Job ID = 2590806 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,535,480 reads read : 39,070,960 reads written : 19,535,480 reads 0-length : 19,535,480 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: 00:07:50 19535480 reads; of these: 19535480 (100.00%) were unpaired; of these: 3514893 (17.99%) aligned 0 times 11777634 (60.29%) aligned exactly 1 time 4242953 (21.72%) aligned >1 times 82.01% 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 8 files... [bam_rmdupse_core] 7130521 / 16020587 = 0.4451 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 23:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.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 23:31:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:31:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.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 23:31:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:31:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:31:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.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 23:31:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:31:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:31:29: 1000000 INFO @ Mon, 12 Aug 2019 23:31:30: 1000000 INFO @ Mon, 12 Aug 2019 23:31:31: 1000000 INFO @ Mon, 12 Aug 2019 23:31:37: 2000000 INFO @ Mon, 12 Aug 2019 23:31:38: 2000000 INFO @ Mon, 12 Aug 2019 23:31:39: 2000000 INFO @ Mon, 12 Aug 2019 23:31:45: 3000000 INFO @ Mon, 12 Aug 2019 23:31:46: 3000000 INFO @ Mon, 12 Aug 2019 23:31:48: 3000000 INFO @ Mon, 12 Aug 2019 23:31:54: 4000000 INFO @ Mon, 12 Aug 2019 23:31:54: 4000000 INFO @ Mon, 12 Aug 2019 23:31:56: 4000000 INFO @ Mon, 12 Aug 2019 23:32:02: 5000000 INFO @ Mon, 12 Aug 2019 23:32:02: 5000000 INFO @ Mon, 12 Aug 2019 23:32:05: 5000000 INFO @ Mon, 12 Aug 2019 23:32:10: 6000000 INFO @ Mon, 12 Aug 2019 23:32:10: 6000000 INFO @ Mon, 12 Aug 2019 23:32:13: 6000000 INFO @ Mon, 12 Aug 2019 23:32:18: 7000000 INFO @ Mon, 12 Aug 2019 23:32:19: 7000000 INFO @ Mon, 12 Aug 2019 23:32:22: 7000000 INFO @ Mon, 12 Aug 2019 23:32:26: 8000000 INFO @ Mon, 12 Aug 2019 23:32:27: 8000000 INFO @ Mon, 12 Aug 2019 23:32:30: 8000000 INFO @ Mon, 12 Aug 2019 23:32:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:32:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:32:33: #1 total tags in treatment: 8890066 INFO @ Mon, 12 Aug 2019 23:32:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:32:33: #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 23:32:34: #1 tags after filtering in treatment: 8890066 INFO @ Mon, 12 Aug 2019 23:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:32:34: #1 finished! INFO @ Mon, 12 Aug 2019 23:32:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:32:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:32:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:32:34: #1 total tags in treatment: 8890066 INFO @ Mon, 12 Aug 2019 23:32:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:32:34: #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 23:32:34: #1 tags after filtering in treatment: 8890066 INFO @ Mon, 12 Aug 2019 23:32:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:32:34: #1 finished! INFO @ Mon, 12 Aug 2019 23:32:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:32:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:32:35: #2 number of paired peaks: 1746 INFO @ Mon, 12 Aug 2019 23:32:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:32:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:32:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:32:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:32:35: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 23:32:35: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 23:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.05_model.r INFO @ Mon, 12 Aug 2019 23:32:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:32:35: #2 number of paired peaks: 1746 INFO @ Mon, 12 Aug 2019 23:32:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:32:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:32:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:32:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:32:35: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 23:32:35: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 23:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.10_model.r INFO @ Mon, 12 Aug 2019 23:32:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:32:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:32:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:32:37: #1 total tags in treatment: 8890066 INFO @ Mon, 12 Aug 2019 23:32:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:32:37: #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 23:32:37: #1 tags after filtering in treatment: 8890066 INFO @ Mon, 12 Aug 2019 23:32:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:32:37: #1 finished! INFO @ Mon, 12 Aug 2019 23:32:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:32:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:32:38: #2 number of paired peaks: 1746 INFO @ Mon, 12 Aug 2019 23:32:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:32:38: start X-correlation... INFO @ Mon, 12 Aug 2019 23:32:38: end of X-cor INFO @ Mon, 12 Aug 2019 23:32:38: #2 finished! INFO @ Mon, 12 Aug 2019 23:32:38: #2 predicted fragment length is 160 bps INFO @ Mon, 12 Aug 2019 23:32:38: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 12 Aug 2019 23:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.20_model.r INFO @ Mon, 12 Aug 2019 23:32:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:32:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:33:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:33:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:33:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.05_summits.bed INFO @ Mon, 12 Aug 2019 23:33:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6059 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:33:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:33:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:33:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.10_summits.bed INFO @ Mon, 12 Aug 2019 23:33:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3848 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:33:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:33:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011048/SRX5011048.20_summits.bed INFO @ Mon, 12 Aug 2019 23:33:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2056 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。