Job ID = 4178608 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,617,151 reads read : 30,617,151 reads written : 30,617,151 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:49 30617151 reads; of these: 30617151 (100.00%) were unpaired; of these: 4961045 (16.20%) aligned 0 times 20933650 (68.37%) aligned exactly 1 time 4722456 (15.42%) aligned >1 times 83.80% overall alignment rate Time searching: 00:07:50 Overall time: 00:07:50 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] 15469268 / 25656106 = 0.6029 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.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 @ Thu, 05 Dec 2019 13:41:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:41:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:42:04: 1000000 INFO @ Thu, 05 Dec 2019 13:42:12: 2000000 INFO @ Thu, 05 Dec 2019 13:42:21: 3000000 INFO @ Thu, 05 Dec 2019 13:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.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 @ Thu, 05 Dec 2019 13:42:25: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:42:25: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:42:29: 4000000 INFO @ Thu, 05 Dec 2019 13:42:32: 1000000 INFO @ Thu, 05 Dec 2019 13:42:37: 5000000 INFO @ Thu, 05 Dec 2019 13:42:39: 2000000 INFO @ Thu, 05 Dec 2019 13:42:44: 6000000 INFO @ Thu, 05 Dec 2019 13:42:46: 3000000 INFO @ Thu, 05 Dec 2019 13:42:52: 7000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:42:53: 4000000 INFO @ Thu, 05 Dec 2019 13:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.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 @ Thu, 05 Dec 2019 13:42:55: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:42:55: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:43:00: 8000000 INFO @ Thu, 05 Dec 2019 13:43:00: 5000000 INFO @ Thu, 05 Dec 2019 13:43:04: 1000000 INFO @ Thu, 05 Dec 2019 13:43:08: 6000000 INFO @ Thu, 05 Dec 2019 13:43:08: 9000000 INFO @ Thu, 05 Dec 2019 13:43:12: 2000000 INFO @ Thu, 05 Dec 2019 13:43:15: 7000000 INFO @ Thu, 05 Dec 2019 13:43:16: 10000000 INFO @ Thu, 05 Dec 2019 13:43:18: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:43:18: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:43:18: #1 total tags in treatment: 10186838 INFO @ Thu, 05 Dec 2019 13:43:18: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:43:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:43:18: #1 tags after filtering in treatment: 10186838 INFO @ Thu, 05 Dec 2019 13:43:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:43:18: #1 finished! INFO @ Thu, 05 Dec 2019 13:43:18: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:43:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:43:19: #2 number of paired peaks: 1345 INFO @ Thu, 05 Dec 2019 13:43:19: start model_add_line... INFO @ Thu, 05 Dec 2019 13:43:19: start X-correlation... INFO @ Thu, 05 Dec 2019 13:43:19: end of X-cor INFO @ Thu, 05 Dec 2019 13:43:19: #2 finished! INFO @ Thu, 05 Dec 2019 13:43:19: #2 predicted fragment length is 155 bps INFO @ Thu, 05 Dec 2019 13:43:19: #2 alternative fragment length(s) may be 155 bps INFO @ Thu, 05 Dec 2019 13:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.05_model.r INFO @ Thu, 05 Dec 2019 13:43:19: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:43:20: 3000000 INFO @ Thu, 05 Dec 2019 13:43:22: 8000000 INFO @ Thu, 05 Dec 2019 13:43:28: 4000000 INFO @ Thu, 05 Dec 2019 13:43:30: 9000000 INFO @ Thu, 05 Dec 2019 13:43:36: 5000000 INFO @ Thu, 05 Dec 2019 13:43:37: 10000000 INFO @ Thu, 05 Dec 2019 13:43:38: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:43:38: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:43:38: #1 total tags in treatment: 10186838 INFO @ Thu, 05 Dec 2019 13:43:38: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:43:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:43:38: #1 tags after filtering in treatment: 10186838 INFO @ Thu, 05 Dec 2019 13:43:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:43:38: #1 finished! INFO @ Thu, 05 Dec 2019 13:43:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:43:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:43:39: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:43:39: #2 number of paired peaks: 1345 INFO @ Thu, 05 Dec 2019 13:43:39: start model_add_line... INFO @ Thu, 05 Dec 2019 13:43:39: start X-correlation... INFO @ Thu, 05 Dec 2019 13:43:39: end of X-cor INFO @ Thu, 05 Dec 2019 13:43:39: #2 finished! INFO @ Thu, 05 Dec 2019 13:43:39: #2 predicted fragment length is 155 bps INFO @ Thu, 05 Dec 2019 13:43:39: #2 alternative fragment length(s) may be 155 bps INFO @ Thu, 05 Dec 2019 13:43:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.10_model.r INFO @ Thu, 05 Dec 2019 13:43:39: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:43:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:43:43: 6000000 INFO @ Thu, 05 Dec 2019 13:43:50: 7000000 INFO @ Thu, 05 Dec 2019 13:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.05_summits.bed INFO @ Thu, 05 Dec 2019 13:43:51: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7779 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:43:58: 8000000 INFO @ Thu, 05 Dec 2019 13:44:00: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:44:04: 9000000 INFO @ Thu, 05 Dec 2019 13:44:11: 10000000 INFO @ Thu, 05 Dec 2019 13:44:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:44:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:44:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.10_summits.bed INFO @ Thu, 05 Dec 2019 13:44:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5383 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:44:12: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 13:44:12: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 13:44:12: #1 total tags in treatment: 10186838 INFO @ Thu, 05 Dec 2019 13:44:12: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:44:12: #1 tags after filtering in treatment: 10186838 INFO @ Thu, 05 Dec 2019 13:44:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:44:12: #1 finished! INFO @ Thu, 05 Dec 2019 13:44:12: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:44:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:44:13: #2 number of paired peaks: 1345 INFO @ Thu, 05 Dec 2019 13:44:13: start model_add_line... INFO @ Thu, 05 Dec 2019 13:44:13: start X-correlation... INFO @ Thu, 05 Dec 2019 13:44:13: end of X-cor INFO @ Thu, 05 Dec 2019 13:44:13: #2 finished! INFO @ Thu, 05 Dec 2019 13:44:13: #2 predicted fragment length is 155 bps INFO @ Thu, 05 Dec 2019 13:44:13: #2 alternative fragment length(s) may be 155 bps INFO @ Thu, 05 Dec 2019 13:44:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.20_model.r INFO @ Thu, 05 Dec 2019 13:44:13: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:44:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:44:33: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:44:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:44:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:44:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6468484/SRX6468484.20_summits.bed INFO @ Thu, 05 Dec 2019 13:44:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2714 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。