Job ID = 1293895 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,833,522 reads read : 29,833,522 reads written : 29,833,522 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: 00:08:29 29833522 reads; of these: 29833522 (100.00%) were unpaired; of these: 1184178 (3.97%) aligned 0 times 21761287 (72.94%) aligned exactly 1 time 6888057 (23.09%) aligned >1 times 96.03% overall alignment rate Time searching: 00:08:29 Overall time: 00:08:29 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] 5854697 / 28649344 = 0.2044 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 03:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.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 03:25:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:25:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.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 03:25:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:25:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:25:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.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 03:25:29: #1 read tag files... INFO @ Mon, 03 Jun 2019 03:25:29: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 03:25:37: 1000000 INFO @ Mon, 03 Jun 2019 03:25:37: 1000000 INFO @ Mon, 03 Jun 2019 03:25:39: 1000000 INFO @ Mon, 03 Jun 2019 03:25:44: 2000000 INFO @ Mon, 03 Jun 2019 03:25:44: 2000000 INFO @ Mon, 03 Jun 2019 03:25:47: 2000000 INFO @ Mon, 03 Jun 2019 03:25:51: 3000000 INFO @ Mon, 03 Jun 2019 03:25:51: 3000000 INFO @ Mon, 03 Jun 2019 03:25:56: 3000000 INFO @ Mon, 03 Jun 2019 03:25:58: 4000000 INFO @ Mon, 03 Jun 2019 03:25:58: 4000000 INFO @ Mon, 03 Jun 2019 03:26:05: 4000000 INFO @ Mon, 03 Jun 2019 03:26:06: 5000000 INFO @ Mon, 03 Jun 2019 03:26:06: 5000000 INFO @ Mon, 03 Jun 2019 03:26:13: 6000000 INFO @ Mon, 03 Jun 2019 03:26:13: 6000000 INFO @ Mon, 03 Jun 2019 03:26:14: 5000000 INFO @ Mon, 03 Jun 2019 03:26:20: 7000000 INFO @ Mon, 03 Jun 2019 03:26:20: 7000000 INFO @ Mon, 03 Jun 2019 03:26:22: 6000000 INFO @ Mon, 03 Jun 2019 03:26:27: 8000000 INFO @ Mon, 03 Jun 2019 03:26:27: 8000000 INFO @ Mon, 03 Jun 2019 03:26:31: 7000000 INFO @ Mon, 03 Jun 2019 03:26:34: 9000000 INFO @ Mon, 03 Jun 2019 03:26:34: 9000000 INFO @ Mon, 03 Jun 2019 03:26:40: 8000000 INFO @ Mon, 03 Jun 2019 03:26:42: 10000000 INFO @ Mon, 03 Jun 2019 03:26:42: 10000000 INFO @ Mon, 03 Jun 2019 03:26:49: 11000000 INFO @ Mon, 03 Jun 2019 03:26:49: 9000000 INFO @ Mon, 03 Jun 2019 03:26:49: 11000000 INFO @ Mon, 03 Jun 2019 03:26:56: 12000000 INFO @ Mon, 03 Jun 2019 03:26:57: 12000000 INFO @ Mon, 03 Jun 2019 03:26:58: 10000000 INFO @ Mon, 03 Jun 2019 03:27:03: 13000000 INFO @ Mon, 03 Jun 2019 03:27:04: 13000000 INFO @ Mon, 03 Jun 2019 03:27:07: 11000000 INFO @ Mon, 03 Jun 2019 03:27:10: 14000000 INFO @ Mon, 03 Jun 2019 03:27:11: 14000000 INFO @ Mon, 03 Jun 2019 03:27:15: 12000000 INFO @ Mon, 03 Jun 2019 03:27:17: 15000000 INFO @ Mon, 03 Jun 2019 03:27:18: 15000000 INFO @ Mon, 03 Jun 2019 03:27:24: 16000000 INFO @ Mon, 03 Jun 2019 03:27:24: 13000000 INFO @ Mon, 03 Jun 2019 03:27:25: 16000000 INFO @ Mon, 03 Jun 2019 03:27:31: 17000000 INFO @ Mon, 03 Jun 2019 03:27:32: 17000000 INFO @ Mon, 03 Jun 2019 03:27:33: 14000000 INFO @ Mon, 03 Jun 2019 03:27:38: 18000000 INFO @ Mon, 03 Jun 2019 03:27:39: 18000000 INFO @ Mon, 03 Jun 2019 03:27:42: 15000000 INFO @ Mon, 03 Jun 2019 03:27:45: 19000000 INFO @ Mon, 03 Jun 2019 03:27:46: 19000000 INFO @ Mon, 03 Jun 2019 03:27:51: 16000000 INFO @ Mon, 03 Jun 2019 03:27:52: 20000000 INFO @ Mon, 03 Jun 2019 03:27:53: 20000000 INFO @ Mon, 03 Jun 2019 03:27:59: 17000000 INFO @ Mon, 03 Jun 2019 03:27:59: 21000000 INFO @ Mon, 03 Jun 2019 03:28:00: 21000000 INFO @ Mon, 03 Jun 2019 03:28:06: 22000000 INFO @ Mon, 03 Jun 2019 03:28:07: 22000000 INFO @ Mon, 03 Jun 2019 03:28:08: 18000000 INFO @ Mon, 03 Jun 2019 03:28:12: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:28:12: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:28:12: #1 total tags in treatment: 22794647 INFO @ Mon, 03 Jun 2019 03:28:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:28:12: #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 03:28:13: #1 tags after filtering in treatment: 22794647 INFO @ Mon, 03 Jun 2019 03:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:28:13: #1 finished! INFO @ Mon, 03 Jun 2019 03:28:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:28:13: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:28:13: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:28:13: #1 total tags in treatment: 