Job ID = 2001576 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,277,714 reads read : 19,277,714 reads written : 19,277,714 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: 00:10:54 19277714 reads; of these: 19277714 (100.00%) were unpaired; of these: 542688 (2.82%) aligned 0 times 14030842 (72.78%) aligned exactly 1 time 4704184 (24.40%) aligned >1 times 97.18% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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] 1063147 / 18735026 = 0.0567 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 05:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.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 05:42:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:42:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.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 05:42:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:42:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:42:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.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 05:42:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:42:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:43:03: 1000000 INFO @ Fri, 05 Jul 2019 05:43:03: 1000000 INFO @ Fri, 05 Jul 2019 05:43:06: 1000000 INFO @ Fri, 05 Jul 2019 05:43:13: 2000000 INFO @ Fri, 05 Jul 2019 05:43:13: 2000000 INFO @ Fri, 05 Jul 2019 05:43:16: 2000000 INFO @ Fri, 05 Jul 2019 05:43:22: 3000000 INFO @ Fri, 05 Jul 2019 05:43:22: 3000000 INFO @ Fri, 05 Jul 2019 05:43:25: 3000000 INFO @ Fri, 05 Jul 2019 05:43:31: 4000000 INFO @ Fri, 05 Jul 2019 05:43:32: 4000000 INFO @ Fri, 05 Jul 2019 05:43:34: 4000000 INFO @ Fri, 05 Jul 2019 05:43:39: 5000000 INFO @ Fri, 05 Jul 2019 05:43:42: 5000000 INFO @ Fri, 05 Jul 2019 05:43:43: 5000000 INFO @ Fri, 05 Jul 2019 05:43:49: 6000000 INFO @ Fri, 05 Jul 2019 05:43:51: 6000000 INFO @ Fri, 05 Jul 2019 05:43:53: 6000000 INFO @ Fri, 05 Jul 2019 05:44:00: 7000000 INFO @ Fri, 05 Jul 2019 05:44:01: 7000000 INFO @ Fri, 05 Jul 2019 05:44:03: 7000000 INFO @ Fri, 05 Jul 2019 05:44:10: 8000000 INFO @ Fri, 05 Jul 2019 05:44:11: 8000000 INFO @ Fri, 05 Jul 2019 05:44:14: 8000000 INFO @ Fri, 05 Jul 2019 05:44:21: 9000000 INFO @ Fri, 05 Jul 2019 05:44:21: 9000000 INFO @ Fri, 05 Jul 2019 05:44:24: 9000000 INFO @ Fri, 05 Jul 2019 05:44:30: 10000000 INFO @ Fri, 05 Jul 2019 05:44:30: 10000000 INFO @ Fri, 05 Jul 2019 05:44:33: 10000000 INFO @ Fri, 05 Jul 2019 05:44:39: 11000000 INFO @ Fri, 05 Jul 2019 05:44:39: 11000000 INFO @ Fri, 05 Jul 2019 05:44:42: 11000000 INFO @ Fri, 05 Jul 2019 05:44:47: 12000000 INFO @ Fri, 05 Jul 2019 05:44:47: 12000000 INFO @ Fri, 05 Jul 2019 05:44:50: 12000000 INFO @ Fri, 05 Jul 2019 05:44:55: 13000000 INFO @ Fri, 05 Jul 2019 05:44:56: 13000000 INFO @ Fri, 05 Jul 2019 05:44:59: 13000000 INFO @ Fri, 05 Jul 2019 05:45:04: 14000000 INFO @ Fri, 05 Jul 2019 05:45:05: 14000000 INFO @ Fri, 05 Jul 2019 05:45:07: 14000000 INFO @ Fri, 05 Jul 2019 05:45:12: 15000000 INFO @ Fri, 05 Jul 2019 05:45:13: 15000000 INFO @ Fri, 05 Jul 2019 05:45:16: 15000000 INFO @ Fri, 05 Jul 2019 05:45:20: 16000000 INFO @ Fri, 05 Jul 2019 05:45:22: 16000000 INFO @ Fri, 05 Jul 2019 05:45:25: 16000000 INFO @ Fri, 05 Jul 2019 05:45:29: 17000000 INFO @ Fri, 05 Jul 2019 05:45:31: 17000000 INFO @ Fri, 05 Jul 2019 05:45:34: 17000000 INFO @ Fri, 05 Jul 2019 05:45:35: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:45:35: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:45:35: #1 total tags in treatment: 17671879 INFO @ Fri, 05 Jul 2019 05:45:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:45:35: #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 05:45:36: #1 tags after filtering in treatment: 17671696 INFO @ Fri, 05 Jul 2019 05:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:45:36: #1 finished! INFO @ Fri, 05 Jul 2019 