Job ID = 1293200 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 61,657,199 reads read : 61,657,199 reads written : 61,657,199 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: 00:17:45 61657199 reads; of these: 61657199 (100.00%) were unpaired; of these: 17472910 (28.34%) aligned 0 times 20496467 (33.24%) aligned exactly 1 time 23687822 (38.42%) aligned >1 times 71.66% overall alignment rate Time searching: 00:17:45 Overall time: 00:17:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 26417262 / 44184289 = 0.5979 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 23:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.bam'] # control file = None # effective genome size = 9.00e+07 # 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 23:11:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:11:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.bam'] # control file = None # effective genome size = 9.00e+07 # 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 23:11:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:11:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.bam'] # control file = None # effective genome size = 9.00e+07 # 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 23:11:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 23:11:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 23:11:15: 1000000 INFO @ Sun, 02 Jun 2019 23:11:16: 1000000 INFO @ Sun, 02 Jun 2019 23:11:16: 1000000 INFO @ Sun, 02 Jun 2019 23:11:24: 2000000 INFO @ Sun, 02 Jun 2019 23:11:25: 2000000 INFO @ Sun, 02 Jun 2019 23:11:25: 2000000 INFO @ Sun, 02 Jun 2019 23:11:32: 3000000 INFO @ Sun, 02 Jun 2019 23:11:34: 3000000 INFO @ Sun, 02 Jun 2019 23:11:34: 3000000 INFO @ Sun, 02 Jun 2019 23:11:40: 4000000 INFO @ Sun, 02 Jun 2019 23:11:42: 4000000 INFO @ Sun, 02 Jun 2019 23:11:42: 4000000 INFO @ Sun, 02 Jun 2019 23:11:49: 5000000 INFO @ Sun, 02 Jun 2019 23:11:51: 5000000 INFO @ Sun, 02 Jun 2019 23:11:51: 5000000 INFO @ Sun, 02 Jun 2019 23:11:57: 6000000 INFO @ Sun, 02 Jun 2019 23:12:00: 6000000 INFO @ Sun, 02 Jun 2019 23:12:00: 6000000 INFO @ Sun, 02 Jun 2019 23:12:05: 7000000 INFO @ Sun, 02 Jun 2019 23:12:09: 7000000 INFO @ Sun, 02 Jun 2019 23:12:09: 7000000 INFO @ Sun, 02 Jun 2019 23:12:14: 8000000 INFO @ Sun, 02 Jun 2019 23:12:18: 8000000 INFO @ Sun, 02 Jun 2019 23:12:18: 8000000 INFO @ Sun, 02 Jun 2019 23:12:22: 9000000 INFO @ Sun, 02 Jun 2019 23:12:26: 9000000 INFO @ Sun, 02 Jun 2019 23:12:26: 9000000 INFO @ Sun, 02 Jun 2019 23:12:30: 10000000 INFO @ Sun, 02 Jun 2019 23:12:35: 10000000 INFO @ Sun, 02 Jun 2019 23:12:35: 10000000 INFO @ Sun, 02 Jun 2019 23:12:38: 11000000 INFO @ Sun, 02 Jun 2019 23:12:43: 11000000 INFO @ Sun, 02 Jun 2019 23:12:43: 11000000 INFO @ Sun, 02 Jun 2019 23:12:47: 12000000 INFO @ Sun, 02 Jun 2019 23:12:50: 12000000 INFO @ Sun, 02 Jun 2019 23:12:51: 12000000 INFO @ Sun, 02 Jun 2019 23:12:55: 13000000 INFO @ Sun, 02 Jun 2019 23:12:57: 13000000 INFO @ Sun, 02 Jun 2019 23:13:00: 13000000 INFO @ Sun, 02 Jun 2019 23:13:03: 14000000 INFO @ Sun, 02 Jun 2019 23:13:05: 14000000 INFO @ Sun, 02 Jun 2019 23:13:08: 14000000 INFO @ Sun, 02 Jun 2019 23:13:12: 15000000 INFO @ Sun, 02 Jun 2019 23:13:12: 15000000 INFO @ Sun, 02 Jun 2019 23:13:16: 15000000 INFO @ Sun, 02 Jun 2019 23:13:20: 16000000 INFO @ Sun, 02 Jun 2019 23:13:20: 16000000 INFO @ Sun, 02 Jun 2019 23:13:24: 16000000 INFO @ Sun, 02 Jun 2019 23:13:27: 17000000 INFO @ Sun, 02 Jun 2019 23:13:28: 17000000 INFO @ Sun, 02 Jun 2019 23:13:33: 17000000 INFO @ Sun, 02 Jun 2019 23:13:33: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:13:33: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:13:33: #1 total tags in treatment: 17767027 INFO @ Sun, 02 Jun 2019 23:13:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:13:33: #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 23:13:33: #1 tags after filtering in treatment: 17767027 INFO @ Sun, 02 Jun 2019 23:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:13:33: #1 finished! INFO @ Sun, 02 Jun 2019 23:13:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:13:35: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:13:35: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:13:35: #1 total tags in treatment: 17767027 INFO @ Sun, 02 Jun 2019 23:13:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:13:35: #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 23:13:35: #1 tags after filtering in treatment: 17767027 INFO @ Sun, 02 Jun 2019 23:13:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:13:35: #1 finished! INFO @ Sun, 02 Jun 2019 23:13:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:13:35: #2 number of paired peaks: 4645 INFO @ Sun, 02 Jun 2019 23:13:35: start model_add_line... INFO @ Sun, 02 Jun 2019 23:13:36: start X-correlation... INFO @ Sun, 02 Jun 2019 23:13:36: end of X-cor INFO @ Sun, 02 Jun 2019 23:13:36: #2 finished! INFO @ Sun, 02 Jun 2019 23:13:36: #2 predicted fragment length is 110 bps INFO @ Sun, 02 Jun 2019 23:13:36: #2 alternative fragment length(s) may be 4,110 bps INFO @ Sun, 02 Jun 2019 23:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.20_model.r INFO @ Sun, 02 Jun 2019 23:13:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:13:37: #2 number of paired peaks: 4645 INFO @ Sun, 02 Jun 2019 23:13:37: start model_add_line... INFO @ Sun, 02 Jun 2019 23:13:38: start X-correlation... INFO @ Sun, 02 Jun 2019 23:13:38: end of X-cor INFO @ Sun, 02 Jun 2019 23:13:38: #2 finished! INFO @ Sun, 02 Jun 2019 23:13:38: #2 predicted fragment length is 110 bps INFO @ Sun, 02 Jun 2019 23:13:38: #2 alternative fragment length(s) may be 4,110 bps INFO @ Sun, 02 Jun 2019 23:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.05_model.r INFO @ Sun, 02 Jun 2019 23:13:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:13:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 23:13:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 23:13:39: #1 total tags in treatment: 17767027 INFO @ Sun, 02 Jun 2019 23:13:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 23:13:39: #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 23:13:40: #1 tags after filtering in treatment: 17767027 INFO @ Sun, 02 Jun 2019 23:13:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 23:13:40: #1 finished! INFO @ Sun, 02 Jun 2019 23:13:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 23:13:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 23:13:42: #2 number of paired peaks: 4645 INFO @ Sun, 02 Jun 2019 23:13:42: start model_add_line... INFO @ Sun, 02 Jun 2019 23:13:42: start X-correlation... INFO @ Sun, 02 Jun 2019 23:13:42: end of X-cor INFO @ Sun, 02 Jun 2019 23:13:42: #2 finished! INFO @ Sun, 02 Jun 2019 23:13:42: #2 predicted fragment length is 110 bps INFO @ Sun, 02 Jun 2019 23:13:42: #2 alternative fragment length(s) may be 4,110 bps INFO @ Sun, 02 Jun 2019 23:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.10_model.r INFO @ Sun, 02 Jun 2019 23:13:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 23:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 23:14:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:14:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:14:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 23:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.20_peaks.xls INFO @ Sun, 02 Jun 2019 23:14:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.20_summits.bed INFO @ Sun, 02 Jun 2019 23:14:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6645 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:14:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.05_peaks.xls INFO @ Sun, 02 Jun 2019 23:14:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:14:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.05_summits.bed INFO @ Sun, 02 Jun 2019 23:14:52: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (12497 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 23:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.10_peaks.xls INFO @ Sun, 02 Jun 2019 23:14:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 23:14:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402753/SRX5402753.10_summits.bed INFO @ Sun, 02 Jun 2019 23:14:55: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9805 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。