Job ID = 2590822 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,982,490 reads read : 63,964,980 reads written : 31,982,490 reads 0-length : 31,982,490 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: 00:11:29 31982490 reads; of these: 31982490 (100.00%) were unpaired; of these: 3149514 (9.85%) aligned 0 times 22989225 (71.88%) aligned exactly 1 time 5843751 (18.27%) aligned >1 times 90.15% overall alignment rate Time searching: 00:11:29 Overall time: 00:11:29 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 12 files... [bam_rmdupse_core] 15007885 / 28832976 = 0.5205 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 23:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.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 23:45:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:45:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.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 23:45:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:45:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.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 23:45:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:45:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:45:43: 1000000 INFO @ Mon, 12 Aug 2019 23:45:43: 1000000 INFO @ Mon, 12 Aug 2019 23:45:44: 1000000 INFO @ Mon, 12 Aug 2019 23:45:51: 2000000 INFO @ Mon, 12 Aug 2019 23:45:52: 2000000 INFO @ Mon, 12 Aug 2019 23:45:52: 2000000 INFO @ Mon, 12 Aug 2019 23:45:58: 3000000 INFO @ Mon, 12 Aug 2019 23:45:59: 3000000 INFO @ Mon, 12 Aug 2019 23:46:01: 3000000 INFO @ Mon, 12 Aug 2019 23:46:06: 4000000 INFO @ Mon, 12 Aug 2019 23:46:07: 4000000 INFO @ Mon, 12 Aug 2019 23:46:09: 4000000 INFO @ Mon, 12 Aug 2019 23:46:13: 5000000 INFO @ Mon, 12 Aug 2019 23:46:14: 5000000 INFO @ Mon, 12 Aug 2019 23:46:17: 5000000 INFO @ Mon, 12 Aug 2019 23:46:21: 6000000 INFO @ Mon, 12 Aug 2019 23:46:21: 6000000 INFO @ Mon, 12 Aug 2019 23:46:26: 6000000 INFO @ Mon, 12 Aug 2019 23:46:28: 7000000 INFO @ Mon, 12 Aug 2019 23:46:29: 7000000 INFO @ Mon, 12 Aug 2019 23:46:34: 7000000 INFO @ Mon, 12 Aug 2019 23:46:36: 8000000 INFO @ Mon, 12 Aug 2019 23:46:36: 8000000 INFO @ Mon, 12 Aug 2019 23:46:43: 8000000 INFO @ Mon, 12 Aug 2019 23:46:43: 9000000 INFO @ Mon, 12 Aug 2019 23:46:44: 9000000 INFO @ Mon, 12 Aug 2019 23:46:50: 10000000 INFO @ Mon, 12 Aug 2019 23:46:51: 10000000 INFO @ Mon, 12 Aug 2019 23:46:51: 9000000 INFO @ Mon, 12 Aug 2019 23:46:58: 11000000 INFO @ Mon, 12 Aug 2019 23:46:58: 11000000 INFO @ Mon, 12 Aug 2019 23:46:59: 10000000 INFO @ Mon, 12 Aug 2019 23:47:05: 12000000 INFO @ Mon, 12 Aug 2019 23:47:06: 12000000 INFO @ Mon, 12 Aug 2019 23:47:07: 11000000 INFO @ Mon, 12 Aug 2019 23:47:12: 13000000 INFO @ Mon, 12 Aug 2019 23:47:13: 13000000 INFO @ Mon, 12 Aug 2019 23:47:16: 12000000 INFO @ Mon, 12 Aug 2019 23:47:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:47:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:47:18: #1 total tags in treatment: 13825091 INFO @ Mon, 12 Aug 2019 23:47:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:47:18: #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 23:47:19: #1 tags after filtering in treatment: 13825091 INFO @ Mon, 12 Aug 2019 23:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:47:19: #1 finished! INFO @ Mon, 12 Aug 2019 23:47:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:47:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:47:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:47:19: #1 total tags in treatment: 13825091 INFO @ Mon, 12 Aug 2019 23:47:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:47:19: #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 23:47:19: #1 tags after filtering in treatment: 13825091 INFO @ Mon, 12 Aug 2019 23:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:47:19: #1 finished! INFO @ Mon, 12 Aug 2019 23:47:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:47:21: #2 number of paired peaks: 6129 INFO @ Mon, 12 Aug 2019 23:47:21: start model_add_line... INFO @ Mon, 12 Aug 2019 23:47:21: start X-correlation... INFO @ Mon, 12 Aug 2019 23:47:21: end of X-cor INFO @ Mon, 12 Aug 2019 23:47:21: #2 finished! INFO @ Mon, 12 Aug 2019 23:47:21: #2 predicted fragment length is 252 bps INFO @ Mon, 12 Aug 2019 23:47:21: #2 alternative fragment length(s) may be 252 bps INFO @ Mon, 12 Aug 2019 23:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.10_model.r INFO @ Mon, 12 Aug 2019 23:47:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:47:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:47:21: #2 number of paired peaks: 6129 INFO @ Mon, 12 Aug 2019 23:47:21: start model_add_line... INFO @ Mon, 12 Aug 2019 23:47:21: start X-correlation... INFO @ Mon, 12 Aug 2019 23:47:21: end of X-cor INFO @ Mon, 12 Aug 2019 23:47:21: #2 finished! INFO @ Mon, 12 Aug 2019 23:47:21: #2 predicted fragment length is 252 bps INFO @ Mon, 12 Aug 2019 23:47:21: #2 alternative fragment length(s) may be 252 bps INFO @ Mon, 12 Aug 2019 23:47:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.20_model.r INFO @ Mon, 12 Aug 2019 23:47:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:47:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:47:24: 13000000 INFO @ Mon, 12 Aug 2019 23:47:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:47:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:47:30: #1 total tags in treatment: 13825091 INFO @ Mon, 12 Aug 2019 23:47:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:47:30: #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 23:47:31: #1 tags after filtering in treatment: 13825091 INFO @ Mon, 12 Aug 2019 23:47:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:47:31: #1 finished! INFO @ Mon, 12 Aug 2019 23:47:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:47:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:47:33: #2 number of paired peaks: 6129 INFO @ Mon, 12 Aug 2019 23:47:33: start model_add_line... INFO @ Mon, 12 Aug 2019 23:47:33: start X-correlation... INFO @ Mon, 12 Aug 2019 23:47:33: end of X-cor INFO @ Mon, 12 Aug 2019 23:47:33: #2 finished! INFO @ Mon, 12 Aug 2019 23:47:33: #2 predicted fragment length is 252 bps INFO @ Mon, 12 Aug 2019 23:47:33: #2 alternative fragment length(s) may be 252 bps INFO @ Mon, 12 Aug 2019 23:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.05_model.r INFO @ Mon, 12 Aug 2019 23:47:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:48:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.10_summits.bed INFO @ Mon, 12 Aug 2019 23:48:34: Done! INFO @ Mon, 12 Aug 2019 23:48:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.20_summits.bed pass1 - making usageList (14 chroms): 5 millis INFO @ Mon, 12 Aug 2019 23:48:34: Done! pass2 - checking and writing primary data (11088 records, 4 fields): 16 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8128 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011061/SRX5011061.05_summits.bed INFO @ Mon, 12 Aug 2019 23:48:49: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (13560 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。