Job ID = 1293909 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,545,230 reads read : 21,545,230 reads written : 21,545,230 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:07:49 21545230 reads; of these: 21545230 (100.00%) were unpaired; of these: 741855 (3.44%) aligned 0 times 14825116 (68.81%) aligned exactly 1 time 5978259 (27.75%) aligned >1 times 96.56% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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] 5062417 / 20803375 = 0.2433 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, 03 Jun 2019 03:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.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, 03 Jun 2019 03:19:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:19:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.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, 03 Jun 2019 03:19:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:19:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:19:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.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, 03 Jun 2019 03:19:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:19:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:19:54: 1000000 INFO @ Mon, 03 Jun 2019 03:19:55: 1000000 INFO @ Mon, 03 Jun 2019 03:19:56: 1000000 INFO @ Mon, 03 Jun 2019 03:20:02: 2000000 INFO @ Mon, 03 Jun 2019 03:20:04: 2000000 INFO @ Mon, 03 Jun 2019 03:20:07: 2000000 INFO @ Mon, 03 Jun 2019 03:20:09: 3000000 INFO @ Mon, 03 Jun 2019 03:20:12: 3000000 INFO @ Mon, 03 Jun 2019 03:20:17: 4000000 INFO @ Mon, 03 Jun 2019 03:20:17: 3000000 INFO @ Mon, 03 Jun 2019 03:20:21: 4000000 INFO @ Mon, 03 Jun 2019 03:20:25: 5000000 INFO @ Mon, 03 Jun 2019 03:20:28: 4000000 INFO @ Mon, 03 Jun 2019 03:20:30: 5000000 INFO @ Mon, 03 Jun 2019 03:20:33: 6000000 INFO @ Mon, 03 Jun 2019 03:20:38: 6000000 INFO @ Mon, 03 Jun 2019 03:20:39: 5000000 INFO @ Mon, 03 Jun 2019 03:20:40: 7000000 INFO @ Mon, 03 Jun 2019 03:20:47: 7000000 INFO @ Mon, 03 Jun 2019 03:20:49: 8000000 INFO @ Mon, 03 Jun 2019 03:20:51: 6000000 INFO @ Mon, 03 Jun 2019 03:20:56: 8000000 INFO @ Mon, 03 Jun 2019 03:20:56: 9000000 INFO @ Mon, 03 Jun 2019 03:21:01: 7000000 INFO @ Mon, 03 Jun 2019 03:21:04: 10000000 INFO @ Mon, 03 Jun 2019 03:21:05: 9000000 INFO @ Mon, 03 Jun 2019 03:21:12: 11000000 INFO @ Mon, 03 Jun 2019 03:21:12: 8000000 INFO @ Mon, 03 Jun 2019 03:21:13: 10000000 INFO @ Mon, 03 Jun 2019 03:21:19: 12000000 INFO @ Mon, 03 Jun 2019 03:21:22: 11000000 INFO @ Mon, 03 Jun 2019 03:21:22: 9000000 INFO @ Mon, 03 Jun 2019 03:21:27: 13000000 INFO @ Mon, 03 Jun 2019 03:21:30: 12000000 INFO @ Mon, 03 Jun 2019 03:21:33: 10000000 INFO @ Mon, 03 Jun 2019 03:21:35: 14000000 INFO @ Mon, 03 Jun 2019 03:21:39: 13000000 INFO @ Mon, 03 Jun 2019 03:21:42: 15000000 INFO @ Mon, 03 Jun 2019 03:21:43: 11000000 INFO @ Mon, 03 Jun 2019 03:21:48: 14000000 INFO @ Mon, 03 Jun 2019 03:21:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:21:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:21:48: #1 total tags in treatment: 15740958 INFO @ Mon, 03 Jun 2019 03:21:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:21:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:21:48: #1 tags after filtering in treatment: 15740958 INFO @ Mon, 03 Jun 2019 03:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:21:48: #1 finished! INFO @ Mon, 03 Jun 2019 03:21:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:21:50: #2 number of paired peaks: 2555 INFO @ Mon, 03 Jun 2019 03:21:50: start model_add_line... INFO @ Mon, 03 Jun 2019 03:21:50: start X-correlation... INFO @ Mon, 03 Jun 2019 03:21:50: end of X-cor INFO @ Mon, 03 Jun 2019 03:21:50: #2 finished! INFO @ Mon, 03 Jun 2019 03:21:50: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 03:21:50: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 03 Jun 2019 03:21:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.10_model.r INFO @ Mon, 03 Jun 2019 03:21:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:21:53: 12000000 INFO @ Mon, 03 Jun 2019 03:21:56: 15000000 INFO @ Mon, 03 Jun 2019 03:22:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:22:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:22:03: #1 total tags in treatment: 15740958 INFO @ Mon, 03 Jun 2019 03:22:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:22:03: #1 tags after filtering in treatment: 15740958 INFO @ Mon, 03 Jun 2019 03:22:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:03: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:03: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:03: 13000000 INFO @ Mon, 03 Jun 2019 03:22:05: #2 number of paired peaks: 2555 INFO @ Mon, 03 Jun 2019 03:22:05: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:05: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:05: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:05: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:05: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 03:22:05: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 03 Jun 2019 03:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.20_model.r INFO @ Mon, 03 Jun 2019 03:22:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:13: 14000000 INFO @ Mon, 03 Jun 2019 03:22:23: 15000000 INFO @ Mon, 03 Jun 2019 03:22:31: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 03:22:31: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 03:22:31: #1 total tags in treatment: 15740958 INFO @ Mon, 03 Jun 2019 03:22:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:22:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 03:22:31: #1 tags after filtering in treatment: 15740958 INFO @ Mon, 03 Jun 2019 03:22:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:22:31: #1 finished! INFO @ Mon, 03 Jun 2019 03:22:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:22:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:22:33: #2 number of paired peaks: 2555 INFO @ Mon, 03 Jun 2019 03:22:33: start model_add_line... INFO @ Mon, 03 Jun 2019 03:22:33: start X-correlation... INFO @ Mon, 03 Jun 2019 03:22:33: end of X-cor INFO @ Mon, 03 Jun 2019 03:22:33: #2 finished! INFO @ Mon, 03 Jun 2019 03:22:33: #2 predicted fragment length is 160 bps INFO @ Mon, 03 Jun 2019 03:22:33: #2 alternative fragment length(s) may be 160 bps INFO @ Mon, 03 Jun 2019 03:22:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.05_model.r INFO @ Mon, 03 Jun 2019 03:22:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:22:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:22:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:22:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.10_summits.bed INFO @ Mon, 03 Jun 2019 03:23:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7716 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.20_summits.bed INFO @ Mon, 03 Jun 2019 03:23:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5411 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:23:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:23:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:23:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:23:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX147003/SRX147003.05_summits.bed INFO @ Mon, 03 Jun 2019 03:23:45: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10119 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。