Job ID = 1295113 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,703,791 reads read : 40,703,791 reads written : 40,703,791 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: 00:07:51 40703791 reads; of these: 40703791 (100.00%) were unpaired; of these: 12083902 (29.69%) aligned 0 times 26061146 (64.03%) aligned exactly 1 time 2558743 (6.29%) aligned >1 times 70.31% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 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] 18764963 / 28619889 = 0.6557 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 12:19:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.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 12:19:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:19:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:19:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.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 12:19:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:19:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:19:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.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 12:19:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:19:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:19:47: 1000000 INFO @ Mon, 03 Jun 2019 12:19:48: 1000000 INFO @ Mon, 03 Jun 2019 12:19:48: 1000000 INFO @ Mon, 03 Jun 2019 12:19:53: 2000000 INFO @ Mon, 03 Jun 2019 12:19:56: 2000000 INFO @ Mon, 03 Jun 2019 12:19:57: 2000000 INFO @ Mon, 03 Jun 2019 12:20:00: 3000000 INFO @ Mon, 03 Jun 2019 12:20:04: 3000000 INFO @ Mon, 03 Jun 2019 12:20:04: 3000000 INFO @ Mon, 03 Jun 2019 12:20:06: 4000000 INFO @ Mon, 03 Jun 2019 12:20:12: 4000000 INFO @ Mon, 03 Jun 2019 12:20:13: 5000000 INFO @ Mon, 03 Jun 2019 12:20:13: 4000000 INFO @ Mon, 03 Jun 2019 12:20:19: 6000000 INFO @ Mon, 03 Jun 2019 12:20:20: 5000000 INFO @ Mon, 03 Jun 2019 12:20:21: 5000000 INFO @ Mon, 03 Jun 2019 12:20:25: 7000000 INFO @ Mon, 03 Jun 2019 12:20:27: 6000000 INFO @ Mon, 03 Jun 2019 12:20:30: 6000000 INFO @ Mon, 03 Jun 2019 12:20:32: 8000000 INFO @ Mon, 03 Jun 2019 12:20:34: 7000000 INFO @ Mon, 03 Jun 2019 12:20:38: 9000000 INFO @ Mon, 03 Jun 2019 12:20:38: 7000000 INFO @ Mon, 03 Jun 2019 12:20:41: 8000000 INFO @ Mon, 03 Jun 2019 12:20:43: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:20:43: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:20:43: #1 total tags in treatment: 9854926 INFO @ Mon, 03 Jun 2019 12:20:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:20:43: #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 12:20:43: #1 tags after filtering in treatment: 9854926 INFO @ Mon, 03 Jun 2019 12:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:20:43: #1 finished! INFO @ Mon, 03 Jun 2019 12:20:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:20:45: #2 number of paired peaks: 3636 INFO @ Mon, 03 Jun 2019 12:20:45: start model_add_line... INFO @ Mon, 03 Jun 2019 12:20:45: start X-correlation... INFO @ Mon, 03 Jun 2019 12:20:45: end of X-cor INFO @ Mon, 03 Jun 2019 12:20:45: #2 finished! INFO @ Mon, 03 Jun 2019 12:20:45: #2 predicted fragment length is 263 bps INFO @ Mon, 03 Jun 2019 12:20:45: #2 alternative fragment length(s) may be 263 bps INFO @ Mon, 03 Jun 2019 12:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.05_model.r INFO @ Mon, 03 Jun 2019 12:20:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:20:46: 8000000 INFO @ Mon, 03 Jun 2019 12:20:47: 9000000 INFO @ Mon, 03 Jun 2019 12:20:53: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:20:53: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:20:53: #1 total tags in treatment: 9854926 INFO @ Mon, 03 Jun 2019 12:20:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:20:53: #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 12:20:53: #1 tags after filtering in treatment: 9854926 INFO @ Mon, 03 Jun 2019 12:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:20:53: #1 finished! INFO @ Mon, 03 Jun 2019 12:20:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:20:54: 9000000 INFO @ Mon, 03 Jun 2019 12:20:54: #2 number of paired peaks: 3636 INFO @ Mon, 03 Jun 2019 12:20:54: start model_add_line... INFO @ Mon, 03 Jun 2019 12:20:55: start X-correlation... INFO @ Mon, 03 Jun 2019 12:20:55: end of X-cor INFO @ Mon, 03 Jun 2019 12:20:55: #2 finished! INFO @ Mon, 03 Jun 2019 12:20:55: #2 predicted fragment length is 263 bps INFO @ Mon, 03 Jun 2019 12:20:55: #2 alternative fragment length(s) may be 263 bps INFO @ Mon, 03 Jun 2019 12:20:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.20_model.r INFO @ Mon, 03 Jun 2019 12:20:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:20:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:21:01: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 12:21:01: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 12:21:01: #1 total tags in treatment: 9854926 INFO @ Mon, 03 Jun 2019 12:21:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:21:01: #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 12:21:01: #1 tags after filtering in treatment: 9854926 INFO @ Mon, 03 Jun 2019 12:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 12:21:01: #1 finished! INFO @ Mon, 03 Jun 2019 12:21:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:21:03: #2 number of paired peaks: 3636 INFO @ Mon, 03 Jun 2019 12:21:03: start model_add_line... INFO @ Mon, 03 Jun 2019 12:21:03: start X-correlation... INFO @ Mon, 03 Jun 2019 12:21:03: end of X-cor INFO @ Mon, 03 Jun 2019 12:21:03: #2 finished! INFO @ Mon, 03 Jun 2019 12:21:03: #2 predicted fragment length is 263 bps INFO @ Mon, 03 Jun 2019 12:21:03: #2 alternative fragment length(s) may be 263 bps INFO @ Mon, 03 Jun 2019 12:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.10_model.r INFO @ Mon, 03 Jun 2019 12:21:03: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:21:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:21:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.05_summits.bed INFO @ Mon, 03 Jun 2019 12:21:37: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (13949 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:21:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.20_summits.bed INFO @ Mon, 03 Jun 2019 12:21:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5304 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:21:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:21:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:21:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX319055/SRX319055.10_summits.bed INFO @ Mon, 03 Jun 2019 12:21:59: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (9711 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。