Job ID = 1291661 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,529,958 reads read : 2,529,958 reads written : 2,529,958 spots read : 2,554,824 reads read : 2,554,824 reads written : 2,554,824 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: 00:00:56 5084782 reads; of these: 5084782 (100.00%) were unpaired; of these: 2490010 (48.97%) aligned 0 times 2181527 (42.90%) aligned exactly 1 time 413245 (8.13%) aligned >1 times 51.03% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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_rmdupse_core] 628793 / 2594772 = 0.2423 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 16:14:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.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 16:14:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:14:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:14:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.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 16:14:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:14:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:14:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.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 16:14:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:14:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:14:20: 1000000 INFO @ Sun, 02 Jun 2019 16:14:22: 1000000 INFO @ Sun, 02 Jun 2019 16:14:22: 1000000 INFO @ Sun, 02 Jun 2019 16:14:28: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:14:28: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:14:28: #1 total tags in treatment: 1965979 INFO @ Sun, 02 Jun 2019 16:14:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:14:28: #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 16:14:28: #1 tags after filtering in treatment: 1965979 INFO @ Sun, 02 Jun 2019 16:14:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:14:28: #1 finished! INFO @ Sun, 02 Jun 2019 16:14:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:14:28: #2 number of paired peaks: 3460 INFO @ Sun, 02 Jun 2019 16:14:28: start model_add_line... INFO @ Sun, 02 Jun 2019 16:14:28: start X-correlation... INFO @ Sun, 02 Jun 2019 16:14:28: end of X-cor INFO @ Sun, 02 Jun 2019 16:14:28: #2 finished! INFO @ Sun, 02 Jun 2019 16:14:28: #2 predicted fragment length is 285 bps INFO @ Sun, 02 Jun 2019 16:14:28: #2 alternative fragment length(s) may be 285 bps INFO @ Sun, 02 Jun 2019 16:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.10_model.r INFO @ Sun, 02 Jun 2019 16:14:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:14:31: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:14:31: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:14:31: #1 total tags in treatment: 1965979 INFO @ Sun, 02 Jun 2019 16:14:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:14:31: #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 16:14:31: #1 tags after filtering in treatment: 1965979 INFO @ Sun, 02 Jun 2019 16:14:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:14:31: #1 finished! INFO @ Sun, 02 Jun 2019 16:14:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:14:31: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:14:31: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:14:31: #1 total tags in treatment: 1965979 INFO @ Sun, 02 Jun 2019 16:14:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:14:31: #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 16:14:31: #1 tags after filtering in treatment: 1965979 INFO @ Sun, 02 Jun 2019 16:14:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:14:31: #1 finished! INFO @ Sun, 02 Jun 2019 16:14:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:14:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:14:31: #2 number of paired peaks: 3460 INFO @ Sun, 02 Jun 2019 16:14:31: start model_add_line... INFO @ Sun, 02 Jun 2019 16:14:31: start X-correlation... INFO @ Sun, 02 Jun 2019 16:14:31: #2 number of paired peaks: 3460 INFO @ Sun, 02 Jun 2019 16:14:31: start model_add_line... INFO @ Sun, 02 Jun 2019 16:14:31: end of X-cor INFO @ Sun, 02 Jun 2019 16:14:31: #2 finished! INFO @ Sun, 02 Jun 2019 16:14:31: #2 predicted fragment length is 285 bps INFO @ Sun, 02 Jun 2019 16:14:31: #2 alternative fragment length(s) may be 285 bps INFO @ Sun, 02 Jun 2019 16:14:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.20_model.r INFO @ Sun, 02 Jun 2019 16:14:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:14:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:14:31: start X-correlation... INFO @ Sun, 02 Jun 2019 16:14:31: end of X-cor INFO @ Sun, 02 Jun 2019 16:14:31: #2 finished! INFO @ Sun, 02 Jun 2019 16:14:31: #2 predicted fragment length is 285 bps INFO @ Sun, 02 Jun 2019 16:14:31: #2 alternative fragment length(s) may be 285 bps INFO @ Sun, 02 Jun 2019 16:14:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.05_model.r INFO @ Sun, 02 Jun 2019 16:14:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:14:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:14:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:14:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:14:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:14:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.10_summits.bed INFO @ Sun, 02 Jun 2019 16:14:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2908 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:14:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:14:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:14:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.20_summits.bed INFO @ Sun, 02 Jun 2019 16:14:43: Done! INFO @ Sun, 02 Jun 2019 16:14:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:14:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.05_peaks.narrowPeak pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2049 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:14:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769989/SRX1769989.05_summits.bed INFO @ Sun, 02 Jun 2019 16:14:43: Done! BedGraph に変換しました。 pass1 - making usageList (7 chroms) : 2 millis BigWig に変換中... pass2 - checking and writing primary data (3946 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。