05:45:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:45:38: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:45:38: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:45:38: #1 total tags in treatment: 17671879 INFO @ Fri, 05 Jul 2019 05:45:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:45:38: #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 05:45:38: #1 tags after filtering in treatment: 17671696 INFO @ Fri, 05 Jul 2019 05:45:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:45:38: #1 finished! INFO @ Fri, 05 Jul 2019 05:45:38: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:45:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:45:40: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:45:40: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:45:40: #1 total tags in treatment: 17671879 INFO @ Fri, 05 Jul 2019 05:45:40: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:45:40: #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 05:45:40: #2 number of paired peaks: 64815 INFO @ Fri, 05 Jul 2019 05:45:40: start model_add_line... INFO @ Fri, 05 Jul 2019 05:45:41: start X-correlation... INFO @ Fri, 05 Jul 2019 05:45:41: #1 tags after filtering in treatment: 17671696 INFO @ Fri, 05 Jul 2019 05:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:45:41: #1 finished! INFO @ Fri, 05 Jul 2019 05:45:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:45:41: end of X-cor INFO @ Fri, 05 Jul 2019 05:45:41: #2 finished! INFO @ Fri, 05 Jul 2019 05:45:41: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 05:45:41: #2 alternative fragment length(s) may be 3,132,497 bps INFO @ Fri, 05 Jul 2019 05:45:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.05_model.r INFO @ Fri, 05 Jul 2019 05:45:41: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:45:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:45:43: #2 number of paired peaks: 64815 INFO @ Fri, 05 Jul 2019 05:45:43: start model_add_line... INFO @ Fri, 05 Jul 2019 05:45:43: start X-correlation... INFO @ Fri, 05 Jul 2019 05:45:43: end of X-cor INFO @ Fri, 05 Jul 2019 05:45:43: #2 finished! INFO @ Fri, 05 Jul 2019 05:45:43: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 05:45:43: #2 alternative fragment length(s) may be 3,132,497 bps INFO @ Fri, 05 Jul 2019 05:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.10_model.r INFO @ Fri, 05 Jul 2019 05:45:43: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:45:45: #2 number of paired peaks: 64815 INFO @ Fri, 05 Jul 2019 05:45:45: start model_add_line... INFO @ Fri, 05 Jul 2019 05:45:46: start X-correlation... INFO @ Fri, 05 Jul 2019 05:45:46: end of X-cor INFO @ Fri, 05 Jul 2019 05:45:46: #2 finished! INFO @ Fri, 05 Jul 2019 05:45:46: #2 predicted fragment length is 132 bps INFO @ Fri, 05 Jul 2019 05:45:46: #2 alternative fragment length(s) may be 3,132,497 bps INFO @ Fri, 05 Jul 2019 05:45:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.20_model.r INFO @ Fri, 05 Jul 2019 05:45:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:45:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:46:43: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:46:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:46:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.05_summits.bed INFO @ Fri, 05 Jul 2019 05:47:14: Done! pass1 - making usageList (60 chroms): 3 millis pass2 - checking and writing primary data (3852 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.10_summits.bed INFO @ Fri, 05 Jul 2019 05:47:16: Done! pass1 - making usageList (38 chroms): 2 millis pass2 - checking and writing primary data (811 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:47:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:47:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:47:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101919/ERX101919.20_summits.bed INFO @ Fri, 05 Jul 2019 05:47:18: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (101 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。