Job ID = 2001518 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,266,357 reads read : 23,266,357 reads written : 23,266,357 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:12 23266357 reads; of these: 23266357 (100.00%) were unpaired; of these: 569804 (2.45%) aligned 0 times 17150307 (73.71%) aligned exactly 1 time 5546246 (23.84%) aligned >1 times 97.55% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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] 1451119 / 22696553 = 0.0639 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 04:29:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.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 04:29:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:29:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:29:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.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 04:29:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:29:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.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 04:29:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:29:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:29:34: 1000000 INFO @ Fri, 05 Jul 2019 04:29:35: 1000000 INFO @ Fri, 05 Jul 2019 04:29:36: 1000000 INFO @ Fri, 05 Jul 2019 04:29:46: 2000000 INFO @ Fri, 05 Jul 2019 04:29:47: 2000000 INFO @ Fri, 05 Jul 2019 04:29:47: 2000000 INFO @ Fri, 05 Jul 2019 04:29:57: 3000000 INFO @ Fri, 05 Jul 2019 04:29:57: 3000000 INFO @ Fri, 05 Jul 2019 04:29:58: 3000000 INFO @ Fri, 05 Jul 2019 04:30:09: 4000000 INFO @ Fri, 05 Jul 2019 04:30:09: 4000000 INFO @ Fri, 05 Jul 2019 04:30:10: 4000000 INFO @ Fri, 05 Jul 2019 04:30:20: 5000000 INFO @ Fri, 05 Jul 2019 04:30:21: 5000000 INFO @ Fri, 05 Jul 2019 04:30:21: 5000000 INFO @ Fri, 05 Jul 2019 04:30:31: 6000000 INFO @ Fri, 05 Jul 2019 04:30:32: 6000000 INFO @ Fri, 05 Jul 2019 04:30:32: 6000000 INFO @ Fri, 05 Jul 2019 04:30:43: 7000000 INFO @ Fri, 05 Jul 2019 04:30:43: 7000000 INFO @ Fri, 05 Jul 2019 04:30:44: 7000000 INFO @ Fri, 05 Jul 2019 04:30:54: 8000000 INFO @ Fri, 05 Jul 2019 04:30:55: 8000000 INFO @ Fri, 05 Jul 2019 04:30:56: 8000000 INFO @ Fri, 05 Jul 2019 04:31:06: 9000000 INFO @ Fri, 05 Jul 2019 04:31:07: 9000000 INFO @ Fri, 05 Jul 2019 04:31:09: 9000000 INFO @ Fri, 05 Jul 2019 04:31:19: 10000000 INFO @ Fri, 05 Jul 2019 04:31:19: 10000000 INFO @ Fri, 05 Jul 2019 04:31:21: 10000000 INFO @ Fri, 05 Jul 2019 04:31:32: 11000000 INFO @ Fri, 05 Jul 2019 04:31:32: 11000000 INFO @ Fri, 05 Jul 2019 04:31:34: 11000000 INFO @ Fri, 05 Jul 2019 04:31:44: 12000000 INFO @ Fri, 05 Jul 2019 04:31:45: 12000000 INFO @ Fri, 05 Jul 2019 04:31:46: 12000000 INFO @ Fri, 05 Jul 2019 04:31:56: 13000000 INFO @ Fri, 05 Jul 2019 04:31:57: 13000000 INFO @ Fri, 05 Jul 2019 04:31:58: 13000000 INFO @ Fri, 05 Jul 2019 04:32:08: 14000000 INFO @ Fri, 05 Jul 2019 04:32:08: 14000000 INFO @ Fri, 05 Jul 2019 04:32:08: 14000000 INFO @ Fri, 05 Jul 2019 04:32:19: 15000000 INFO @ Fri, 05 Jul 2019 04:32:19: 15000000 INFO @ Fri, 05 Jul 2019 04:32:20: 15000000 INFO @ Fri, 05 Jul 2019 04:32:31: 16000000 INFO @ Fri, 05 Jul 2019 04:32:31: 16000000 INFO @ Fri, 05 Jul 2019 04:32:32: 16000000 INFO @ Fri, 05 Jul 2019 04:32:41: 17000000 INFO @ Fri, 05 Jul 2019 04:32:42: 17000000 INFO @ Fri, 05 Jul 2019 04:32:43: 17000000 INFO @ Fri, 05 Jul 2019 04:32:52: 18000000 INFO @ Fri, 05 Jul 2019 04:32:53: 18000000 INFO @ Fri, 05 Jul 2019 04:32:54: 18000000 INFO @ Fri, 05 Jul 2019 04:33:02: 19000000 INFO @ Fri, 05 Jul 2019 04:33:05: 19000000 INFO @ Fri, 05 Jul 2019 04:33:05: 19000000 INFO @ Fri, 05 Jul 2019 04:33:12: 20000000 INFO @ Fri, 05 Jul 2019 04:33:16: 20000000 INFO @ Fri, 05 Jul 2019 04:33:17: 20000000 INFO @ Fri, 05 Jul 2019 04:33:22: 21000000 INFO @ Fri, 05 Jul 2019 04:33:24: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:33:24: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:33:24: #1 total tags in treatment: 21245434 INFO @ Fri, 05 Jul 2019 04:33:24: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:33:24: #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 