Job ID = 1292774 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,595,990 reads read : 19,595,990 reads written : 19,595,990 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: 00:03:15 19595990 reads; of these: 19595990 (100.00%) were unpaired; of these: 3607431 (18.41%) aligned 0 times 13946374 (71.17%) aligned exactly 1 time 2042185 (10.42%) aligned >1 times 81.59% overall alignment rate Time searching: 00:03:15 Overall time: 00:03:15 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] 4724949 / 15988559 = 0.2955 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 20:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.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 20:41:42: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:41:42: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.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 20:41:42: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:41:42: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.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 20:41:42: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:41:42: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:41:52: 1000000 INFO @ Sun, 02 Jun 2019 20:41:52: 1000000 INFO @ Sun, 02 Jun 2019 20:41:53: 1000000 INFO @ Sun, 02 Jun 2019 20:42:02: 2000000 INFO @ Sun, 02 Jun 2019 20:42:04: 2000000 INFO @ Sun, 02 Jun 2019 20:42:04: 2000000 INFO @ Sun, 02 Jun 2019 20:42:12: 3000000 INFO @ Sun, 02 Jun 2019 20:42:13: 3000000 INFO @ Sun, 02 Jun 2019 20:42:14: 3000000 INFO @ Sun, 02 Jun 2019 20:42:21: 4000000 INFO @ Sun, 02 Jun 2019 20:42:23: 4000000 INFO @ Sun, 02 Jun 2019 20:42:23: 4000000 INFO @ Sun, 02 Jun 2019 20:42:30: 5000000 INFO @ Sun, 02 Jun 2019 20:42:33: 5000000 INFO @ Sun, 02 Jun 2019 20:42:33: 5000000 INFO @ Sun, 02 Jun 2019 20:42:40: 6000000 INFO @ Sun, 02 Jun 2019 20:42:43: 6000000 INFO @ Sun, 02 Jun 2019 20:42:43: 6000000 INFO @ Sun, 02 Jun 2019 20:42:49: 7000000 INFO @ Sun, 02 Jun 2019 20:42:52: 7000000 INFO @ Sun, 02 Jun 2019 20:42:52: 7000000 INFO @ Sun, 02 Jun 2019 20:42:59: 8000000 INFO @ Sun, 02 Jun 2019 20:43:02: 8000000 INFO @ Sun, 02 Jun 2019 20:43:02: 8000000 INFO @ Sun, 02 Jun 2019 20:43:07: 9000000 INFO @ Sun, 02 Jun 2019 20:43:11: 9000000 INFO @ Sun, 02 Jun 2019 20:43:11: 9000000 INFO @ Sun, 02 Jun 2019 20:43:17: 10000000 INFO @ Sun, 02 Jun 2019 20:43:20: 10000000 INFO @ Sun, 02 Jun 2019 20:43:20: 10000000 INFO @ Sun, 02 Jun 2019 20:43:25: 11000000 INFO @ Sun, 02 Jun 2019 20:43:28: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:43:28: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:43:28: #1 total tags in treatment: 11263610 INFO @ Sun, 02 Jun 2019 20:43:28: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:43:28: #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 20:43:28: #1 tags after filtering in treatment: 11263610 INFO @ Sun, 02 Jun 2019 20:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:43:28: #1 finished! INFO @ Sun, 02 Jun 2019 20:43:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:43:29: 11000000 INFO @ Sun, 02 Jun 2019 20:43:29: 11000000 INFO @ Sun, 02 Jun 2019 20:43:29: #2 number of paired peaks: 2780 INFO @ Sun, 02 Jun 2019 20:43:29: start model_add_line... INFO @ Sun, 02 Jun 2019 20:43:30: start X-correlation... INFO @ Sun, 02 Jun 2019 20:43:30: end of X-cor INFO @ Sun, 02 Jun 2019 20:43:30: #2 finished! INFO @ Sun, 02 Jun 2019 20:43:30: #2 predicted fragment length is 230 bps INFO @ Sun, 02 Jun 2019 20:43:30: #2 alternative fragment length(s) may be 4,230 bps INFO @ Sun, 02 Jun 2019 20:43:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.10_model.r INFO @ Sun, 02 Jun 2019 20:43:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:43:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:43:32: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:43:32: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:43:32: #1 total tags in treatment: 11263610 INFO @ Sun, 02 Jun 2019 20:43:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:43:32: #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 20:43:32: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:43:32: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:43:32: #1 total tags in treatment: 11263610 INFO @ Sun, 02 Jun 2019 20:43:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:43:32: #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 20:43:32: #1 tags after filtering in treatment: 11263610 INFO @ Sun, 02 Jun 2019 20:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:43:32: #1 finished! INFO @ Sun, 02 Jun 2019 20:43:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:43:32: #1 tags after filtering in treatment: 11263610 INFO @ Sun, 02 Jun 2019 20:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:43:32: #1 finished! INFO @ Sun, 02 Jun 2019 20:43:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:43:33: #2 number of paired peaks: 2780 INFO @ Sun, 02 Jun 2019 20:43:33: start model_add_line... INFO @ Sun, 02 Jun 2019 20:43:33: #2 number of paired peaks: 2780 INFO @ Sun, 02 Jun 2019 20:43:33: start model_add_line... INFO @ Sun, 02 Jun 2019 20:43:33: start X-correlation... INFO @ Sun, 02 Jun 2019 20:43:33: end of X-cor INFO @ Sun, 02 Jun 2019 20:43:33: #2 finished! INFO @ Sun, 02 Jun 2019 20:43:33: #2 predicted fragment length is 230 bps INFO @ Sun, 02 Jun 2019 20:43:33: #2 alternative fragment length(s) may be 4,230 bps INFO @ Sun, 02 Jun 2019 20:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.05_model.r INFO @ Sun, 02 Jun 2019 20:43:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:43:33: start X-correlation... INFO @ Sun, 02 Jun 2019 20:43:33: end of X-cor INFO @ Sun, 02 Jun 2019 20:43:33: #2 finished! INFO @ Sun, 02 Jun 2019 20:43:33: #2 predicted fragment length is 230 bps INFO @ Sun, 02 Jun 2019 20:43:33: #2 alternative fragment length(s) may be 4,230 bps INFO @ Sun, 02 Jun 2019 20:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.20_model.r INFO @ Sun, 02 Jun 2019 20:43:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:44:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:44:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:44:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:44:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:44:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:44:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.10_summits.bed INFO @ Sun, 02 Jun 2019 20:44:29: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4368 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.20_summits.bed INFO @ Sun, 02 Jun 2019 20:44:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1931 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495004/SRX495004.05_summits.bed INFO @ Sun, 02 Jun 2019 20:44:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7639 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。