Job ID = 2590593 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,390,258 reads read : 36,780,516 reads written : 18,390,258 reads 0-length : 18,390,258 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: 00:06:15 18390258 reads; of these: 18390258 (100.00%) were unpaired; of these: 365858 (1.99%) aligned 0 times 14577208 (79.27%) aligned exactly 1 time 3447192 (18.74%) aligned >1 times 98.01% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 5390302 / 18024400 = 0.2991 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 22:45:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.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 22:45:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.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 22:45:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.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 22:45:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:45:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:45:09: 1000000 INFO @ Mon, 12 Aug 2019 22:45:10: 1000000 INFO @ Mon, 12 Aug 2019 22:45:13: 1000000 INFO @ Mon, 12 Aug 2019 22:45:16: 2000000 INFO @ Mon, 12 Aug 2019 22:45:17: 2000000 INFO @ Mon, 12 Aug 2019 22:45:21: 2000000 INFO @ Mon, 12 Aug 2019 22:45:23: 3000000 INFO @ Mon, 12 Aug 2019 22:45:24: 3000000 INFO @ Mon, 12 Aug 2019 22:45:30: 3000000 INFO @ Mon, 12 Aug 2019 22:45:30: 4000000 INFO @ Mon, 12 Aug 2019 22:45:31: 4000000 INFO @ Mon, 12 Aug 2019 22:45:37: 5000000 INFO @ Mon, 12 Aug 2019 22:45:38: 5000000 INFO @ Mon, 12 Aug 2019 22:45:38: 4000000 INFO @ Mon, 12 Aug 2019 22:45:44: 6000000 INFO @ Mon, 12 Aug 2019 22:45:45: 6000000 INFO @ Mon, 12 Aug 2019 22:45:47: 5000000 INFO @ Mon, 12 Aug 2019 22:45:51: 7000000 INFO @ Mon, 12 Aug 2019 22:45:52: 7000000 INFO @ Mon, 12 Aug 2019 22:45:56: 6000000 INFO @ Mon, 12 Aug 2019 22:45:58: 8000000 INFO @ Mon, 12 Aug 2019 22:45:59: 8000000 INFO @ Mon, 12 Aug 2019 22:46:04: 7000000 INFO @ Mon, 12 Aug 2019 22:46:05: 9000000 INFO @ Mon, 12 Aug 2019 22:46:06: 9000000 INFO @ Mon, 12 Aug 2019 22:46:12: 10000000 INFO @ Mon, 12 Aug 2019 22:46:13: 8000000 INFO @ Mon, 12 Aug 2019 22:46:14: 10000000 INFO @ Mon, 12 Aug 2019 22:46:19: 11000000 INFO @ Mon, 12 Aug 2019 22:46:21: 11000000 INFO @ Mon, 12 Aug 2019 22:46:21: 9000000 INFO @ Mon, 12 Aug 2019 22:46:26: 12000000 INFO @ Mon, 12 Aug 2019 22:46:28: 12000000 INFO @ Mon, 12 Aug 2019 22:46:30: 10000000 INFO @ Mon, 12 Aug 2019 22:46:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:46:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:46:31: #1 total tags in treatment: 12634098 INFO @ Mon, 12 Aug 2019 22:46:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:46:31: #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 22:46:31: #1 tags after filtering in treatment: 12634098 INFO @ Mon, 12 Aug 2019 22:46:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:46:31: #1 finished! INFO @ Mon, 12 Aug 2019 22:46:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:46:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:46:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:46:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:46:32: #1 total tags in treatment: 12634098 INFO @ Mon, 12 Aug 2019 22:46:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:46:32: #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 22:46:33: #1 tags after filtering in treatment: 12634098 INFO @ Mon, 12 Aug 2019 22:46:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:46:33: #1 finished! INFO @ Mon, 12 Aug 2019 22:46:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:46:33: #2 number of paired peaks: 8538 INFO @ Mon, 12 Aug 2019 22:46:33: start model_add_line... INFO @ Mon, 12 Aug 2019 22:46:33: start X-correlation... INFO @ Mon, 12 Aug 2019 22:46:33: end of X-cor INFO @ Mon, 12 Aug 2019 22:46:33: #2 finished! INFO @ Mon, 12 Aug 2019 22:46:33: #2 predicted fragment length is 142 bps INFO @ Mon, 12 Aug 2019 22:46:33: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 12 Aug 2019 22:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.05_model.r INFO @ Mon, 12 Aug 2019 22:46:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:46:35: #2 number of paired peaks: 8538 INFO @ Mon, 12 Aug 2019 22:46:35: start model_add_line... INFO @ Mon, 12 Aug 2019 22:46:35: start X-correlation... INFO @ Mon, 12 Aug 2019 22:46:35: end of X-cor INFO @ Mon, 12 Aug 2019 22:46:35: #2 finished! INFO @ Mon, 12 Aug 2019 22:46:35: #2 predicted fragment length is 142 bps INFO @ Mon, 12 Aug 2019 22:46:35: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 12 Aug 2019 22:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.10_model.r INFO @ Mon, 12 Aug 2019 22:46:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:46:38: 11000000 INFO @ Mon, 12 Aug 2019 22:46:47: 12000000 INFO @ Mon, 12 Aug 2019 22:46:52: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:46:52: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:46:52: #1 total tags in treatment: 12634098 INFO @ Mon, 12 Aug 2019 22:46:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:46:52: #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 22:46:52: #1 tags after filtering in treatment: 12634098 INFO @ Mon, 12 Aug 2019 22:46:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:46:52: #1 finished! INFO @ Mon, 12 Aug 2019 22:46:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:46:54: #2 number of paired peaks: 8538 INFO @ Mon, 12 Aug 2019 22:46:54: start model_add_line... INFO @ Mon, 12 Aug 2019 22:46:54: start X-correlation... INFO @ Mon, 12 Aug 2019 22:46:54: end of X-cor INFO @ Mon, 12 Aug 2019 22:46:54: #2 finished! INFO @ Mon, 12 Aug 2019 22:46:54: #2 predicted fragment length is 142 bps INFO @ Mon, 12 Aug 2019 22:46:54: #2 alternative fragment length(s) may be 142 bps INFO @ Mon, 12 Aug 2019 22:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.20_model.r INFO @ Mon, 12 Aug 2019 22:46:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:47:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.05_summits.bed INFO @ Mon, 12 Aug 2019 22:47:31: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (9244 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.10_summits.bed INFO @ Mon, 12 Aug 2019 22:47:32: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (8215 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:47:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:47:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:47:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:47:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923182/SRX4923182.20_summits.bed INFO @ Mon, 12 Aug 2019 22:47:52: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6827 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。