Job ID = 2590280 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,349,784 reads read : 16,349,784 reads written : 16,349,784 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: 00:10:01 16349784 reads; of these: 16349784 (100.00%) were unpaired; of these: 465602 (2.85%) aligned 0 times 5116587 (31.29%) aligned exactly 1 time 10767595 (65.86%) aligned >1 times 97.15% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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_rmdupse_core] 2813811 / 15884182 = 0.1771 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 20:44:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.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 20:44:46: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:44:46: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:44:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.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 20:44:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:44:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.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 20:44:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:44:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:44:53: 1000000 INFO @ Mon, 12 Aug 2019 20:44:54: 1000000 INFO @ Mon, 12 Aug 2019 20:44:55: 1000000 INFO @ Mon, 12 Aug 2019 20:44:59: 2000000 INFO @ Mon, 12 Aug 2019 20:45:01: 2000000 INFO @ Mon, 12 Aug 2019 20:45:02: 2000000 INFO @ Mon, 12 Aug 2019 20:45:06: 3000000 INFO @ Mon, 12 Aug 2019 20:45:08: 3000000 INFO @ Mon, 12 Aug 2019 20:45:09: 3000000 INFO @ Mon, 12 Aug 2019 20:45:12: 4000000 INFO @ Mon, 12 Aug 2019 20:45:15: 4000000 INFO @ Mon, 12 Aug 2019 20:45:16: 4000000 INFO @ Mon, 12 Aug 2019 20:45:18: 5000000 INFO @ Mon, 12 Aug 2019 20:45:22: 5000000 INFO @ Mon, 12 Aug 2019 20:45:23: 5000000 INFO @ Mon, 12 Aug 2019 20:45:25: 6000000 INFO @ Mon, 12 Aug 2019 20:45:29: 6000000 INFO @ Mon, 12 Aug 2019 20:45:30: 6000000 INFO @ Mon, 12 Aug 2019 20:45:31: 7000000 INFO @ Mon, 12 Aug 2019 20:45:36: 7000000 INFO @ Mon, 12 Aug 2019 20:45:37: 7000000 INFO @ Mon, 12 Aug 2019 20:45:38: 8000000 INFO @ Mon, 12 Aug 2019 20:45:43: 8000000 INFO @ Mon, 12 Aug 2019 20:45:44: 8000000 INFO @ Mon, 12 Aug 2019 20:45:44: 9000000 INFO @ Mon, 12 Aug 2019 20:45:50: 9000000 INFO @ Mon, 12 Aug 2019 20:45:50: 10000000 INFO @ Mon, 12 Aug 2019 20:45:51: 9000000 INFO @ Mon, 12 Aug 2019 20:45:57: 10000000 INFO @ Mon, 12 Aug 2019 20:45:57: 11000000 INFO @ Mon, 12 Aug 2019 20:45:58: 10000000 INFO @ Mon, 12 Aug 2019 20:46:04: 11000000 INFO @ Mon, 12 Aug 2019 20:46:04: 11000000 INFO @ Mon, 12 Aug 2019 20:46:05: 12000000 INFO @ Mon, 12 Aug 2019 20:46:10: 12000000 INFO @ Mon, 12 Aug 2019 20:46:11: 12000000 INFO @ Mon, 12 Aug 2019 20:46:12: 13000000 INFO @ Mon, 12 Aug 2019 20:46:12: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:46:12: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:46:12: #1 total tags in treatment: 13070371 INFO @ Mon, 12 Aug 2019 20:46:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:46:12: #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 20:46:13: #1 tags after filtering in treatment: 13070371 INFO @ Mon, 12 Aug 2019 20:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:46:13: #1 finished! INFO @ Mon, 12 Aug 2019 20:46:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:46:14: #2 number of paired peaks: 1115 INFO @ Mon, 12 Aug 2019 20:46:14: start model_add_line... INFO @ Mon, 12 Aug 2019 20:46:14: start X-correlation... INFO @ Mon, 12 Aug 2019 20:46:14: end of X-cor INFO @ Mon, 12 Aug 2019 20:46:14: #2 finished! INFO @ Mon, 12 Aug 2019 20:46:14: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 20:46:14: #2 alternative fragment length(s) may be 107 bps INFO @ Mon, 12 Aug 2019 20:46:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.05_model.r INFO @ Mon, 12 Aug 2019 20:46:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:46:17: 13000000 INFO @ Mon, 12 Aug 2019 20:46:18: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:46:18: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:46:18: #1 total tags in treatment: 13070371 INFO @ Mon, 12 Aug 2019 20:46:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:46:18: #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 20:46:18: #1 tags after filtering in treatment: 13070371 INFO @ Mon, 12 Aug 2019 20:46:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:46:18: #1 finished! INFO @ Mon, 12 Aug 2019 20:46:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:46:18: 13000000 INFO @ Mon, 12 Aug 2019 20:46:19: #1 tag size is determined as 36 bps INFO @ Mon, 12 Aug 2019 20:46:19: #1 tag size = 36 INFO @ Mon, 12 Aug 2019 20:46:19: #1 total tags in treatment: 13070371 INFO @ Mon, 12 Aug 2019 20:46:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:46:19: #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 20:46:19: #1 tags after filtering in treatment: 13070371 INFO @ Mon, 12 Aug 2019 20:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:46:19: #1 finished! INFO @ Mon, 12 Aug 2019 20:46:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:46:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:46:20: #2 number of paired peaks: 1115 INFO @ Mon, 12 Aug 2019 20:46:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:46:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:46:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:46:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:46:20: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 20:46:20: #2 alternative fragment length(s) may be 107 bps INFO @ Mon, 12 Aug 2019 20:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.10_model.r INFO @ Mon, 12 Aug 2019 20:46:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:46:20: #2 number of paired peaks: 1115 INFO @ Mon, 12 Aug 2019 20:46:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:46:21: start X-correlation... INFO @ Mon, 12 Aug 2019 20:46:21: end of X-cor INFO @ Mon, 12 Aug 2019 20:46:21: #2 finished! INFO @ Mon, 12 Aug 2019 20:46:21: #2 predicted fragment length is 107 bps INFO @ Mon, 12 Aug 2019 20:46:21: #2 alternative fragment length(s) may be 107 bps INFO @ Mon, 12 Aug 2019 20:46:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.20_model.r INFO @ Mon, 12 Aug 2019 20:46:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:46:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:46:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:46:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:46:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:47:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.05_summits.bed INFO @ Mon, 12 Aug 2019 20:47:11: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (10694 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.10_summits.bed INFO @ Mon, 12 Aug 2019 20:47:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4233 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:47:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:47:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:47:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287565/SRX287565.20_summits.bed INFO @ Mon, 12 Aug 2019 20:47:16: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1603 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。