Job ID = 2001526 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,741,664 reads read : 19,741,664 reads written : 19,741,664 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: 00:04:08 19741664 reads; of these: 19741664 (100.00%) were unpaired; of these: 498831 (2.53%) aligned 0 times 17444280 (88.36%) aligned exactly 1 time 1798553 (9.11%) aligned >1 times 97.47% overall alignment rate Time searching: 00:04:09 Overall time: 00:04:09 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] 9398066 / 19242833 = 0.4884 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 04:29:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.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 04:29:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:29:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.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 04:29:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:29:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.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 04:29:37: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:29:37: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:29:44: 1000000 INFO @ Fri, 05 Jul 2019 04:29:45: 1000000 INFO @ Fri, 05 Jul 2019 04:29:46: 1000000 INFO @ Fri, 05 Jul 2019 04:29:50: 2000000 INFO @ Fri, 05 Jul 2019 04:29:54: 2000000 INFO @ Fri, 05 Jul 2019 04:29:55: 2000000 INFO @ Fri, 05 Jul 2019 04:29:57: 3000000 INFO @ Fri, 05 Jul 2019 04:30:02: 3000000 INFO @ Fri, 05 Jul 2019 04:30:03: 3000000 INFO @ Fri, 05 Jul 2019 04:30:04: 4000000 INFO @ Fri, 05 Jul 2019 04:30:11: 5000000 INFO @ Fri, 05 Jul 2019 04:30:11: 4000000 INFO @ Fri, 05 Jul 2019 04:30:12: 4000000 INFO @ Fri, 05 Jul 2019 04:30:17: 6000000 INFO @ Fri, 05 Jul 2019 04:30:19: 5000000 INFO @ Fri, 05 Jul 2019 04:30:20: 5000000 INFO @ Fri, 05 Jul 2019 04:30:24: 7000000 INFO @ Fri, 05 Jul 2019 04:30:28: 6000000 INFO @ Fri, 05 Jul 2019 04:30:29: 6000000 INFO @ Fri, 05 Jul 2019 04:30:30: 8000000 INFO @ Fri, 05 Jul 2019 04:30:37: 9000000 INFO @ Fri, 05 Jul 2019 04:30:37: 7000000 INFO @ Fri, 05 Jul 2019 04:30:38: 7000000 INFO @ Fri, 05 Jul 2019 04:30:42: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:30:42: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:30:42: #1 total tags in treatment: 9844767 INFO @ Fri, 05 Jul 2019 04:30:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:30:42: #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 04:30:43: #1 tags after filtering in treatment: 9844497 INFO @ Fri, 05 Jul 2019 04:30:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:30:43: #1 finished! INFO @ Fri, 05 Jul 2019 04:30:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:30:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:30:45: 8000000 INFO @ Fri, 05 Jul 2019 04:30:45: #2 number of paired peaks: 37458 INFO @ Fri, 05 Jul 2019 04:30:45: start model_add_line... INFO @ Fri, 05 Jul 2019 04:30:45: start X-correlation... INFO @ Fri, 05 Jul 2019 04:30:45: end of X-cor INFO @ Fri, 05 Jul 2019 04:30:45: #2 finished! INFO @ Fri, 05 Jul 2019 04:30:45: #2 predicted fragment length is 146 bps INFO @ Fri, 05 Jul 2019 04:30:45: #2 alternative fragment length(s) may be 3,146 bps INFO @ Fri, 05 Jul 2019 04:30:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.10_model.r INFO @ Fri, 05 Jul 2019 04:30:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:30:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:30:46: 8000000 INFO @ Fri, 05 Jul 2019 04:30:53: 9000000 INFO @ Fri, 05 Jul 2019 04:30:55: 9000000 INFO @ Fri, 05 Jul 2019 04:30:59: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:30:59: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:30:59: #1 total tags in treatment: 9844767 INFO @ Fri, 05 Jul 2019 04:30:59: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:30:59: #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 04:30:59: #1 tags after filtering in treatment: 9844497 INFO @ Fri, 05 Jul 2019 04:30:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:30:59: #1 finished! INFO @ Fri, 05 Jul 2019 04:30:59: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:30:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:31:02: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:31:02: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:31:02: #1 total tags in treatment: 9844767 INFO @ Fri, 05 Jul 2019 04:31:02: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:31:02: #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 04:31:02: #2 number of paired peaks: 37458 INFO @ Fri, 05 Jul 2019 04:31:02: start model_add_line... INFO @ Fri, 05 Jul 2019 04:31:02: start X-correlation... INFO @ Fri, 05 Jul 2019 04:31:02: end of X-cor INFO @ Fri, 05 Jul 2019 04:31:02: #2 finished! INFO @ Fri, 05 Jul 2019 04:31:02: #2 predicted fragment length is 146 bps INFO @ Fri, 05 Jul 2019 04:31:02: #2 alternative fragment length(s) may be 3,146 bps INFO @ Fri, 05 Jul 2019 04:31:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.20_model.r INFO @ Fri, 05 Jul 2019 04:31:02: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:31:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:31:02: #1 tags after filtering in treatment: 9844497 INFO @ Fri, 05 Jul 2019 04:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:31:02: #1 finished! INFO @ Fri, 05 Jul 2019 04:31:02: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:31:05: #2 number of paired peaks: 37458 INFO @ Fri, 05 Jul 2019 04:31:05: start model_add_line... INFO @ Fri, 05 Jul 2019 04:31:05: start X-correlation... INFO @ Fri, 05 Jul 2019 04:31:05: end of X-cor INFO @ Fri, 05 Jul 2019 04:31:05: #2 finished! INFO @ Fri, 05 Jul 2019 04:31:05: #2 predicted fragment length is 146 bps INFO @ Fri, 05 Jul 2019 04:31:05: #2 alternative fragment length(s) may be 3,146 bps INFO @ Fri, 05 Jul 2019 04:31:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.05_model.r INFO @ Fri, 05 Jul 2019 04:31:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:31:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:31:16: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:31:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:31:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.10_summits.bed INFO @ Fri, 05 Jul 2019 04:31:34: Done! pass1 - making usageList (107 chroms): 10 millis pass2 - checking and writing primary data (30192 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:31:36: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.20_summits.bed INFO @ Fri, 05 Jul 2019 04:31:50: Done! pass1 - making usageList (80 chroms): 10 millis pass2 - checking and writing primary data (21284 records, 4 fields): 298 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:31:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:31:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:31:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101871/ERX101871.05_summits.bed INFO @ Fri, 05 Jul 2019 04:31:55: Done! pass1 - making usageList (129 chroms): 8 millis pass2 - checking and writing primary data (37359 records, 4 fields): 56 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。