Job ID = 2001517 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,910,655 reads read : 16,910,655 reads written : 16,910,655 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:52 16910655 reads; of these: 16910655 (100.00%) were unpaired; of these: 945174 (5.59%) aligned 0 times 10511209 (62.16%) aligned exactly 1 time 5454272 (32.25%) aligned >1 times 94.41% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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] 675366 / 15965481 = 0.0423 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 04:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.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 04:25:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:25:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.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 04:25:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:25:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.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 04:25:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:25:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:25:11: 1000000 INFO @ Fri, 05 Jul 2019 04:25:11: 1000000 INFO @ Fri, 05 Jul 2019 04:25:13: 1000000 INFO @ Fri, 05 Jul 2019 04:25:20: 2000000 INFO @ Fri, 05 Jul 2019 04:25:21: 2000000 INFO @ Fri, 05 Jul 2019 04:25:24: 2000000 INFO @ Fri, 05 Jul 2019 04:25:29: 3000000 INFO @ Fri, 05 Jul 2019 04:25:32: 3000000 INFO @ Fri, 05 Jul 2019 04:25:35: 3000000 INFO @ Fri, 05 Jul 2019 04:25:38: 4000000 INFO @ Fri, 05 Jul 2019 04:25:43: 4000000 INFO @ Fri, 05 Jul 2019 04:25:46: 4000000 INFO @ Fri, 05 Jul 2019 04:25:48: 5000000 INFO @ Fri, 05 Jul 2019 04:25:52: 5000000 INFO @ Fri, 05 Jul 2019 04:25:56: 5000000 INFO @ Fri, 05 Jul 2019 04:25:56: 6000000 INFO @ Fri, 05 Jul 2019 04:26:02: 6000000 INFO @ Fri, 05 Jul 2019 04:26:05: 7000000 INFO @ Fri, 05 Jul 2019 04:26:07: 6000000 INFO @ Fri, 05 Jul 2019 04:26:12: 7000000 INFO @ Fri, 05 Jul 2019 04:26:14: 8000000 INFO @ Fri, 05 Jul 2019 04:26:18: 7000000 INFO @ Fri, 05 Jul 2019 04:26:21: 8000000 INFO @ Fri, 05 Jul 2019 04:26:22: 9000000 INFO @ Fri, 05 Jul 2019 04:26:29: 8000000 INFO @ Fri, 05 Jul 2019 04:26:30: 9000000 INFO @ Fri, 05 Jul 2019 04:26:31: 10000000 INFO @ Fri, 05 Jul 2019 04:26:39: 10000000 INFO @ Fri, 05 Jul 2019 04:26:39: 9000000 INFO @ Fri, 05 Jul 2019 04:26:40: 11000000 INFO @ Fri, 05 Jul 2019 04:26:48: 11000000 INFO @ Fri, 05 Jul 2019 04:26:48: 12000000 INFO @ Fri, 05 Jul 2019 04:26:50: 10000000 INFO @ Fri, 05 Jul 2019 04:26:56: 13000000 INFO @ Fri, 05 Jul 2019 04:26:57: 12000000 INFO @ Fri, 05 Jul 2019 04:27:00: 11000000 INFO @ Fri, 05 Jul 2019 04:27:06: 14000000 INFO @ Fri, 05 Jul 2019 04:27:07: 13000000 INFO @ Fri, 05 Jul 2019 04:27:11: 12000000 INFO @ Fri, 05 Jul 2019 04:27:14: 15000000 INFO @ Fri, 05 Jul 2019 04:27:16: 14000000 INFO @ Fri, 05 Jul 2019 04:27:17: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:27:17: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:27:17: #1 total tags in treatment: 15290115 INFO @ Fri, 05 Jul 2019 04:27:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:27:17: #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 04:27:17: #1 tags after filtering in treatment: 15289940 INFO @ Fri, 05 Jul 2019 04:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:27:17: #1 finished! INFO @ Fri, 05 Jul 2019 04:27:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:27:20: #2 number of paired peaks: 14378 INFO @ Fri, 05 Jul 2019 04:27:20: start model_add_line... INFO @ Fri, 05 Jul 2019 04:27:20: start X-correlation... INFO @ Fri, 05 Jul 2019 04:27:20: end of X-cor INFO @ Fri, 05 Jul 2019 04:27:20: #2 finished! INFO @ Fri, 05 Jul 2019 04:27:20: #2 predicted fragment length is 95 bps INFO @ Fri, 05 Jul 2019 04:27:20: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 05 Jul 2019 04:27:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.10_model.r INFO @ Fri, 05 Jul 2019 04:27:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:27:21: 13000000 INFO @ Fri, 05 Jul 2019 04:27:25: 15000000 INFO @ Fri, 05 Jul 2019 04:27:28: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:27:28: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:27:28: #1 total tags in treatment: 15290115 INFO @ Fri, 05 Jul 2019 04:27:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:27:28: #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 04:27:29: #1 tags after filtering in treatment: 15289940 INFO @ Fri, 05 Jul 2019 04:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:27:29: #1 finished! INFO @ Fri, 05 Jul 2019 04:27:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:27:30: 14000000 INFO @ Fri, 05 Jul 2019 04:27:31: #2 number of paired peaks: 14378 INFO @ Fri, 05 Jul 2019 04:27:31: start model_add_line... INFO @ Fri, 05 Jul 2019 04:27:31: start X-correlation... INFO @ Fri, 05 Jul 2019 04:27:31: end of X-cor INFO @ Fri, 05 Jul 2019 04:27:31: #2 finished! INFO @ Fri, 05 Jul 2019 04:27:31: #2 predicted fragment length is 95 bps INFO @ Fri, 05 Jul 2019 04:27:31: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 05 Jul 2019 04:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.05_model.r INFO @ Fri, 05 Jul 2019 04:27:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:27:41: 15000000 INFO @ Fri, 05 Jul 2019 04:27:44: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:27:44: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:27:44: #1 total tags in treatment: 15290115 INFO @ Fri, 05 Jul 2019 04:27:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:27:44: #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 04:27:44: #1 tags after filtering in treatment: 15289940 INFO @ Fri, 05 Jul 2019 04:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:27:44: #1 finished! INFO @ Fri, 05 Jul 2019 04:27:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:27:47: #2 number of paired peaks: 14378 INFO @ Fri, 05 Jul 2019 04:27:47: start model_add_line... INFO @ Fri, 05 Jul 2019 04:27:48: start X-correlation... INFO @ Fri, 05 Jul 2019 04:27:48: end of X-cor INFO @ Fri, 05 Jul 2019 04:27:48: #2 finished! INFO @ Fri, 05 Jul 2019 04:27:48: #2 predicted fragment length is 95 bps INFO @ Fri, 05 Jul 2019 04:27:48: #2 alternative fragment length(s) may be 95 bps INFO @ Fri, 05 Jul 2019 04:27:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.20_model.r INFO @ Fri, 05 Jul 2019 04:27:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:27:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:28:12: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:28:30: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.10_summits.bed INFO @ Fri, 05 Jul 2019 04:28:40: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (2409 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:28:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:28:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:28:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:28:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.05_summits.bed INFO @ Fri, 05 Jul 2019 04:28:57: Done! pass1 - making usageList (75 chroms): 3 millis pass2 - checking and writing primary data (10310 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:29:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101864/ERX101864.20_summits.bed INFO @ Fri, 05 Jul 2019 04:29:13: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (317 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。