Job ID = 1292345 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,834,267 reads read : 10,834,267 reads written : 10,834,267 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: 00:00:01 Multiseed full-index search: 00:03:24 10834267 reads; of these: 10834267 (100.00%) were unpaired; of these: 937429 (8.65%) aligned 0 times 8742583 (80.69%) aligned exactly 1 time 1154255 (10.65%) aligned >1 times 91.35% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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 8 files... [bam_rmdupse_core] 4981988 / 9896838 = 0.5034 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 18:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.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 18:00:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:00:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.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 18:00:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:00:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.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 18:00:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:00:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:00:37: 1000000 INFO @ Sun, 02 Jun 2019 18:00:38: 1000000 INFO @ Sun, 02 Jun 2019 18:00:39: 1000000 INFO @ Sun, 02 Jun 2019 18:00:47: 2000000 INFO @ Sun, 02 Jun 2019 18:00:48: 2000000 INFO @ Sun, 02 Jun 2019 18:00:50: 2000000 INFO @ Sun, 02 Jun 2019 18:00:56: 3000000 INFO @ Sun, 02 Jun 2019 18:00:58: 3000000 INFO @ Sun, 02 Jun 2019 18:01:00: 3000000 INFO @ Sun, 02 Jun 2019 18:01:05: 4000000 INFO @ Sun, 02 Jun 2019 18:01:07: 4000000 INFO @ Sun, 02 Jun 2019 18:01:10: 4000000 INFO @ Sun, 02 Jun 2019 18:01:13: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:01:13: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:01:13: #1 total tags in treatment: 4914850 INFO @ Sun, 02 Jun 2019 18:01:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:01:13: #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 18:01:13: #1 tags after filtering in treatment: 4914850 INFO @ Sun, 02 Jun 2019 18:01:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:01:13: #1 finished! INFO @ Sun, 02 Jun 2019 18:01:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:01:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:01:14: #2 number of paired peaks: 1150 INFO @ Sun, 02 Jun 2019 18:01:14: start model_add_line... INFO @ Sun, 02 Jun 2019 18:01:14: start X-correlation... INFO @ Sun, 02 Jun 2019 18:01:14: end of X-cor INFO @ Sun, 02 Jun 2019 18:01:14: #2 finished! INFO @ Sun, 02 Jun 2019 18:01:14: #2 predicted fragment length is 337 bps INFO @ Sun, 02 Jun 2019 18:01:14: #2 alternative fragment length(s) may be 337 bps INFO @ Sun, 02 Jun 2019 18:01:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.05_model.r INFO @ Sun, 02 Jun 2019 18:01:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:01:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:01:16: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:01:16: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:01:16: #1 total tags in treatment: 4914850 INFO @ Sun, 02 Jun 2019 18:01:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:01:16: #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 18:01:17: #1 tags after filtering in treatment: 4914850 INFO @ Sun, 02 Jun 2019 18:01:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:01:17: #1 finished! INFO @ Sun, 02 Jun 2019 18:01:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:01:17: #2 number of paired peaks: 1150 INFO @ Sun, 02 Jun 2019 18:01:17: start model_add_line... INFO @ Sun, 02 Jun 2019 18:01:17: start X-correlation... INFO @ Sun, 02 Jun 2019 18:01:17: end of X-cor INFO @ Sun, 02 Jun 2019 18:01:17: #2 finished! INFO @ Sun, 02 Jun 2019 18:01:17: #2 predicted fragment length is 337 bps INFO @ Sun, 02 Jun 2019 18:01:17: #2 alternative fragment length(s) may be 337 bps INFO @ Sun, 02 Jun 2019 18:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.20_model.r INFO @ Sun, 02 Jun 2019 18:01:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:01:19: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:01:19: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:01:19: #1 total tags in treatment: 4914850 INFO @ Sun, 02 Jun 2019 18:01:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:01:19: #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 18:01:19: #1 tags after filtering in treatment: 4914850 INFO @ Sun, 02 Jun 2019 18:01:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:01:19: #1 finished! INFO @ Sun, 02 Jun 2019 18:01:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:01:20: #2 number of paired peaks: 1150 INFO @ Sun, 02 Jun 2019 18:01:20: start model_add_line... INFO @ Sun, 02 Jun 2019 18:01:20: start X-correlation... INFO @ Sun, 02 Jun 2019 18:01:20: end of X-cor INFO @ Sun, 02 Jun 2019 18:01:20: #2 finished! INFO @ Sun, 02 Jun 2019 18:01:20: #2 predicted fragment length is 337 bps INFO @ Sun, 02 Jun 2019 18:01:20: #2 alternative fragment length(s) may be 337 bps INFO @ Sun, 02 Jun 2019 18:01:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.10_model.r INFO @ Sun, 02 Jun 2019 18:01:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:01:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:01:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:01:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:01:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.05_summits.bed INFO @ Sun, 02 Jun 2019 18:01:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3178 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:01:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.20_summits.bed INFO @ Sun, 02 Jun 2019 18:01:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1419 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341784/SRX341784.10_summits.bed INFO @ Sun, 02 Jun 2019 18:01:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2278 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。