Job ID = 2590858 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,403,332 reads read : 22,403,332 reads written : 22,403,332 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: 00:05:12 22403332 reads; of these: 22403332 (100.00%) were unpaired; of these: 11432096 (51.03%) aligned 0 times 8554840 (38.19%) aligned exactly 1 time 2416396 (10.79%) aligned >1 times 48.97% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 3542023 / 10971236 = 0.3228 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 23:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.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 23:54:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.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 23:54:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.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 23:54:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:54:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:54:44: 1000000 INFO @ Mon, 12 Aug 2019 23:54:45: 1000000 INFO @ Mon, 12 Aug 2019 23:54:45: 1000000 INFO @ Mon, 12 Aug 2019 23:54:54: 2000000 INFO @ Mon, 12 Aug 2019 23:54:54: 2000000 INFO @ Mon, 12 Aug 2019 23:54:55: 2000000 INFO @ Mon, 12 Aug 2019 23:55:04: 3000000 INFO @ Mon, 12 Aug 2019 23:55:04: 3000000 INFO @ Mon, 12 Aug 2019 23:55:04: 3000000 INFO @ Mon, 12 Aug 2019 23:55:14: 4000000 INFO @ Mon, 12 Aug 2019 23:55:14: 4000000 INFO @ Mon, 12 Aug 2019 23:55:15: 4000000 INFO @ Mon, 12 Aug 2019 23:55:23: 5000000 INFO @ Mon, 12 Aug 2019 23:55:24: 5000000 INFO @ Mon, 12 Aug 2019 23:55:25: 5000000 INFO @ Mon, 12 Aug 2019 23:55:33: 6000000 INFO @ Mon, 12 Aug 2019 23:55:35: 6000000 INFO @ Mon, 12 Aug 2019 23:55:35: 6000000 INFO @ Mon, 12 Aug 2019 23:55:44: 7000000 INFO @ Mon, 12 Aug 2019 23:55:45: 7000000 INFO @ Mon, 12 Aug 2019 23:55:47: 7000000 INFO @ Mon, 12 Aug 2019 23:55:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:55:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:55:49: #1 total tags in treatment: 7429213 INFO @ Mon, 12 Aug 2019 23:55:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:49: #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 23:55:49: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:55:49: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:55:49: #1 total tags in treatment: 7429213 INFO @ Mon, 12 Aug 2019 23:55:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:49: #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 23:55:49: #1 tags after filtering in treatment: 7429213 INFO @ Mon, 12 Aug 2019 23:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:49: #1 tags after filtering in treatment: 7429213 INFO @ Mon, 12 Aug 2019 23:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:50: #2 number of paired peaks: 3460 INFO @ Mon, 12 Aug 2019 23:55:50: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:50: #2 number of paired peaks: 3460 INFO @ Mon, 12 Aug 2019 23:55:50: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:50: #2 predicted fragment length is 183 bps INFO @ Mon, 12 Aug 2019 23:55:50: #2 alternative fragment length(s) may be 183 bps INFO @ Mon, 12 Aug 2019 23:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.20_model.r INFO @ Mon, 12 Aug 2019 23:55:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:55:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:50: #2 predicted fragment length is 183 bps INFO @ Mon, 12 Aug 2019 23:55:50: #2 alternative fragment length(s) may be 183 bps INFO @ Mon, 12 Aug 2019 23:55:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.10_model.r INFO @ Mon, 12 Aug 2019 23:55:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:55:51: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:55:51: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:55:51: #1 total tags in treatment: 7429213 INFO @ Mon, 12 Aug 2019 23:55:51: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:55:51: #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 23:55:51: #1 tags after filtering in treatment: 7429213 INFO @ Mon, 12 Aug 2019 23:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:55:51: #1 finished! INFO @ Mon, 12 Aug 2019 23:55:51: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:55:52: #2 number of paired peaks: 3460 INFO @ Mon, 12 Aug 2019 23:55:52: start model_add_line... INFO @ Mon, 12 Aug 2019 23:55:52: start X-correlation... INFO @ Mon, 12 Aug 2019 23:55:52: end of X-cor INFO @ Mon, 12 Aug 2019 23:55:52: #2 finished! INFO @ Mon, 12 Aug 2019 23:55:52: #2 predicted fragment length is 183 bps INFO @ Mon, 12 Aug 2019 23:55:52: #2 alternative fragment length(s) may be 183 bps INFO @ Mon, 12 Aug 2019 23:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.05_model.r INFO @ Mon, 12 Aug 2019 23:55:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:56:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.20_summits.bed INFO @ Mon, 12 Aug 2019 23:56:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3816 records, 4 fields): 11 millis INFO @ Mon, 12 Aug 2019 23:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.10_peaks.xls CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.10_summits.bed INFO @ Mon, 12 Aug 2019 23:56:26: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6761 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011092/SRX5011092.05_summits.bed INFO @ Mon, 12 Aug 2019 23:56:28: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10078 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。