Job ID = 2590685 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,524,806 reads read : 35,049,612 reads written : 17,524,806 reads 0-length : 17,524,806 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:37 17524806 reads; of these: 17524806 (100.00%) were unpaired; of these: 910530 (5.20%) aligned 0 times 12359832 (70.53%) aligned exactly 1 time 4254444 (24.28%) aligned >1 times 94.80% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 6298971 / 16614276 = 0.3791 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 @ Mon, 12 Aug 2019 23:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:22:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:22:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:22:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:22:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:22:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:22:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Mon, 12 Aug 2019 23:22:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:22:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:22:14: 1000000 INFO @ Mon, 12 Aug 2019 23:22:15: 1000000 INFO @ Mon, 12 Aug 2019 23:22:16: 1000000 INFO @ Mon, 12 Aug 2019 23:22:21: 2000000 INFO @ Mon, 12 Aug 2019 23:22:23: 2000000 INFO @ Mon, 12 Aug 2019 23:22:23: 2000000 INFO @ Mon, 12 Aug 2019 23:22:28: 3000000 INFO @ Mon, 12 Aug 2019 23:22:30: 3000000 INFO @ Mon, 12 Aug 2019 23:22:31: 3000000 INFO @ Mon, 12 Aug 2019 23:22:35: 4000000 INFO @ Mon, 12 Aug 2019 23:22:37: 4000000 INFO @ Mon, 12 Aug 2019 23:22:39: 4000000 INFO @ Mon, 12 Aug 2019 23:22:42: 5000000 INFO @ Mon, 12 Aug 2019 23:22:44: 5000000 INFO @ Mon, 12 Aug 2019 23:22:47: 5000000 INFO @ Mon, 12 Aug 2019 23:22:48: 6000000 INFO @ Mon, 12 Aug 2019 23:22:51: 6000000 INFO @ Mon, 12 Aug 2019 23:22:55: 7000000 INFO @ Mon, 12 Aug 2019 23:22:55: 6000000 INFO @ Mon, 12 Aug 2019 23:22:58: 7000000 INFO @ Mon, 12 Aug 2019 23:23:01: 8000000 INFO @ Mon, 12 Aug 2019 23:23:03: 7000000 INFO @ Mon, 12 Aug 2019 23:23:05: 8000000 INFO @ Mon, 12 Aug 2019 23:23:07: 9000000 INFO @ Mon, 12 Aug 2019 23:23:11: 8000000 INFO @ Mon, 12 Aug 2019 23:23:12: 9000000 INFO @ Mon, 12 Aug 2019 23:23:14: 10000000 INFO @ Mon, 12 Aug 2019 23:23:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:23:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:23:16: #1 total tags in treatment: 10315305 INFO @ Mon, 12 Aug 2019 23:23:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:23:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:23:16: #1 tags after filtering in treatment: 10315305 INFO @ Mon, 12 Aug 2019 23:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:23:16: #1 finished! INFO @ Mon, 12 Aug 2019 23:23:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:23:17: #2 number of paired peaks: 1303 INFO @ Mon, 12 Aug 2019 23:23:17: start model_add_line... INFO @ Mon, 12 Aug 2019 23:23:17: start X-correlation... INFO @ Mon, 12 Aug 2019 23:23:17: end of X-cor INFO @ Mon, 12 Aug 2019 23:23:17: #2 finished! INFO @ Mon, 12 Aug 2019 23:23:17: #2 predicted fragment length is 195 bps INFO @ Mon, 12 Aug 2019 23:23:17: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 12 Aug 2019 23:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.10_model.r INFO @ Mon, 12 Aug 2019 23:23:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:23:18: 10000000 INFO @ Mon, 12 Aug 2019 23:23:19: 9000000 INFO @ Mon, 12 Aug 2019 23:23:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:23:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:23:21: #1 total tags in treatment: 10315305 INFO @ Mon, 12 Aug 2019 23:23:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:23:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:23:21: #1 tags after filtering in treatment: 10315305 INFO @ Mon, 12 Aug 2019 23:23:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:23:21: #1 finished! INFO @ Mon, 12 Aug 2019 23:23:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:23:22: #2 number of paired peaks: 1303 INFO @ Mon, 12 Aug 2019 23:23:22: start model_add_line... INFO @ Mon, 12 Aug 2019 23:23:22: start X-correlation... INFO @ Mon, 12 Aug 2019 23:23:22: end of X-cor INFO @ Mon, 12 Aug 2019 23:23:22: #2 finished! INFO @ Mon, 12 Aug 2019 23:23:22: #2 predicted fragment length is 195 bps INFO @ Mon, 12 Aug 2019 23:23:22: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 12 Aug 2019 23:23:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.20_model.r INFO @ Mon, 12 Aug 2019 23:23:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:23:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:23:26: 10000000 INFO @ Mon, 12 Aug 2019 23:23:29: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:23:29: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:23:29: #1 total tags in treatment: 10315305 INFO @ Mon, 12 Aug 2019 23:23:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:23:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:23:29: #1 tags after filtering in treatment: 10315305 INFO @ Mon, 12 Aug 2019 23:23:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:23:29: #1 finished! INFO @ Mon, 12 Aug 2019 23:23:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:23:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:23:30: #2 number of paired peaks: 1303 INFO @ Mon, 12 Aug 2019 23:23:30: start model_add_line... INFO @ Mon, 12 Aug 2019 23:23:30: start X-correlation... INFO @ Mon, 12 Aug 2019 23:23:30: end of X-cor INFO @ Mon, 12 Aug 2019 23:23:30: #2 finished! INFO @ Mon, 12 Aug 2019 23:23:30: #2 predicted fragment length is 195 bps INFO @ Mon, 12 Aug 2019 23:23:30: #2 alternative fragment length(s) may be 195 bps INFO @ Mon, 12 Aug 2019 23:23:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.05_model.r INFO @ Mon, 12 Aug 2019 23:23:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:23:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:23:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:24:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:24:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.10_summits.bed INFO @ Mon, 12 Aug 2019 23:24:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4546 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.20_summits.bed INFO @ Mon, 12 Aug 2019 23:24:10: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2305 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:24:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:24:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:24:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011030/SRX5011030.05_summits.bed INFO @ Mon, 12 Aug 2019 23:24:19: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7341 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。