Job ID = 2001149 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,893,863 reads read : 13,893,863 reads written : 13,893,863 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: 00:06:59 13893863 reads; of these: 13893863 (100.00%) were unpaired; of these: 341783 (2.46%) aligned 0 times 10351005 (74.50%) aligned exactly 1 time 3201075 (23.04%) aligned >1 times 97.54% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 684098 / 13552080 = 0.0505 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 03:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.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 03:57:46: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:57:46: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.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 03:57:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:57:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:57:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.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 03:57:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 03:57:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 03:57:55: 1000000 INFO @ Fri, 05 Jul 2019 03:57:56: 1000000 INFO @ Fri, 05 Jul 2019 03:57:59: 1000000 INFO @ Fri, 05 Jul 2019 03:58:03: 2000000 INFO @ Fri, 05 Jul 2019 03:58:04: 2000000 INFO @ Fri, 05 Jul 2019 03:58:09: 2000000 INFO @ Fri, 05 Jul 2019 03:58:11: 3000000 INFO @ Fri, 05 Jul 2019 03:58:11: 3000000 INFO @ Fri, 05 Jul 2019 03:58:18: 3000000 INFO @ Fri, 05 Jul 2019 03:58:19: 4000000 INFO @ Fri, 05 Jul 2019 03:58:21: 4000000 INFO @ Fri, 05 Jul 2019 03:58:26: 5000000 INFO @ Fri, 05 Jul 2019 03:58:27: 4000000 INFO @ Fri, 05 Jul 2019 03:58:30: 5000000 INFO @ Fri, 05 Jul 2019 03:58:33: 6000000 INFO @ Fri, 05 Jul 2019 03:58:36: 5000000 INFO @ Fri, 05 Jul 2019 03:58:39: 6000000 INFO @ Fri, 05 Jul 2019 03:58:41: 7000000 INFO @ Fri, 05 Jul 2019 03:58:45: 6000000 INFO @ Fri, 05 Jul 2019 03:58:47: 7000000 INFO @ Fri, 05 Jul 2019 03:58:48: 8000000 INFO @ Fri, 05 Jul 2019 03:58:55: 7000000 INFO @ Fri, 05 Jul 2019 03:58:55: 8000000 INFO @ Fri, 05 Jul 2019 03:58:55: 9000000 INFO @ Fri, 05 Jul 2019 03:59:02: 10000000 INFO @ Fri, 05 Jul 2019 03:59:03: 9000000 INFO @ Fri, 05 Jul 2019 03:59:03: 8000000 INFO @ Fri, 05 Jul 2019 03:59:10: 11000000 INFO @ Fri, 05 Jul 2019 03:59:10: 10000000 INFO @ Fri, 05 Jul 2019 03:59:12: 9000000 INFO @ Fri, 05 Jul 2019 03:59:18: 12000000 INFO @ Fri, 05 Jul 2019 03:59:18: 11000000 INFO @ Fri, 05 Jul 2019 03:59:21: 10000000 INFO @ Fri, 05 Jul 2019 03:59:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:59:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:59:25: #1 total tags in treatment: 12867982 INFO @ Fri, 05 Jul 2019 03:59:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:59:25: #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 03:59:26: #1 tags after filtering in treatment: 12867759 INFO @ Fri, 05 Jul 2019 03:59:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:59:26: #1 finished! INFO @ Fri, 05 Jul 2019 03:59:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:59:26: 12000000 INFO @ Fri, 05 Jul 2019 03:59:30: 11000000 INFO @ Fri, 05 Jul 2019 03:59:31: #2 number of paired peaks: 71537 INFO @ Fri, 05 Jul 2019 03:59:31: start model_add_line... INFO @ Fri, 05 Jul 2019 03:59:31: start X-correlation... INFO @ Fri, 05 Jul 2019 03:59:31: end of X-cor INFO @ Fri, 05 Jul 2019 03:59:31: #2 finished! INFO @ Fri, 05 Jul 2019 03:59:31: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 03:59:31: #2 alternative fragment length(s) may be 4,127,291 bps INFO @ Fri, 05 Jul 2019 03:59:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.10_model.r INFO @ Fri, 05 Jul 2019 03:59:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:59:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:59:33: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:59:33: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:59:33: #1 total tags in treatment: 12867982 INFO @ Fri, 05 Jul 2019 03:59:33: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:59:33: #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 03:59:33: #1 tags after filtering in treatment: 12867759 INFO @ Fri, 05 Jul 2019 03:59:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:59:33: #1 finished! INFO @ Fri, 05 Jul 2019 03:59:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:59:38: #2 number of paired peaks: 71537 INFO @ Fri, 05 Jul 2019 03:59:38: start model_add_line... INFO @ Fri, 05 Jul 2019 03:59:38: start X-correlation... INFO @ Fri, 05 Jul 2019 03:59:38: end of X-cor INFO @ Fri, 05 Jul 2019 03:59:38: #2 finished! INFO @ Fri, 05 Jul 2019 03:59:38: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 03:59:38: #2 alternative fragment length(s) may be 4,127,291 bps INFO @ Fri, 05 Jul 2019 03:59:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.05_model.r INFO @ Fri, 05 Jul 2019 03:59:38: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:59:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 03:59:39: 12000000 INFO @ Fri, 05 Jul 2019 03:59:47: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 03:59:47: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 03:59:47: #1 total tags in treatment: 12867982 INFO @ Fri, 05 Jul 2019 03:59:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 03:59:47: #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 03:59:48: #1 tags after filtering in treatment: 12867759 INFO @ Fri, 05 Jul 2019 03:59:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 03:59:48: #1 finished! INFO @ Fri, 05 Jul 2019 03:59:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 03:59:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 03:59:52: #2 number of paired peaks: 71537 INFO @ Fri, 05 Jul 2019 03:59:52: start model_add_line... INFO @ Fri, 05 Jul 2019 03:59:53: start X-correlation... INFO @ Fri, 05 Jul 2019 03:59:53: end of X-cor INFO @ Fri, 05 Jul 2019 03:59:53: #2 finished! INFO @ Fri, 05 Jul 2019 03:59:53: #2 predicted fragment length is 127 bps INFO @ Fri, 05 Jul 2019 03:59:53: #2 alternative fragment length(s) may be 4,127,291 bps INFO @ Fri, 05 Jul 2019 03:59:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.20_model.r INFO @ Fri, 05 Jul 2019 03:59:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 03:59:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:00:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:00:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.10_summits.bed INFO @ Fri, 05 Jul 2019 04:00:40: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:00:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:00:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:00:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.05_summits.bed INFO @ Fri, 05 Jul 2019 04:00:47: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1565 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101839/ERX101839.20_summits.bed INFO @ Fri, 05 Jul 2019 04:01:05: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。