Job ID = 1294986 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,285,409 reads read : 16,285,409 reads written : 16,285,409 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: 00:04:41 16285409 reads; of these: 16285409 (100.00%) were unpaired; of these: 991580 (6.09%) aligned 0 times 13069262 (80.25%) aligned exactly 1 time 2224567 (13.66%) aligned >1 times 93.91% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 2400119 / 15293829 = 0.1569 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 11:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.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 11:19:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:19:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.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 11:19:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:19:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.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 11:19:22: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:19:22: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:19:29: 1000000 INFO @ Mon, 03 Jun 2019 11:19:30: 1000000 INFO @ Mon, 03 Jun 2019 11:19:31: 1000000 INFO @ Mon, 03 Jun 2019 11:19:36: 2000000 INFO @ Mon, 03 Jun 2019 11:19:38: 2000000 INFO @ Mon, 03 Jun 2019 11:19:39: 2000000 INFO @ Mon, 03 Jun 2019 11:19:43: 3000000 INFO @ Mon, 03 Jun 2019 11:19:45: 3000000 INFO @ Mon, 03 Jun 2019 11:19:47: 3000000 INFO @ Mon, 03 Jun 2019 11:19:50: 4000000 INFO @ Mon, 03 Jun 2019 11:19:53: 4000000 INFO @ Mon, 03 Jun 2019 11:19:56: 4000000 INFO @ Mon, 03 Jun 2019 11:19:57: 5000000 INFO @ Mon, 03 Jun 2019 11:20:00: 5000000 INFO @ Mon, 03 Jun 2019 11:20:04: 6000000 INFO @ Mon, 03 Jun 2019 11:20:04: 5000000 INFO @ Mon, 03 Jun 2019 11:20:08: 6000000 INFO @ Mon, 03 Jun 2019 11:20:10: 7000000 INFO @ Mon, 03 Jun 2019 11:20:12: 6000000 INFO @ Mon, 03 Jun 2019 11:20:15: 7000000 INFO @ Mon, 03 Jun 2019 11:20:17: 8000000 INFO @ Mon, 03 Jun 2019 11:20:21: 7000000 INFO @ Mon, 03 Jun 2019 11:20:22: 8000000 INFO @ Mon, 03 Jun 2019 11:20:24: 9000000 INFO @ Mon, 03 Jun 2019 11:20:29: 8000000 INFO @ Mon, 03 Jun 2019 11:20:30: 9000000 INFO @ Mon, 03 Jun 2019 11:20:31: 10000000 INFO @ Mon, 03 Jun 2019 11:20:37: 10000000 INFO @ Mon, 03 Jun 2019 11:20:37: 9000000 INFO @ Mon, 03 Jun 2019 11:20:38: 11000000 INFO @ Mon, 03 Jun 2019 11:20:44: 12000000 INFO @ Mon, 03 Jun 2019 11:20:44: 11000000 INFO @ Mon, 03 Jun 2019 11:20:45: 10000000 INFO @ Mon, 03 Jun 2019 11:20:51: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:20:51: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:20:51: #1 total tags in treatment: 12893710 INFO @ Mon, 03 Jun 2019 11:20:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:20:51: #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 11:20:51: #1 tags after filtering in treatment: 12893710 INFO @ Mon, 03 Jun 2019 11:20:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:20:51: #1 finished! INFO @ Mon, 03 Jun 2019 11:20:51: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:20:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:20:52: 12000000 INFO @ Mon, 03 Jun 2019 11:20:52: #2 number of paired peaks: 3464 INFO @ Mon, 03 Jun 2019 11:20:52: start model_add_line... INFO @ Mon, 03 Jun 2019 11:20:53: start X-correlation... INFO @ Mon, 03 Jun 2019 11:20:53: end of X-cor INFO @ Mon, 03 Jun 2019 11:20:53: #2 finished! INFO @ Mon, 03 Jun 2019 11:20:53: #2 predicted fragment length is 251 bps INFO @ Mon, 03 Jun 2019 11:20:53: #2 alternative fragment length(s) may be 3,251 bps INFO @ Mon, 03 Jun 2019 11:20:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.10_model.r INFO @ Mon, 03 Jun 2019 11:20:53: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:20:54: 11000000 INFO @ Mon, 03 Jun 2019 11:20:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:20:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:20:59: #1 total tags in treatment: 12893710 INFO @ Mon, 03 Jun 2019 11:20:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:20:59: #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 11:20:59: #1 tags after filtering in treatment: 12893710 INFO @ Mon, 03 Jun 2019 11:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:20:59: #1 finished! INFO @ Mon, 03 Jun 2019 11:20:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:21:00: #2 number of paired peaks: 3464 INFO @ Mon, 03 Jun 2019 11:21:00: start model_add_line... INFO @ Mon, 03 Jun 2019 11:21:01: start X-correlation... INFO @ Mon, 03 Jun 2019 11:21:01: end of X-cor INFO @ Mon, 03 Jun 2019 11:21:01: #2 finished! INFO @ Mon, 03 Jun 2019 11:21:01: #2 predicted fragment length is 251 bps INFO @ Mon, 03 Jun 2019 11:21:01: #2 alternative fragment length(s) may be 3,251 bps INFO @ Mon, 03 Jun 2019 11:21:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.20_model.r INFO @ Mon, 03 Jun 2019 11:21:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:21:02: 12000000 INFO @ Mon, 03 Jun 2019 11:21:10: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:21:10: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:21:10: #1 total tags in treatment: 12893710 INFO @ Mon, 03 Jun 2019 11:21:10: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:21:10: #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 11:21:10: #1 tags after filtering in treatment: 12893710 INFO @ Mon, 03 Jun 2019 11:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:21:10: #1 finished! INFO @ Mon, 03 Jun 2019 11:21:10: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:21:12: #2 number of paired peaks: 3464 INFO @ Mon, 03 Jun 2019 11:21:12: start model_add_line... INFO @ Mon, 03 Jun 2019 11:21:12: start X-correlation... INFO @ Mon, 03 Jun 2019 11:21:12: end of X-cor INFO @ Mon, 03 Jun 2019 11:21:12: #2 finished! INFO @ Mon, 03 Jun 2019 11:21:12: #2 predicted fragment length is 251 bps INFO @ Mon, 03 Jun 2019 11:21:12: #2 alternative fragment length(s) may be 3,251 bps INFO @ Mon, 03 Jun 2019 11:21:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.05_model.r INFO @ Mon, 03 Jun 2019 11:21:12: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:21:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:21:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:21:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:21:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:21:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:21:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.10_summits.bed INFO @ Mon, 03 Jun 2019 11:21:54: Done! INFO @ Mon, 03 Jun 2019 11:21:54: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4766 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:22:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:22:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:22:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.20_summits.bed INFO @ Mon, 03 Jun 2019 11:22:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1670 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:22:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:22:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:22:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288041/SRX288041.05_summits.bed INFO @ Mon, 03 Jun 2019 11:22:16: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7807 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。