Job ID = 2590856 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,523,431 reads read : 22,523,431 reads written : 22,523,431 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: 00:07:48 22523431 reads; of these: 22523431 (100.00%) were unpaired; of these: 2606999 (11.57%) aligned 0 times 15869606 (70.46%) aligned exactly 1 time 4046826 (17.97%) aligned >1 times 88.43% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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] 12314378 / 19916432 = 0.6183 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 23:56:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.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 23:56:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.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 23:56:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.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 23:56:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:24: 1000000 INFO @ Mon, 12 Aug 2019 23:56:25: 1000000 INFO @ Mon, 12 Aug 2019 23:56:25: 1000000 INFO @ Mon, 12 Aug 2019 23:56:31: 2000000 INFO @ Mon, 12 Aug 2019 23:56:31: 2000000 INFO @ Mon, 12 Aug 2019 23:56:33: 2000000 INFO @ Mon, 12 Aug 2019 23:56:37: 3000000 INFO @ Mon, 12 Aug 2019 23:56:38: 3000000 INFO @ Mon, 12 Aug 2019 23:56:40: 3000000 INFO @ Mon, 12 Aug 2019 23:56:43: 4000000 INFO @ Mon, 12 Aug 2019 23:56:45: 4000000 INFO @ Mon, 12 Aug 2019 23:56:48: 4000000 INFO @ Mon, 12 Aug 2019 23:56:49: 5000000 INFO @ Mon, 12 Aug 2019 23:56:51: 5000000 INFO @ Mon, 12 Aug 2019 23:56:55: 6000000 INFO @ Mon, 12 Aug 2019 23:56:56: 5000000 INFO @ Mon, 12 Aug 2019 23:56:58: 6000000 INFO @ Mon, 12 Aug 2019 23:57:01: 7000000 INFO @ Mon, 12 Aug 2019 23:57:04: 6000000 INFO @ Mon, 12 Aug 2019 23:57:05: 7000000 INFO @ Mon, 12 Aug 2019 23:57:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:57:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:57:05: #1 total tags in treatment: 7602054 INFO @ Mon, 12 Aug 2019 23:57:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:57:05: #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 23:57:05: #1 tags after filtering in treatment: 7602054 INFO @ Mon, 12 Aug 2019 23:57:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:57:05: #1 finished! INFO @ Mon, 12 Aug 2019 23:57:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:57:06: #2 number of paired peaks: 4841 INFO @ Mon, 12 Aug 2019 23:57:06: start model_add_line... INFO @ Mon, 12 Aug 2019 23:57:07: start X-correlation... INFO @ Mon, 12 Aug 2019 23:57:07: end of X-cor INFO @ Mon, 12 Aug 2019 23:57:07: #2 finished! INFO @ Mon, 12 Aug 2019 23:57:07: #2 predicted fragment length is 170 bps INFO @ Mon, 12 Aug 2019 23:57:07: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 12 Aug 2019 23:57:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.20_model.r INFO @ Mon, 12 Aug 2019 23:57:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:57:09: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:57:09: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:57:09: #1 total tags in treatment: 7602054 INFO @ Mon, 12 Aug 2019 23:57:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:57:09: #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 23:57:09: #1 tags after filtering in treatment: 7602054 INFO @ Mon, 12 Aug 2019 23:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:57:09: #1 finished! INFO @ Mon, 12 Aug 2019 23:57:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:57:10: #2 number of paired peaks: 4841 INFO @ Mon, 12 Aug 2019 23:57:10: start model_add_line... INFO @ Mon, 12 Aug 2019 23:57:10: start X-correlation... INFO @ Mon, 12 Aug 2019 23:57:10: end of X-cor INFO @ Mon, 12 Aug 2019 23:57:10: #2 finished! INFO @ Mon, 12 Aug 2019 23:57:10: #2 predicted fragment length is 170 bps INFO @ Mon, 12 Aug 2019 23:57:10: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 12 Aug 2019 23:57:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.10_model.r INFO @ Mon, 12 Aug 2019 23:57:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:57:12: 7000000 INFO @ Mon, 12 Aug 2019 23:57:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:57:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:57:17: #1 total tags in treatment: 7602054 INFO @ Mon, 12 Aug 2019 23:57:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:57:17: #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 23:57:17: #1 tags after filtering in treatment: 7602054 INFO @ Mon, 12 Aug 2019 23:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:57:17: #1 finished! INFO @ Mon, 12 Aug 2019 23:57:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:57:18: #2 number of paired peaks: 4841 INFO @ Mon, 12 Aug 2019 23:57:18: start model_add_line... INFO @ Mon, 12 Aug 2019 23:57:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:57:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:57:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:57:18: #2 predicted fragment length is 170 bps INFO @ Mon, 12 Aug 2019 23:57:18: #2 alternative fragment length(s) may be 170 bps INFO @ Mon, 12 Aug 2019 23:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.05_model.r INFO @ Mon, 12 Aug 2019 23:57:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:57:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:57:35: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:57:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.20_summits.bed INFO @ Mon, 12 Aug 2019 23:57:44: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (4849 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:57:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:57:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:57:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.10_summits.bed INFO @ Mon, 12 Aug 2019 23:57:47: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (8468 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:57:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:57:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:57:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011090/SRX5011090.05_summits.bed INFO @ Mon, 12 Aug 2019 23:57:57: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (12189 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。