Job ID = 2590809 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,903,026 reads read : 49,806,052 reads written : 24,903,026 reads 0-length : 24,903,026 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: 00:08:30 24903026 reads; of these: 24903026 (100.00%) were unpaired; of these: 6578190 (26.42%) aligned 0 times 13673891 (54.91%) aligned exactly 1 time 4650945 (18.68%) aligned >1 times 73.58% overall alignment rate Time searching: 00:08:30 Overall time: 00:08:30 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] 11142869 / 18324836 = 0.6081 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 23:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.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 23:34:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.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 23:34:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.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 23:34:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:16: 1000000 INFO @ Mon, 12 Aug 2019 23:34:18: 1000000 INFO @ Mon, 12 Aug 2019 23:34:19: 1000000 INFO @ Mon, 12 Aug 2019 23:34:23: 2000000 INFO @ Mon, 12 Aug 2019 23:34:27: 2000000 INFO @ Mon, 12 Aug 2019 23:34:28: 2000000 INFO @ Mon, 12 Aug 2019 23:34:30: 3000000 INFO @ Mon, 12 Aug 2019 23:34:35: 3000000 INFO @ Mon, 12 Aug 2019 23:34:37: 3000000 INFO @ Mon, 12 Aug 2019 23:34:37: 4000000 INFO @ Mon, 12 Aug 2019 23:34:44: 5000000 INFO @ Mon, 12 Aug 2019 23:34:44: 4000000 INFO @ Mon, 12 Aug 2019 23:34:45: 4000000 INFO @ Mon, 12 Aug 2019 23:34:51: 6000000 INFO @ Mon, 12 Aug 2019 23:34:53: 5000000 INFO @ Mon, 12 Aug 2019 23:34:54: 5000000 INFO @ Mon, 12 Aug 2019 23:34:58: 7000000 INFO @ Mon, 12 Aug 2019 23:34:59: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:34:59: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:34:59: #1 total tags in treatment: 7181967 INFO @ Mon, 12 Aug 2019 23:34:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:34:59: #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 23:34:59: #1 tags after filtering in treatment: 7181967 INFO @ Mon, 12 Aug 2019 23:34:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:34:59: #1 finished! INFO @ Mon, 12 Aug 2019 23:34:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:35:00: #2 number of paired peaks: 3404 INFO @ Mon, 12 Aug 2019 23:35:00: start model_add_line... INFO @ Mon, 12 Aug 2019 23:35:00: start X-correlation... INFO @ Mon, 12 Aug 2019 23:35:00: end of X-cor INFO @ Mon, 12 Aug 2019 23:35:00: #2 finished! INFO @ Mon, 12 Aug 2019 23:35:00: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 23:35:00: #2 alternative fragment length(s) may be 134,596 bps INFO @ Mon, 12 Aug 2019 23:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.05_model.r INFO @ Mon, 12 Aug 2019 23:35:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:35:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:35:01: 6000000 INFO @ Mon, 12 Aug 2019 23:35:02: 6000000 INFO @ Mon, 12 Aug 2019 23:35:10: 7000000 INFO @ Mon, 12 Aug 2019 23:35:11: 7000000 INFO @ Mon, 12 Aug 2019 23:35:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:35:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:35:11: #1 total tags in treatment: 7181967 INFO @ Mon, 12 Aug 2019 23:35:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:35:11: #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 23:35:11: #1 tags after filtering in treatment: 7181967 INFO @ Mon, 12 Aug 2019 23:35:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:35:11: #1 finished! INFO @ Mon, 12 Aug 2019 23:35:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:35:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:35:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:35:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:35:12: #1 total tags in treatment: 7181967 INFO @ Mon, 12 Aug 2019 23:35:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:35:12: #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 23:35:12: #1 tags after filtering in treatment: 7181967 INFO @ Mon, 12 Aug 2019 23:35:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:35:12: #1 finished! INFO @ Mon, 12 Aug 2019 23:35:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:35:12: #2 number of paired peaks: 3404 INFO @ Mon, 12 Aug 2019 23:35:12: start model_add_line... INFO @ Mon, 12 Aug 2019 23:35:12: start X-correlation... INFO @ Mon, 12 Aug 2019 23:35:12: end of X-cor INFO @ Mon, 12 Aug 2019 23:35:12: #2 finished! INFO @ Mon, 12 Aug 2019 23:35:12: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 23:35:12: #2 alternative fragment length(s) may be 134,596 bps INFO @ Mon, 12 Aug 2019 23:35:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.10_model.r INFO @ Mon, 12 Aug 2019 23:35:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:35:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:35:13: #2 number of paired peaks: 3404 INFO @ Mon, 12 Aug 2019 23:35:13: start model_add_line... INFO @ Mon, 12 Aug 2019 23:35:13: start X-correlation... INFO @ Mon, 12 Aug 2019 23:35:13: end of X-cor INFO @ Mon, 12 Aug 2019 23:35:13: #2 finished! INFO @ Mon, 12 Aug 2019 23:35:13: #2 predicted fragment length is 134 bps INFO @ Mon, 12 Aug 2019 23:35:13: #2 alternative fragment length(s) may be 134,596 bps INFO @ Mon, 12 Aug 2019 23:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.20_model.r INFO @ Mon, 12 Aug 2019 23:35:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:35:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:35:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.05_summits.bed INFO @ Mon, 12 Aug 2019 23:35:33: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7195 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:35:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:35:36: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.10_summits.bed INFO @ Mon, 12 Aug 2019 23:35:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4831 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011051/SRX5011051.20_summits.bed INFO @ Mon, 12 Aug 2019 23:35:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2840 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。