Job ID = 2001158 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,971,098 reads read : 19,971,098 reads written : 19,971,098 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: 00:08:29 19971098 reads; of these: 19971098 (100.00%) were unpaired; of these: 588149 (2.95%) aligned 0 times 14656498 (73.39%) aligned exactly 1 time 4726451 (23.67%) aligned >1 times 97.05% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 1173440 / 19382949 = 0.0605 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 04:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.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 04:16:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:16:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.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 04:16:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:16:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:16:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.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 04:16:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 04:16:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 04:16:33: 1000000 INFO @ Fri, 05 Jul 2019 04:16:35: 1000000 INFO @ Fri, 05 Jul 2019 04:16:35: 1000000 INFO @ Fri, 05 Jul 2019 04:16:43: 2000000 INFO @ Fri, 05 Jul 2019 04:16:44: 2000000 INFO @ Fri, 05 Jul 2019 04:16:45: 2000000 INFO @ Fri, 05 Jul 2019 04:16:53: 3000000 INFO @ Fri, 05 Jul 2019 04:16:53: 3000000 INFO @ Fri, 05 Jul 2019 04:16:56: 3000000 INFO @ Fri, 05 Jul 2019 04:17:02: 4000000 INFO @ Fri, 05 Jul 2019 04:17:03: 4000000 INFO @ Fri, 05 Jul 2019 04:17:07: 4000000 INFO @ Fri, 05 Jul 2019 04:17:10: 5000000 INFO @ Fri, 05 Jul 2019 04:17:12: 5000000 INFO @ Fri, 05 Jul 2019 04:17:17: 5000000 INFO @ Fri, 05 Jul 2019 04:17:19: 6000000 INFO @ Fri, 05 Jul 2019 04:17:22: 6000000 INFO @ Fri, 05 Jul 2019 04:17:28: 6000000 INFO @ Fri, 05 Jul 2019 04:17:28: 7000000 INFO @ Fri, 05 Jul 2019 04:17:31: 7000000 INFO @ Fri, 05 Jul 2019 04:17:37: 8000000 INFO @ Fri, 05 Jul 2019 04:17:37: 7000000 INFO @ Fri, 05 Jul 2019 04:17:41: 8000000 INFO @ Fri, 05 Jul 2019 04:17:45: 9000000 INFO @ Fri, 05 Jul 2019 04:17:47: 8000000 INFO @ Fri, 05 Jul 2019 04:17:50: 9000000 INFO @ Fri, 05 Jul 2019 04:17:54: 10000000 INFO @ Fri, 05 Jul 2019 04:17:57: 9000000 INFO @ Fri, 05 Jul 2019 04:17:59: 10000000 INFO @ Fri, 05 Jul 2019 04:18:02: 11000000 INFO @ Fri, 05 Jul 2019 04:18:07: 10000000 INFO @ Fri, 05 Jul 2019 04:18:09: 11000000 INFO @ Fri, 05 Jul 2019 04:18:11: 12000000 INFO @ Fri, 05 Jul 2019 04:18:17: 11000000 INFO @ Fri, 05 Jul 2019 04:18:18: 12000000 INFO @ Fri, 05 Jul 2019 04:18:19: 13000000 INFO @ Fri, 05 Jul 2019 04:18:26: 12000000 INFO @ Fri, 05 Jul 2019 04:18:27: 13000000 INFO @ Fri, 05 Jul 2019 04:18:28: 14000000 INFO @ Fri, 05 Jul 2019 04:18:36: 13000000 INFO @ Fri, 05 Jul 2019 04:18:36: 14000000 INFO @ Fri, 05 Jul 2019 04:18:36: 15000000 INFO @ Fri, 05 Jul 2019 04:18:45: 16000000 INFO @ Fri, 05 Jul 2019 04:18:45: 14000000 INFO @ Fri, 05 Jul 2019 04:18:46: 15000000 INFO @ Fri, 05 Jul 2019 04:18:53: 17000000 INFO @ Fri, 05 Jul 2019 04:18:55: 15000000 INFO @ Fri, 05 Jul 2019 04:18:55: 16000000 INFO @ Fri, 05 Jul 2019 04:19:02: 18000000 INFO @ Fri, 05 Jul 2019 04:19:04: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:19:04: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:19:04: #1 total tags in treatment: 18209509 INFO @ Fri, 05 Jul 2019 04:19:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:19:04: #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 04:19:04: #1 tags after filtering in treatment: 18209305 INFO @ Fri, 05 Jul 2019 04:19:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:19:04: #1 finished! INFO @ Fri, 05 Jul 2019 04:19:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:19:04: 17000000 INFO @ Fri, 05 Jul 2019 04:19:04: 16000000 INFO @ Fri, 05 Jul 2019 04:19:09: #2 number of paired peaks: 59017 INFO @ Fri, 05 Jul 2019 04:19:09: start model_add_line... INFO @ Fri, 05 Jul 2019 04:19:09: start X-correlation... INFO @ Fri, 05 Jul 2019 04:19:09: end of X-cor INFO @ Fri, 05 Jul 2019 04:19:09: #2 finished! INFO @ Fri, 05 Jul 2019 