Job ID = 1293272 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,793,011 reads read : 25,793,011 reads written : 25,793,011 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:47 25793011 reads; of these: 25793011 (100.00%) were unpaired; of these: 888385 (3.44%) aligned 0 times 22456113 (87.06%) aligned exactly 1 time 2448513 (9.49%) aligned >1 times 96.56% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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 8 files... [bam_rmdupse_core] 7488405 / 24904626 = 0.3007 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 @ Sun, 02 Jun 2019 22:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.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 @ Sun, 02 Jun 2019 22:55:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:55:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.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 @ Sun, 02 Jun 2019 22:55:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:55:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.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 @ Sun, 02 Jun 2019 22:55:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:55:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:55:56: 1000000 INFO @ Sun, 02 Jun 2019 22:55:56: 1000000 INFO @ Sun, 02 Jun 2019 22:55:57: 1000000 INFO @ Sun, 02 Jun 2019 22:56:02: 2000000 INFO @ Sun, 02 Jun 2019 22:56:03: 2000000 INFO @ Sun, 02 Jun 2019 22:56:05: 2000000 INFO @ Sun, 02 Jun 2019 22:56:08: 3000000 INFO @ Sun, 02 Jun 2019 22:56:10: 3000000 INFO @ Sun, 02 Jun 2019 22:56:14: 3000000 INFO @ Sun, 02 Jun 2019 22:56:14: 4000000 INFO @ Sun, 02 Jun 2019 22:56:17: 4000000 INFO @ Sun, 02 Jun 2019 22:56:20: 5000000 INFO @ Sun, 02 Jun 2019 22:56:22: 4000000 INFO @ Sun, 02 Jun 2019 22:56:24: 5000000 INFO @ Sun, 02 Jun 2019 22:56:26: 6000000 INFO @ Sun, 02 Jun 2019 22:56:30: 5000000 INFO @ Sun, 02 Jun 2019 22:56:30: 6000000 INFO @ Sun, 02 Jun 2019 22:56:32: 7000000 INFO @ Sun, 02 Jun 2019 22:56:37: 7000000 INFO @ Sun, 02 Jun 2019 22:56:38: 6000000 INFO @ Sun, 02 Jun 2019 22:56:38: 8000000 INFO @ Sun, 02 Jun 2019 22:56:43: 8000000 INFO @ Sun, 02 Jun 2019 22:56:44: 9000000 INFO @ Sun, 02 Jun 2019 22:56:45: 7000000 INFO @ Sun, 02 Jun 2019 22:56:50: 9000000 INFO @ Sun, 02 Jun 2019 22:56:50: 10000000 INFO @ Sun, 02 Jun 2019 22:56:53: 8000000 INFO @ Sun, 02 Jun 2019 22:56:56: 11000000 INFO @ Sun, 02 Jun 2019 22:56:56: 10000000 INFO @ Sun, 02 Jun 2019 22:57:00: 9000000 INFO @ Sun, 02 Jun 2019 22:57:02: 12000000 INFO @ Sun, 02 Jun 2019 22:57:03: 11000000 INFO @ Sun, 02 Jun 2019 22:57:08: 13000000 INFO @ Sun, 02 Jun 2019 22:57:08: 10000000 INFO @ Sun, 02 Jun 2019 22:57:09: 12000000 INFO @ Sun, 02 Jun 2019 22:57:14: 14000000 INFO @ Sun, 02 Jun 2019 22:57:15: 11000000 INFO @ Sun, 02 Jun 2019 22:57:16: 13000000 INFO @ Sun, 02 Jun 2019 22:57:20: 15000000 INFO @ Sun, 02 Jun 2019 22:57:22: 14000000 INFO @ Sun, 02 Jun 2019 22:57:23: 12000000 INFO @ Sun, 02 Jun 2019 22:57:26: 16000000 INFO @ Sun, 02 Jun 2019 22:57:29: 15000000 INFO @ Sun, 02 Jun 2019 22:57:30: 13000000 INFO @ Sun, 02 Jun 2019 22:57:32: 17000000 INFO @ Sun, 02 Jun 2019 22:57:35: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:57:35: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:57:35: #1 total tags in treatment: 17416221 INFO @ Sun, 02 Jun 2019 22:57:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:57:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:57:35: #1 tags after filtering in treatment: 17416220 INFO @ Sun, 02 Jun 2019 22:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:57:35: #1 finished! INFO @ Sun, 02 Jun 2019 22:57:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:57:36: 16000000 INFO @ Sun, 02 Jun 2019 22:57:37: #2 number of paired peaks: 2964 INFO @ Sun, 02 Jun 2019 22:57:37: start model_add_line... INFO @ Sun, 02 Jun 2019 22:57:37: start X-correlation... INFO @ Sun, 02 Jun 2019 22:57:37: end of X-cor INFO @ Sun, 02 Jun 2019 22:57:37: #2 finished! INFO @ Sun, 02 Jun 2019 22:57:37: #2 predicted fragment length is 176 bps INFO @ Sun, 02 Jun 2019 22:57:37: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 02 Jun 2019 22:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.05_model.r INFO @ Sun, 02 Jun 2019 22:57:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:57:38: 14000000 INFO @ Sun, 02 Jun 2019 22:57:42: 17000000 INFO @ Sun, 02 Jun 2019 22:57:45: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:57:45: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:57:45: #1 total tags in treatment: 17416221 INFO @ Sun, 02 Jun 2019 22:57:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:57:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:57:45: #1 tags after filtering in treatment: 17416220 INFO @ Sun, 02 Jun 2019 22:57:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:57:45: #1 finished! INFO @ Sun, 02 Jun 2019 22:57:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:57:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:57:46: 15000000 INFO @ Sun, 02 Jun 2019 22:57:47: #2 number of paired peaks: 2964 INFO @ Sun, 02 Jun 2019 22:57:47: start model_add_line... INFO @ Sun, 02 Jun 2019 22:57:47: start X-correlation... INFO @ Sun, 02 Jun 2019 22:57:48: end of X-cor INFO @ Sun, 02 Jun 2019 22:57:48: #2 finished! INFO @ Sun, 02 Jun 2019 22:57:48: #2 predicted fragment length is 176 bps INFO @ Sun, 02 Jun 2019 22:57:48: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 02 Jun 2019 22:57:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.20_model.r INFO @ Sun, 02 Jun 2019 22:57:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:57:53: 16000000 INFO @ Sun, 02 Jun 2019 22:58:01: 17000000 INFO @ Sun, 02 Jun 2019 22:58:04: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:58:04: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:58:04: #1 total tags in treatment: 17416221 INFO @ Sun, 02 Jun 2019 22:58:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:58:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:58:04: #1 tags after filtering in treatment: 17416220 INFO @ Sun, 02 Jun 2019 22:58:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:58:04: #1 finished! INFO @ Sun, 02 Jun 2019 22:58:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:58:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:58:06: #2 number of paired peaks: 2964 INFO @ Sun, 02 Jun 2019 22:58:06: start model_add_line... INFO @ Sun, 02 Jun 2019 22:58:06: start X-correlation... INFO @ Sun, 02 Jun 2019 22:58:06: end of X-cor INFO @ Sun, 02 Jun 2019 22:58:06: #2 finished! INFO @ Sun, 02 Jun 2019 22:58:06: #2 predicted fragment length is 176 bps INFO @ Sun, 02 Jun 2019 22:58:06: #2 alternative fragment length(s) may be 176 bps INFO @ Sun, 02 Jun 2019 22:58:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.10_model.r INFO @ Sun, 02 Jun 2019 22:58:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:58:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:58:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:58:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.05_summits.bed INFO @ Sun, 02 Jun 2019 22:58:55: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (14151 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:59:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.20_summits.bed INFO @ Sun, 02 Jun 2019 22:59:04: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (4393 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:59:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:59:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:59:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011411/ERX011411.10_summits.bed INFO @ Sun, 02 Jun 2019 22:59:23: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (9283 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。