Job ID = 1292544 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,156,918 reads read : 14,156,918 reads written : 14,156,918 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: 00:02:42 14156918 reads; of these: 14156918 (100.00%) were unpaired; of these: 174522 (1.23%) aligned 0 times 12309982 (86.95%) aligned exactly 1 time 1672414 (11.81%) aligned >1 times 98.77% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 3966814 / 13982396 = 0.2837 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 19:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.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 19:31:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:31:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.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 19:31:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:31:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.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 19:31:48: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:31:48: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:31:56: 1000000 INFO @ Sun, 02 Jun 2019 19:31:57: 1000000 INFO @ Sun, 02 Jun 2019 19:31:59: 1000000 INFO @ Sun, 02 Jun 2019 19:32:03: 2000000 INFO @ Sun, 02 Jun 2019 19:32:05: 2000000 INFO @ Sun, 02 Jun 2019 19:32:10: 2000000 INFO @ Sun, 02 Jun 2019 19:32:10: 3000000 INFO @ Sun, 02 Jun 2019 19:32:13: 3000000 INFO @ Sun, 02 Jun 2019 19:32:17: 4000000 INFO @ Sun, 02 Jun 2019 19:32:20: 3000000 INFO @ Sun, 02 Jun 2019 19:32:21: 4000000 INFO @ Sun, 02 Jun 2019 19:32:24: 5000000 INFO @ Sun, 02 Jun 2019 19:32:28: 5000000 INFO @ Sun, 02 Jun 2019 19:32:30: 4000000 INFO @ Sun, 02 Jun 2019 19:32:31: 6000000 INFO @ Sun, 02 Jun 2019 19:32:36: 6000000 INFO @ Sun, 02 Jun 2019 19:32:38: 7000000 INFO @ Sun, 02 Jun 2019 19:32:41: 5000000 INFO @ Sun, 02 Jun 2019 19:32:44: 7000000 INFO @ Sun, 02 Jun 2019 19:32:45: 8000000 INFO @ Sun, 02 Jun 2019 19:32:51: 6000000 INFO @ Sun, 02 Jun 2019 19:32:52: 8000000 INFO @ Sun, 02 Jun 2019 19:32:53: 9000000 INFO @ Sun, 02 Jun 2019 19:33:00: 10000000 INFO @ Sun, 02 Jun 2019 19:33:00: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:33:00: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:33:00: #1 total tags in treatment: 10015582 INFO @ Sun, 02 Jun 2019 19:33:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:33:00: #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 19:33:00: 9000000 INFO @ Sun, 02 Jun 2019 19:33:00: #1 tags after filtering in treatment: 10015582 INFO @ Sun, 02 Jun 2019 19:33:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:33:00: #1 finished! INFO @ Sun, 02 Jun 2019 19:33:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:33:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:33:01: #2 number of paired peaks: 2347 INFO @ Sun, 02 Jun 2019 19:33:01: start model_add_line... INFO @ Sun, 02 Jun 2019 19:33:01: start X-correlation... INFO @ Sun, 02 Jun 2019 19:33:01: end of X-cor INFO @ Sun, 02 Jun 2019 19:33:01: #2 finished! INFO @ Sun, 02 Jun 2019 19:33:01: #2 predicted fragment length is 261 bps INFO @ Sun, 02 Jun 2019 19:33:01: #2 alternative fragment length(s) may be 4,261 bps INFO @ Sun, 02 Jun 2019 19:33:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.05_model.r INFO @ Sun, 02 Jun 2019 19:33:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:33:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:33:01: 7000000 INFO @ Sun, 02 Jun 2019 19:33:08: 10000000 INFO @ Sun, 02 Jun 2019 19:33:08: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:33:08: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:33:08: #1 total tags in treatment: 10015582 INFO @ Sun, 02 Jun 2019 19:33:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:33:08: #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 19:33:08: #1 tags after filtering in treatment: 10015582 INFO @ Sun, 02 Jun 2019 19:33:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:33:08: #1 finished! INFO @ Sun, 02 Jun 2019 19:33:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:33:09: #2 number of paired peaks: 2347 INFO @ Sun, 02 Jun 2019 19:33:09: start model_add_line... INFO @ Sun, 02 Jun 2019 19:33:10: start X-correlation... INFO @ Sun, 02 Jun 2019 19:33:10: end of X-cor INFO @ Sun, 02 Jun 2019 19:33:10: #2 finished! INFO @ Sun, 02 Jun 2019 19:33:10: #2 predicted fragment length is 261 bps INFO @ Sun, 02 Jun 2019 19:33:10: #2 alternative fragment length(s) may be 4,261 bps INFO @ Sun, 02 Jun 2019 19:33:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.20_model.r INFO @ Sun, 02 Jun 2019 19:33:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:33:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:33:12: 8000000 INFO @ Sun, 02 Jun 2019 19:33:22: 9000000 INFO @ Sun, 02 Jun 2019 19:33:32: 10000000 INFO @ Sun, 02 Jun 2019 19:33:32: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:33:32: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:33:32: #1 total tags in treatment: 10015582 INFO @ Sun, 02 Jun 2019 19:33:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:33:32: #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 19:33:32: #1 tags after filtering in treatment: 10015582 INFO @ Sun, 02 Jun 2019 19:33:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:33:32: #1 finished! INFO @ Sun, 02 Jun 2019 19:33:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:33:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:33:34: #2 number of paired peaks: 2347 INFO @ Sun, 02 Jun 2019 19:33:34: start model_add_line... INFO @ Sun, 02 Jun 2019 19:33:34: start X-correlation... INFO @ Sun, 02 Jun 2019 19:33:34: end of X-cor INFO @ Sun, 02 Jun 2019 19:33:34: #2 finished! INFO @ Sun, 02 Jun 2019 19:33:34: #2 predicted fragment length is 261 bps INFO @ Sun, 02 Jun 2019 19:33:34: #2 alternative fragment length(s) may be 4,261 bps INFO @ Sun, 02 Jun 2019 19:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.10_model.r INFO @ Sun, 02 Jun 2019 19:33:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:33:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:33:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:33:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:33:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:33:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.05_summits.bed INFO @ Sun, 02 Jun 2019 19:33:53: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4290 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:34:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:34:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:34:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.20_summits.bed INFO @ Sun, 02 Jun 2019 19:34:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1229 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:34:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:34:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:34:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:34:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466558/SRX466558.10_summits.bed INFO @ Sun, 02 Jun 2019 19:34:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2531 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。