ Fri, 05 Jul 2019 08:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:33:27: #1 finished! INFO @ Fri, 05 Jul 2019 08:33:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:33:31: #2 number of paired peaks: 52779 INFO @ Fri, 05 Jul 2019 08:33:31: start model_add_line... INFO @ Fri, 05 Jul 2019 08:33:31: start X-correlation... INFO @ Fri, 05 Jul 2019 08:33:31: end of X-cor INFO @ Fri, 05 Jul 2019 08:33:31: #2 finished! INFO @ Fri, 05 Jul 2019 08:33:31: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 08:33:31: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 08:33:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.20_model.r INFO @ Fri, 05 Jul 2019 08:33:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:33:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:33:31: 13000000 INFO @ Fri, 05 Jul 2019 08:33:32: 13000000 INFO @ Fri, 05 Jul 2019 08:33:33: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:33:33: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:33:33: #1 total tags in treatment: 13206930 INFO @ Fri, 05 Jul 2019 08:33:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:33:33: #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 08:33:33: #1 tags after filtering in treatment: 13206682 INFO @ Fri, 05 Jul 2019 08:33:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:33:33: #1 finished! INFO @ Fri, 05 Jul 2019 08:33:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:33:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:33:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:33:34: #1 total tags in treatment: 13206930 INFO @ Fri, 05 Jul 2019 08:33:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:33:34: #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 08:33:34: #1 tags after filtering in treatment: 13206682 INFO @ Fri, 05 Jul 2019 08:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:33:34: #1 finished! INFO @ Fri, 05 Jul 2019 08:33:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:33:37: #2 number of paired peaks: 52779 INFO @ Fri, 05 Jul 2019 08:33:37: start model_add_line... INFO @ Fri, 05 Jul 2019 08:33:37: start X-correlation... INFO @ Fri, 05 Jul 2019 08:33:37: end of X-cor INFO @ Fri, 05 Jul 2019 08:33:37: #2 finished! INFO @ Fri, 05 Jul 2019 08:33:37: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 08:33:37: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 08:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.10_model.r INFO @ Fri, 05 Jul 2019 08:33:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:33:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:33:38: #2 number of paired peaks: 52779 INFO @ Fri, 05 Jul 2019 08:33:38: start model_add_line... INFO @ Fri, 05 Jul 2019 08:33:38: start X-correlation... INFO @ Fri, 05 Jul 2019 08:33:38: end of X-cor INFO @ Fri, 05 Jul 2019 08:33:38: #2 finished! INFO @ Fri, 05 Jul 2019 08:33:38: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 08:33:38: #2 alternative fragment length(s) may be 4,142 bps INFO @ Fri, 05 Jul 2019 08:33:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.05_model.r INFO @ Fri, 05 Jul 2019 08:33:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:33:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:34:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:34:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:34:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.20_summits.bed INFO @ Fri, 05 Jul 2019 08:34:36: Done! pass1 - making usageList (73 chroms): 7 millis pass2 - checking and writing primary data (17470 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:34:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:34:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:34:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.05_summits.bed INFO @ Fri, 05 Jul 2019 08:34:41: Done! pass1 - making usageList (128 chroms): 8 millis pass2 - checking and writing primary data (39200 records, 4 fields): 54 millis INFO @ Fri, 05 Jul 2019 08:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.10_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101993/ERX101993.10_summits.bed INFO @ Fri, 05 Jul 2019 08:34:43: Done! pass1 - making usageList (105 chroms): 8 millis pass2 - checking and writing primary data (29566 records, 4 fields): 41 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。