Job ID = 2590300 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,452,880 reads read : 24,452,880 reads written : 24,452,880 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: 00:07:23 24452880 reads; of these: 24452880 (100.00%) were unpaired; of these: 3666953 (15.00%) aligned 0 times 16398133 (67.06%) aligned exactly 1 time 4387794 (17.94%) aligned >1 times 85.00% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 7671439 / 20785927 = 0.3691 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 20:57:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.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 20:57:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.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 20:57:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.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 20:57:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:57:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:57:37: 1000000 INFO @ Mon, 12 Aug 2019 20:57:38: 1000000 INFO @ Mon, 12 Aug 2019 20:57:39: 1000000 INFO @ Mon, 12 Aug 2019 20:57:45: 2000000 INFO @ Mon, 12 Aug 2019 20:57:46: 2000000 INFO @ Mon, 12 Aug 2019 20:57:47: 2000000 INFO @ Mon, 12 Aug 2019 20:57:54: 3000000 INFO @ Mon, 12 Aug 2019 20:57:54: 3000000 INFO @ Mon, 12 Aug 2019 20:57:55: 3000000 INFO @ Mon, 12 Aug 2019 20:58:02: 4000000 INFO @ Mon, 12 Aug 2019 20:58:03: 4000000 INFO @ Mon, 12 Aug 2019 20:58:04: 4000000 INFO @ Mon, 12 Aug 2019 20:58:10: 5000000 INFO @ Mon, 12 Aug 2019 20:58:11: 5000000 INFO @ Mon, 12 Aug 2019 20:58:12: 5000000 INFO @ Mon, 12 Aug 2019 20:58:18: 6000000 INFO @ Mon, 12 Aug 2019 20:58:19: 6000000 INFO @ Mon, 12 Aug 2019 20:58:20: 6000000 INFO @ Mon, 12 Aug 2019 20:58:27: 7000000 INFO @ Mon, 12 Aug 2019 20:58:29: 7000000 INFO @ Mon, 12 Aug 2019 20:58:29: 7000000 INFO @ Mon, 12 Aug 2019 20:58:35: 8000000 INFO @ Mon, 12 Aug 2019 20:58:37: 8000000 INFO @ Mon, 12 Aug 2019 20:58:37: 8000000 INFO @ Mon, 12 Aug 2019 20:58:43: 9000000 INFO @ Mon, 12 Aug 2019 20:58:46: 9000000 INFO @ Mon, 12 Aug 2019 20:58:46: 9000000 INFO @ Mon, 12 Aug 2019 20:58:52: 10000000 INFO @ Mon, 12 Aug 2019 20:58:54: 10000000 INFO @ Mon, 12 Aug 2019 20:58:54: 10000000 INFO @ Mon, 12 Aug 2019 20:59:00: 11000000 INFO @ Mon, 12 Aug 2019 20:59:03: 11000000 INFO @ Mon, 12 Aug 2019 20:59:03: 11000000 INFO @ Mon, 12 Aug 2019 20:59:08: 12000000 INFO @ Mon, 12 Aug 2019 20:59:11: 12000000 INFO @ Mon, 12 Aug 2019 20:59:11: 12000000 INFO @ Mon, 12 Aug 2019 20:59:16: 13000000 INFO @ Mon, 12 Aug 2019 20:59:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:59:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:59:17: #1 total tags in treatment: 13114488 INFO @ Mon, 12 Aug 2019 20:59:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:59:17: #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 20:59:18: #1 tags after filtering in treatment: 13114488 INFO @ Mon, 12 Aug 2019 20:59:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:59:18: #1 finished! INFO @ Mon, 12 Aug 2019 20:59:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:59:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:59:20: 13000000 INFO @ Mon, 12 Aug 2019 20:59:20: 13000000 INFO @ Mon, 12 Aug 2019 20:59:20: #2 number of paired peaks: 9538 INFO @ Mon, 12 Aug 2019 20:59:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:59:20: start X-correlation... INFO @ Mon, 12 Aug 2019 20:59:20: end of X-cor INFO @ Mon, 12 Aug 2019 20:59:20: #2 finished! INFO @ Mon, 12 Aug 2019 20:59:20: #2 predicted fragment length is 231 bps INFO @ Mon, 12 Aug 2019 20:59:20: #2 alternative fragment length(s) may be 231 bps INFO @ Mon, 12 Aug 2019 20:59:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.05_model.r INFO @ Mon, 12 Aug 2019 20:59:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:59:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:59:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:59:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:59:21: #1 total tags in treatment: 13114488 INFO @ Mon, 12 Aug 2019 20:59:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:59:21: #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 20:59:21: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:59:21: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:59:21: #1 total tags in treatment: 13114488 INFO @ Mon, 12 Aug 2019 20:59:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:59:21: #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 20:59:21: #1 tags after filtering in treatment: 13114488 INFO @ Mon, 12 Aug 2019 20:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:59:21: #1 finished! INFO @ Mon, 12 Aug 2019 20:59:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:59:21: #1 tags after filtering in treatment: 13114488 INFO @ Mon, 12 Aug 2019 20:59:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:59:21: #1 finished! INFO @ Mon, 12 Aug 2019 20:59:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:59:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:59:23: #2 number of paired peaks: 9538 INFO @ Mon, 12 Aug 2019 20:59:23: start model_add_line... INFO @ Mon, 12 Aug 2019 20:59:23: #2 number of paired peaks: 9538 INFO @ Mon, 12 Aug 2019 20:59:23: start model_add_line... INFO @ Mon, 12 Aug 2019 20:59:23: start X-correlation... INFO @ Mon, 12 Aug 2019 20:59:23: end of X-cor INFO @ Mon, 12 Aug 2019 20:59:23: #2 finished! INFO @ Mon, 12 Aug 2019 20:59:23: #2 predicted fragment length is 231 bps INFO @ Mon, 12 Aug 2019 20:59:23: #2 alternative fragment length(s) may be 231 bps INFO @ Mon, 12 Aug 2019 20:59:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.10_model.r INFO @ Mon, 12 Aug 2019 20:59:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:59:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:59:24: start X-correlation... INFO @ Mon, 12 Aug 2019 20:59:24: end of X-cor INFO @ Mon, 12 Aug 2019 20:59:24: #2 finished! INFO @ Mon, 12 Aug 2019 20:59:24: #2 predicted fragment length is 231 bps INFO @ Mon, 12 Aug 2019 20:59:24: #2 alternative fragment length(s) may be 231 bps INFO @ Mon, 12 Aug 2019 20:59:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.20_model.r INFO @ Mon, 12 Aug 2019 20:59:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:59:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:00:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:00:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.05_summits.bed INFO @ Mon, 12 Aug 2019 21:00:34: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10064 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:00:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:00:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.10_summits.bed INFO @ Mon, 12 Aug 2019 21:00:37: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (8777 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318796/SRX318796.20_summits.bed INFO @ Mon, 12 Aug 2019 21:00:40: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7332 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。