Job ID = 2002169 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,318,952 reads read : 19,318,952 reads written : 19,318,952 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR235747.sra.cache’: 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: 00:00:01 Multiseed full-index search: 00:05:54 19318952 reads; of these: 19318952 (100.00%) were unpaired; of these: 6144106 (31.80%) aligned 0 times 9373025 (48.52%) aligned exactly 1 time 3801821 (19.68%) aligned >1 times 68.20% overall alignment rate Time searching: 00:05:57 Overall time: 00:05:57 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] 1907954 / 13174846 = 0.1448 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 10:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.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 10:55:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:55:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.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 10:55:07: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:55:07: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:55:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.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 10:55:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 10:55:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 10:55:15: 1000000 INFO @ Fri, 05 Jul 2019 10:55:15: 1000000 INFO @ Fri, 05 Jul 2019 10:55:16: 1000000 INFO @ Fri, 05 Jul 2019 10:55:22: 2000000 INFO @ Fri, 05 Jul 2019 10:55:23: 2000000 INFO @ Fri, 05 Jul 2019 10:55:23: 2000000 INFO @ Fri, 05 Jul 2019 10:55:30: 3000000 INFO @ Fri, 05 Jul 2019 10:55:30: 3000000 INFO @ Fri, 05 Jul 2019 10:55:30: 3000000 INFO @ Fri, 05 Jul 2019 10:55:36: 4000000 INFO @ Fri, 05 Jul 2019 10:55:37: 4000000 INFO @ Fri, 05 Jul 2019 10:55:38: 4000000 INFO @ Fri, 05 Jul 2019 10:55:43: 5000000 INFO @ Fri, 05 Jul 2019 10:55:45: 5000000 INFO @ Fri, 05 Jul 2019 10:55:45: 5000000 INFO @ Fri, 05 Jul 2019 10:55:50: 6000000 INFO @ Fri, 05 Jul 2019 10:55:53: 6000000 INFO @ Fri, 05 Jul 2019 10:55:53: 6000000 INFO @ Fri, 05 Jul 2019 10:55:57: 7000000 INFO @ Fri, 05 Jul 2019 10:56:01: 7000000 INFO @ Fri, 05 Jul 2019 10:56:01: 7000000 INFO @ Fri, 05 Jul 2019 10:56:04: 8000000 INFO @ Fri, 05 Jul 2019 10:56:09: 8000000 INFO @ Fri, 05 Jul 2019 10:56:09: 8000000 INFO @ Fri, 05 Jul 2019 10:56:11: 9000000 INFO @ Fri, 05 Jul 2019 10:56:16: 9000000 INFO @ Fri, 05 Jul 2019 10:56:17: 9000000 INFO @ Fri, 05 Jul 2019 10:56:18: 10000000 INFO @ Fri, 05 Jul 2019 10:56:24: 10000000 INFO @ Fri, 05 Jul 2019 10:56:24: 10000000 INFO @ Fri, 05 Jul 2019 10:56:25: 11000000 INFO @ Fri, 05 Jul 2019 10:56:27: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:56:27: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:56:27: #1 total tags in treatment: 11266892 INFO @ Fri, 05 Jul 2019 10:56:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:56:27: #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 10:56:27: #1 tags after filtering in treatment: 11266680 INFO @ Fri, 05 Jul 2019 10:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:56:27: #1 finished! INFO @ Fri, 05 Jul 2019 10:56:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:56:30: #2 number of paired peaks: 32630 INFO @ Fri, 05 Jul 2019 10:56:31: start model_add_line... INFO @ Fri, 05 Jul 2019 10:56:31: start X-correlation... INFO @ Fri, 05 Jul 2019 10:56:31: end of X-cor INFO @ Fri, 05 Jul 2019 10:56:31: #2 finished! INFO @ Fri, 05 Jul 2019 10:56:31: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 10:56:31: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 05 Jul 2019 10:56:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.10_model.r INFO @ Fri, 05 Jul 2019 10:56:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:56:32: 11000000 INFO @ Fri, 05 Jul 2019 10:56:32: 11000000 INFO @ Fri, 05 Jul 2019 10:56:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:56:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:56:34: #1 total tags in treatment: 11266892 INFO @ Fri, 05 Jul 2019 10:56:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:56:34: #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 10:56:34: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 10:56:34: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 10:56:34: #1 total tags in treatment: 11266892 INFO @ Fri, 05 Jul 2019 10:56:34: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 10:56:34: #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 10:56:34: #1 tags after filtering in treatment: 11266680 INFO @ Fri, 05 Jul 2019 10:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:56:34: #1 finished! INFO @ Fri, 05 Jul 2019 10:56:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:56:34: #1 tags after filtering in treatment: 11266680 INFO @ Fri, 05 Jul 2019 10:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 10:56:34: #1 finished! INFO @ Fri, 05 Jul 2019 10:56:34: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 10:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 10:56:37: #2 number of paired peaks: 32630 INFO @ Fri, 05 Jul 2019 10:56:37: #2 number of paired peaks: 32630 INFO @ Fri, 05 Jul 2019 10:56:37: start model_add_line... INFO @ Fri, 05 Jul 2019 10:56:37: start model_add_line... INFO @ Fri, 05 Jul 2019 10:56:37: start X-correlation... INFO @ Fri, 05 Jul 2019 10:56:37: start X-correlation... INFO @ Fri, 05 Jul 2019 10:56:37: end of X-cor INFO @ Fri, 05 Jul 2019 10:56:37: #2 finished! INFO @ Fri, 05 Jul 2019 10:56:37: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 10:56:37: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 05 Jul 2019 10:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.05_model.r INFO @ Fri, 05 Jul 2019 10:56:37: end of X-cor INFO @ Fri, 05 Jul 2019 10:56:37: #2 finished! INFO @ Fri, 05 Jul 2019 10:56:37: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 10:56:37: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 05 Jul 2019 10:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.20_model.r INFO @ Fri, 05 Jul 2019 10:56:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:56:37: #3 Call peaks... INFO @ Fri, 05 Jul 2019 10:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 10:57:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:57:13: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:57:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 10:57:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.10_peaks.xls INFO @ Fri, 05 Jul 2019 10:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:57:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.10_summits.bed INFO @ Fri, 05 Jul 2019 10:57:29: Done! pass1 - making usageList (108 chroms): 8 millis pass2 - checking and writing primary data (15506 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 10:57:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.20_peaks.xls INFO @ Fri, 05 Jul 2019 10:57:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 10:57:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.05_peaks.xls INFO @ Fri, 05 Jul 2019 10:57:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.20_summits.bed INFO @ Fri, 05 Jul 2019 10:57:33: Done! INFO @ Fri, 05 Jul 2019 10:57:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.05_peaks.narrowPeak pass1 - making usageList (78 chroms): 5 millis pass2 - checking and writing primary data (9165 records, 4 fields): 57 millis INFO @ Fri, 05 Jul 2019 10:57:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210225/ERX210225.05_summits.bed INFO @ Fri, 05 Jul 2019 10:57:35: Done! pass1 - making usageList (129 chroms): 5 millis pass2 - checking and writing primary data (23303 records, 4 fields): 35 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。