04:33:25: #1 tags after filtering in treatment: 21245261 INFO @ Fri, 05 Jul 2019 04:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:33:25: #1 finished! INFO @ Fri, 05 Jul 2019 04:33:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:33:28: 21000000 INFO @ Fri, 05 Jul 2019 04:33:28: 21000000 INFO @ Fri, 05 Jul 2019 04:33:29: #2 number of paired peaks: 58073 INFO @ Fri, 05 Jul 2019 04:33:29: start model_add_line... INFO @ Fri, 05 Jul 2019 04:33:30: start X-correlation... INFO @ Fri, 05 Jul 2019 04:33:30: end of X-cor INFO @ Fri, 05 Jul 2019 04:33:30: #2 finished! INFO @ Fri, 05 Jul 2019 04:33:30: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:33:30: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 04:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.20_model.r INFO @ Fri, 05 Jul 2019 04:33:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:33:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:33:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:33:30: #1 total tags in treatment: 21245434 INFO @ Fri, 05 Jul 2019 04:33:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:33:30: #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 04:33:30: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:33:30: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:33:30: #1 total tags in treatment: 21245434 INFO @ Fri, 05 Jul 2019 04:33:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:33:30: #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 04:33:31: #1 tags after filtering in treatment: 21245261 INFO @ Fri, 05 Jul 2019 04:33:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:33:31: #1 finished! INFO @ Fri, 05 Jul 2019 04:33:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:33:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:33:31: #1 tags after filtering in treatment: 21245261 INFO @ Fri, 05 Jul 2019 04:33:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:33:31: #1 finished! INFO @ Fri, 05 Jul 2019 04:33:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:33:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:33:36: #2 number of paired peaks: 58073 INFO @ Fri, 05 Jul 2019 04:33:36: start model_add_line... INFO @ Fri, 05 Jul 2019 04:33:36: #2 number of paired peaks: 58073 INFO @ Fri, 05 Jul 2019 04:33:36: start model_add_line... INFO @ Fri, 05 Jul 2019 04:33:36: start X-correlation... INFO @ Fri, 05 Jul 2019 04:33:36: end of X-cor INFO @ Fri, 05 Jul 2019 04:33:36: #2 finished! INFO @ Fri, 05 Jul 2019 04:33:36: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:33:36: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 04:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.05_model.r INFO @ Fri, 05 Jul 2019 04:33:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:33:36: start X-correlation... INFO @ Fri, 05 Jul 2019 04:33:36: end of X-cor INFO @ Fri, 05 Jul 2019 04:33:36: #2 finished! INFO @ Fri, 05 Jul 2019 04:33:36: #2 predicted fragment length is 130 bps INFO @ Fri, 05 Jul 2019 04:33:36: #2 alternative fragment length(s) may be 4,130 bps INFO @ Fri, 05 Jul 2019 04:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.10_model.r INFO @ Fri, 05 Jul 2019 04:33:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:34:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:34:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:34:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:35:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:35:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:35:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.20_summits.bed INFO @ Fri, 05 Jul 2019 04:35:14: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (148 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.10_summits.bed INFO @ Fri, 05 Jul 2019 04:35:20: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (1193 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101865/ERX101865.05_summits.bed INFO @ Fri, 05 Jul 2019 04:35:20: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (5267 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。