Job ID = 4288950 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,961,804 reads read : 23,923,608 reads written : 11,961,804 reads 0-length : 11,961,804 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:38 11961804 reads; of these: 11961804 (100.00%) were unpaired; of these: 573705 (4.80%) aligned 0 times 9583138 (80.11%) aligned exactly 1 time 1804961 (15.09%) aligned >1 times 95.20% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 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] 1131514 / 11388099 = 0.0994 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.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 @ Tue, 10 Dec 2019 13:11:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:11:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:11:30: 1000000 INFO @ Tue, 10 Dec 2019 13:11:40: 2000000 INFO @ Tue, 10 Dec 2019 13:11:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.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 @ Tue, 10 Dec 2019 13:11:49: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:11:49: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:11:51: 3000000 INFO @ Tue, 10 Dec 2019 13:11:58: 1000000 INFO @ Tue, 10 Dec 2019 13:12:01: 4000000 INFO @ Tue, 10 Dec 2019 13:12:06: 2000000 INFO @ Tue, 10 Dec 2019 13:12:12: 5000000 INFO @ Tue, 10 Dec 2019 13:12:14: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.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 @ Tue, 10 Dec 2019 13:12:19: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:12:19: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:12:21: 6000000 INFO @ Tue, 10 Dec 2019 13:12:23: 4000000 INFO @ Tue, 10 Dec 2019 13:12:30: 1000000 INFO @ Tue, 10 Dec 2019 13:12:31: 7000000 INFO @ Tue, 10 Dec 2019 13:12:32: 5000000 INFO @ Tue, 10 Dec 2019 13:12:40: 8000000 INFO @ Tue, 10 Dec 2019 13:12:41: 2000000 INFO @ Tue, 10 Dec 2019 13:12:41: 6000000 INFO @ Tue, 10 Dec 2019 13:12:49: 9000000 INFO @ Tue, 10 Dec 2019 13:12:50: 7000000 INFO @ Tue, 10 Dec 2019 13:12:52: 3000000 INFO @ Tue, 10 Dec 2019 13:12:59: 10000000 INFO @ Tue, 10 Dec 2019 13:12:59: 8000000 INFO @ Tue, 10 Dec 2019 13:13:02: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:13:02: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:13:02: #1 total tags in treatment: 10256585 INFO @ Tue, 10 Dec 2019 13:13:02: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:13:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:13:02: #1 tags after filtering in treatment: 10256334 INFO @ Tue, 10 Dec 2019 13:13:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:13:02: #1 finished! INFO @ Tue, 10 Dec 2019 13:13:02: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:13:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:13:04: 4000000 INFO @ Tue, 10 Dec 2019 13:13:05: #2 number of paired peaks: 61077 INFO @ Tue, 10 Dec 2019 13:13:05: start model_add_line... INFO @ Tue, 10 Dec 2019 13:13:06: start X-correlation... INFO @ Tue, 10 Dec 2019 13:13:06: end of X-cor INFO @ Tue, 10 Dec 2019 13:13:06: #2 finished! INFO @ Tue, 10 Dec 2019 13:13:06: #2 predicted fragment length is 190 bps INFO @ Tue, 10 Dec 2019 13:13:06: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 10 Dec 2019 13:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.05_model.r INFO @ Tue, 10 Dec 2019 13:13:06: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:13:08: 9000000 INFO @ Tue, 10 Dec 2019 13:13:14: 5000000 INFO @ Tue, 10 Dec 2019 13:13:17: 10000000 INFO @ Tue, 10 Dec 2019 13:13:19: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:13:19: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:13:19: #1 total tags in treatment: 10256585 INFO @ Tue, 10 Dec 2019 13:13:19: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:13:20: #1 tags after filtering in treatment: 10256334 INFO @ Tue, 10 Dec 2019 13:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:13:20: #1 finished! INFO @ Tue, 10 Dec 2019 13:13:20: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:13:23: #2 number of paired peaks: 61077 INFO @ Tue, 10 Dec 2019 13:13:23: start model_add_line... INFO @ Tue, 10 Dec 2019 13:13:23: start X-correlation... INFO @ Tue, 10 Dec 2019 13:13:23: end of X-cor INFO @ Tue, 10 Dec 2019 13:13:23: #2 finished! INFO @ Tue, 10 Dec 2019 13:13:23: #2 predicted fragment length is 190 bps INFO @ Tue, 10 Dec 2019 13:13:23: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 10 Dec 2019 13:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.10_model.r INFO @ Tue, 10 Dec 2019 13:13:23: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:13:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:13:25: 6000000 INFO @ Tue, 10 Dec 2019 13:13:36: 7000000 INFO @ Tue, 10 Dec 2019 13:13:38: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:13:46: 8000000 INFO @ Tue, 10 Dec 2019 13:13:56: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.05_summits.bed INFO @ Tue, 10 Dec 2019 13:13:56: Done! pass1 - making usageList (60 chroms): 4 millis pass2 - checking and writing primary data (6363 records, 4 fields): 62 millis INFO @ Tue, 10 Dec 2019 13:13:57: 9000000 CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:14:07: 10000000 INFO @ Tue, 10 Dec 2019 13:14:10: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:14:10: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:14:10: #1 total tags in treatment: 10256585 INFO @ Tue, 10 Dec 2019 13:14:10: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:14:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:14:10: #1 tags after filtering in treatment: 10256334 INFO @ Tue, 10 Dec 2019 13:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:14:10: #1 finished! INFO @ Tue, 10 Dec 2019 13:14:10: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.10_summits.bed INFO @ Tue, 10 Dec 2019 13:14:13: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (1451 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:14:13: #2 number of paired peaks: 61077 INFO @ Tue, 10 Dec 2019 13:14:13: start model_add_line... INFO @ Tue, 10 Dec 2019 13:14:14: start X-correlation... INFO @ Tue, 10 Dec 2019 13:14:14: end of X-cor INFO @ Tue, 10 Dec 2019 13:14:14: #2 finished! INFO @ Tue, 10 Dec 2019 13:14:14: #2 predicted fragment length is 190 bps INFO @ Tue, 10 Dec 2019 13:14:14: #2 alternative fragment length(s) may be 190 bps INFO @ Tue, 10 Dec 2019 13:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.20_model.r INFO @ Tue, 10 Dec 2019 13:14:14: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:14:46: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460576/SRX5460576.20_summits.bed INFO @ Tue, 10 Dec 2019 13:15:03: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (288 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。