Job ID = 2590318 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,426,648 reads read : 18,426,648 reads written : 18,426,648 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: 00:07:04 18426648 reads; of these: 18426648 (100.00%) were unpaired; of these: 715377 (3.88%) aligned 0 times 13437586 (72.92%) aligned exactly 1 time 4273685 (23.19%) aligned >1 times 96.12% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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] 5107755 / 17711271 = 0.2884 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 20:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.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 20:59:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:59:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.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 20:59:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:59:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:59:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.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 20:59:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:59:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:59:25: 1000000 INFO @ Mon, 12 Aug 2019 20:59:26: 1000000 INFO @ Mon, 12 Aug 2019 20:59:28: 1000000 INFO @ Mon, 12 Aug 2019 20:59:32: 2000000 INFO @ Mon, 12 Aug 2019 20:59:36: 2000000 INFO @ Mon, 12 Aug 2019 20:59:38: 2000000 INFO @ Mon, 12 Aug 2019 20:59:39: 3000000 INFO @ Mon, 12 Aug 2019 20:59:45: 3000000 INFO @ Mon, 12 Aug 2019 20:59:47: 4000000 INFO @ Mon, 12 Aug 2019 20:59:47: 3000000 INFO @ Mon, 12 Aug 2019 20:59:54: 5000000 INFO @ Mon, 12 Aug 2019 20:59:55: 4000000 INFO @ Mon, 12 Aug 2019 20:59:56: 4000000 INFO @ Mon, 12 Aug 2019 21:00:01: 6000000 INFO @ Mon, 12 Aug 2019 21:00:04: 5000000 INFO @ Mon, 12 Aug 2019 21:00:06: 5000000 INFO @ Mon, 12 Aug 2019 21:00:08: 7000000 INFO @ Mon, 12 Aug 2019 21:00:14: 6000000 INFO @ Mon, 12 Aug 2019 21:00:15: 6000000 INFO @ Mon, 12 Aug 2019 21:00:16: 8000000 INFO @ Mon, 12 Aug 2019 21:00:23: 9000000 INFO @ Mon, 12 Aug 2019 21:00:23: 7000000 INFO @ Mon, 12 Aug 2019 21:00:25: 7000000 INFO @ Mon, 12 Aug 2019 21:00:30: 10000000 INFO @ Mon, 12 Aug 2019 21:00:32: 8000000 INFO @ Mon, 12 Aug 2019 21:00:34: 8000000 INFO @ Mon, 12 Aug 2019 21:00:37: 11000000 INFO @ Mon, 12 Aug 2019 21:00:42: 9000000 INFO @ Mon, 12 Aug 2019 21:00:44: 9000000 INFO @ Mon, 12 Aug 2019 21:00:45: 12000000 INFO @ Mon, 12 Aug 2019 21:00:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:00:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:00:49: #1 total tags in treatment: 12603516 INFO @ Mon, 12 Aug 2019 21:00:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:49: #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 21:00:49: #1 tags after filtering in treatment: 12603516 INFO @ Mon, 12 Aug 2019 21:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:49: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:51: 10000000 INFO @ Mon, 12 Aug 2019 21:00:51: #2 number of paired peaks: 6740 INFO @ Mon, 12 Aug 2019 21:00:51: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:52: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:52: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:52: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:52: #2 predicted fragment length is 229 bps INFO @ Mon, 12 Aug 2019 21:00:52: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 12 Aug 2019 21:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.10_model.r INFO @ Mon, 12 Aug 2019 21:00:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:53: 10000000 INFO @ Mon, 12 Aug 2019 21:01:01: 11000000 INFO @ Mon, 12 Aug 2019 21:01:02: 11000000 INFO @ Mon, 12 Aug 2019 21:01:10: 12000000 INFO @ Mon, 12 Aug 2019 21:01:12: 12000000 INFO @ Mon, 12 Aug 2019 21:01:15: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:01:15: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:01:15: #1 total tags in treatment: 12603516 INFO @ Mon, 12 Aug 2019 21:01:15: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:15: #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 21:01:16: #1 tags after filtering in treatment: 12603516 INFO @ Mon, 12 Aug 2019 21:01:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:16: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:01:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:01:17: #1 total tags in treatment: 12603516 INFO @ Mon, 12 Aug 2019 21:01:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:17: #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 21:01:17: #1 tags after filtering in treatment: 12603516 INFO @ Mon, 12 Aug 2019 21:01:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:17: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:18: #2 number of paired peaks: 6740 INFO @ Mon, 12 Aug 2019 21:01:18: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:18: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:18: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:18: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:18: #2 predicted fragment length is 229 bps INFO @ Mon, 12 Aug 2019 21:01:18: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 12 Aug 2019 21:01:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.05_model.r INFO @ Mon, 12 Aug 2019 21:01:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:19: #2 number of paired peaks: 6740 INFO @ Mon, 12 Aug 2019 21:01:19: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:20: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:20: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:20: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:20: #2 predicted fragment length is 229 bps INFO @ Mon, 12 Aug 2019 21:01:20: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 12 Aug 2019 21:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.20_model.r INFO @ Mon, 12 Aug 2019 21:01:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:41: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.10_summits.bed INFO @ Mon, 12 Aug 2019 21:01:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7485 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:02:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:02:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.05_summits.bed INFO @ Mon, 12 Aug 2019 21:02:26: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8756 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331424/SRX331424.20_summits.bed INFO @ Mon, 12 Aug 2019 21:02:27: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (5996 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。