Job ID = 1291665 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,925,488 reads read : 18,925,488 reads written : 18,925,488 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: 00:04:37 18925488 reads; of these: 18925488 (100.00%) were unpaired; of these: 8182265 (43.23%) aligned 0 times 5972226 (31.56%) aligned exactly 1 time 4770997 (25.21%) aligned >1 times 56.77% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 5898197 / 10743223 = 0.5490 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 16:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.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 16:20:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:20:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.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 16:20:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:20:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.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 16:20:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:20:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:20:43: 1000000 INFO @ Sun, 02 Jun 2019 16:20:44: 1000000 INFO @ Sun, 02 Jun 2019 16:20:44: 1000000 INFO @ Sun, 02 Jun 2019 16:20:53: 2000000 INFO @ Sun, 02 Jun 2019 16:20:54: 2000000 INFO @ Sun, 02 Jun 2019 16:20:55: 2000000 INFO @ Sun, 02 Jun 2019 16:21:02: 3000000 INFO @ Sun, 02 Jun 2019 16:21:04: 3000000 INFO @ Sun, 02 Jun 2019 16:21:05: 3000000 INFO @ Sun, 02 Jun 2019 16:21:11: 4000000 INFO @ Sun, 02 Jun 2019 16:21:15: 4000000 INFO @ Sun, 02 Jun 2019 16:21:15: 4000000 INFO @ Sun, 02 Jun 2019 16:21:19: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:21:19: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:21:19: #1 total tags in treatment: 4845026 INFO @ Sun, 02 Jun 2019 16:21:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:21:19: #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 16:21:19: #1 tags after filtering in treatment: 4845026 INFO @ Sun, 02 Jun 2019 16:21:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:21:19: #1 finished! INFO @ Sun, 02 Jun 2019 16:21:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:21:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:21:19: #2 number of paired peaks: 1067 INFO @ Sun, 02 Jun 2019 16:21:19: start model_add_line... INFO @ Sun, 02 Jun 2019 16:21:19: start X-correlation... INFO @ Sun, 02 Jun 2019 16:21:19: end of X-cor INFO @ Sun, 02 Jun 2019 16:21:19: #2 finished! INFO @ Sun, 02 Jun 2019 16:21:19: #2 predicted fragment length is 221 bps INFO @ Sun, 02 Jun 2019 16:21:19: #2 alternative fragment length(s) may be 221 bps INFO @ Sun, 02 Jun 2019 16:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.20_model.r INFO @ Sun, 02 Jun 2019 16:21:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:21:23: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:21:23: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:21:23: #1 total tags in treatment: 4845026 INFO @ Sun, 02 Jun 2019 16:21:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:21:23: #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 16:21:23: #1 tags after filtering in treatment: 4845026 INFO @ Sun, 02 Jun 2019 16:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:21:23: #1 finished! INFO @ Sun, 02 Jun 2019 16:21:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:21:23: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:21:23: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:21:23: #1 total tags in treatment: 4845026 INFO @ Sun, 02 Jun 2019 16:21:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:21:23: #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 16:21:23: #1 tags after filtering in treatment: 4845026 INFO @ Sun, 02 Jun 2019 16:21:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:21:23: #1 finished! INFO @ Sun, 02 Jun 2019 16:21:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:21:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:21:23: #2 number of paired peaks: 1067 INFO @ Sun, 02 Jun 2019 16:21:23: start model_add_line... INFO @ Sun, 02 Jun 2019 16:21:23: start X-correlation... INFO @ Sun, 02 Jun 2019 16:21:24: end of X-cor INFO @ Sun, 02 Jun 2019 16:21:24: #2 finished! INFO @ Sun, 02 Jun 2019 16:21:24: #2 predicted fragment length is 221 bps INFO @ Sun, 02 Jun 2019 16:21:24: #2 alternative fragment length(s) may be 221 bps INFO @ Sun, 02 Jun 2019 16:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.10_model.r INFO @ Sun, 02 Jun 2019 16:21:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:21:24: #2 number of paired peaks: 1067 INFO @ Sun, 02 Jun 2019 16:21:24: start model_add_line... INFO @ Sun, 02 Jun 2019 16:21:24: start X-correlation... INFO @ Sun, 02 Jun 2019 16:21:24: end of X-cor INFO @ Sun, 02 Jun 2019 16:21:24: #2 finished! INFO @ Sun, 02 Jun 2019 16:21:24: #2 predicted fragment length is 221 bps INFO @ Sun, 02 Jun 2019 16:21:24: #2 alternative fragment length(s) may be 221 bps INFO @ Sun, 02 Jun 2019 16:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.05_model.r INFO @ Sun, 02 Jun 2019 16:21:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:21:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:21:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:21:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.20_summits.bed INFO @ Sun, 02 Jun 2019 16:21:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (528 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:21:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:21:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:21:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.10_summits.bed INFO @ Sun, 02 Jun 2019 16:21:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (657 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:21:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:21:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:21:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769993/SRX1769993.05_summits.bed INFO @ Sun, 02 Jun 2019 16:21:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (842 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。