22794647 INFO @ Mon, 03 Jun 2019 03:28:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:28:13: #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 03:28:13: #1 tags after filtering in treatment: 22794647 INFO @ Mon, 03 Jun 2019 03:28:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:28:13: #1 finished! INFO @ Mon, 03 Jun 2019 03:28:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:28:15: #2 number of paired peaks: 518 WARNING @ Mon, 03 Jun 2019 03:28:15: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Mon, 03 Jun 2019 03:28:15: start model_add_line... INFO @ Mon, 03 Jun 2019 03:28:15: start X-correlation... INFO @ Mon, 03 Jun 2019 03:28:15: end of X-cor INFO @ Mon, 03 Jun 2019 03:28:15: #2 finished! INFO @ Mon, 03 Jun 2019 03:28:15: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 03:28:15: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 03 Jun 2019 03:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.10_model.r INFO @ Mon, 03 Jun 2019 03:28:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:28:15: #2 number of paired peaks: 518 WARNING @ Mon, 03 Jun 2019 03:28:15: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Mon, 03 Jun 2019 03:28:15: start model_add_line... INFO @ Mon, 03 Jun 2019 03:28:16: start X-correlation... INFO @ Mon, 03 Jun 2019 03:28:16: end of X-cor INFO @ Mon, 03 Jun 2019 03:28:16: #2 finished! INFO @ Mon, 03 Jun 2019 03:28:16: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 03:28:16: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 03 Jun 2019 03:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.20_model.r INFO @ Mon, 03 Jun 2019 03:28:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:28:17: 19000000 INFO @ Mon, 03 Jun 2019 03:28:24: 20000000 INFO @ Mon, 03 Jun 2019 03:28:32: 21000000 INFO @ Mon, 03 Jun 2019 03:28:41: 22000000 INFO @ Mon, 03 Jun 2019 03:28:47: #1 tag size is determined as 38 bps INFO @ Mon, 03 Jun 2019 03:28:47: #1 tag size = 38 INFO @ Mon, 03 Jun 2019 03:28:47: #1 total tags in treatment: 22794647 INFO @ Mon, 03 Jun 2019 03:28:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 03:28:47: #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 03:28:48: #1 tags after filtering in treatment: 22794647 INFO @ Mon, 03 Jun 2019 03:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 03:28:48: #1 finished! INFO @ Mon, 03 Jun 2019 03:28:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 03:28:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 03:28:50: #2 number of paired peaks: 518 WARNING @ Mon, 03 Jun 2019 03:28:50: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Mon, 03 Jun 2019 03:28:50: start model_add_line... INFO @ Mon, 03 Jun 2019 03:28:50: start X-correlation... INFO @ Mon, 03 Jun 2019 03:28:50: end of X-cor INFO @ Mon, 03 Jun 2019 03:28:50: #2 finished! INFO @ Mon, 03 Jun 2019 03:28:50: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 03:28:50: #2 alternative fragment length(s) may be 4,77 bps INFO @ Mon, 03 Jun 2019 03:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.05_model.r INFO @ Mon, 03 Jun 2019 03:28:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 03:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 03:29:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:29:13: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:29:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.10_peaks.xls INFO @ Mon, 03 Jun 2019 03:29:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:29:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.10_summits.bed INFO @ Mon, 03 Jun 2019 03:29:41: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7202 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:29:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.20_peaks.xls INFO @ Mon, 03 Jun 2019 03:29:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:29:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.20_summits.bed INFO @ Mon, 03 Jun 2019 03:29:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2784 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 03:29:48: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 03:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.05_peaks.xls INFO @ Mon, 03 Jun 2019 03:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 03:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX146992/SRX146992.05_summits.bed INFO @ Mon, 03 Jun 2019 03:30:16: Done! pass1 - making usageList (15 chroms): 8 millis pass2 - checking and writing primary data (17182 records, 4 fields): 22 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。