04:19:09: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:19:09: #2 alternative fragment length(s) may be 4,135,501 bps INFO @ Fri, 05 Jul 2019 04:19:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.20_model.r INFO @ Fri, 05 Jul 2019 04:19:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:19:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:19:14: 18000000 INFO @ Fri, 05 Jul 2019 04:19:14: 17000000 INFO @ Fri, 05 Jul 2019 04:19:16: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:19:16: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:19:16: #1 total tags in treatment: 18209509 INFO @ Fri, 05 Jul 2019 04:19:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:19:16: #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 04:19:16: #1 tags after filtering in treatment: 18209305 INFO @ Fri, 05 Jul 2019 04:19:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:19:16: #1 finished! INFO @ Fri, 05 Jul 2019 04:19:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:19:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:19:20: #2 number of paired peaks: 59017 INFO @ Fri, 05 Jul 2019 04:19:20: start model_add_line... INFO @ Fri, 05 Jul 2019 04:19:21: start X-correlation... INFO @ Fri, 05 Jul 2019 04:19:21: end of X-cor INFO @ Fri, 05 Jul 2019 04:19:21: #2 finished! INFO @ Fri, 05 Jul 2019 04:19:21: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:19:21: #2 alternative fragment length(s) may be 4,135,501 bps INFO @ Fri, 05 Jul 2019 04:19:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.05_model.r INFO @ Fri, 05 Jul 2019 04:19:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:19:23: 18000000 INFO @ Fri, 05 Jul 2019 04:19:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 04:19:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 04:19:25: #1 total tags in treatment: 18209509 INFO @ Fri, 05 Jul 2019 04:19:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 04:19:25: #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 04:19:25: #1 tags after filtering in treatment: 18209305 INFO @ Fri, 05 Jul 2019 04:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 04:19:25: #1 finished! INFO @ Fri, 05 Jul 2019 04:19:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 04:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 04:19:30: #2 number of paired peaks: 59017 INFO @ Fri, 05 Jul 2019 04:19:30: start model_add_line... INFO @ Fri, 05 Jul 2019 04:19:30: start X-correlation... INFO @ Fri, 05 Jul 2019 04:19:30: end of X-cor INFO @ Fri, 05 Jul 2019 04:19:30: #2 finished! INFO @ Fri, 05 Jul 2019 04:19:30: #2 predicted fragment length is 135 bps INFO @ Fri, 05 Jul 2019 04:19:30: #2 alternative fragment length(s) may be 4,135,501 bps INFO @ Fri, 05 Jul 2019 04:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.10_model.r INFO @ Fri, 05 Jul 2019 04:19:30: #3 Call peaks... INFO @ Fri, 05 Jul 2019 04:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 04:20:11: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:20:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:20:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 04:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.20_peaks.xls INFO @ Fri, 05 Jul 2019 04:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.20_summits.bed INFO @ Fri, 05 Jul 2019 04:20:44: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:20:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.05_peaks.xls INFO @ Fri, 05 Jul 2019 04:20:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:20:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.05_summits.bed INFO @ Fri, 05 Jul 2019 04:20:55: Done! pass1 - making usageList (63 chroms): 3 millis pass2 - checking and writing primary data (4110 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 04:21:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.10_peaks.xls INFO @ Fri, 05 Jul 2019 04:21:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 04:21:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101848/ERX101848.10_summits.bed INFO @ Fri, 05 Jul 2019 04:21:03: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (800 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。