Job ID = 1292350 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,555,672 reads read : 20,555,672 reads written : 20,555,672 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:42 20555672 reads; of these: 20555672 (100.00%) were unpaired; of these: 1970893 (9.59%) aligned 0 times 17235459 (83.85%) aligned exactly 1 time 1349320 (6.56%) aligned >1 times 90.41% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 10226943 / 18584779 = 0.5503 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 18:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.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 18:15:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:15:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.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 18:15:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:15:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:15:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.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 18:15:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:15:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:15:38: 1000000 INFO @ Sun, 02 Jun 2019 18:15:39: 1000000 INFO @ Sun, 02 Jun 2019 18:15:40: 1000000 INFO @ Sun, 02 Jun 2019 18:15:46: 2000000 INFO @ Sun, 02 Jun 2019 18:15:47: 2000000 INFO @ Sun, 02 Jun 2019 18:15:49: 2000000 INFO @ Sun, 02 Jun 2019 18:15:54: 3000000 INFO @ Sun, 02 Jun 2019 18:15:56: 3000000 INFO @ Sun, 02 Jun 2019 18:15:58: 3000000 INFO @ Sun, 02 Jun 2019 18:16:01: 4000000 INFO @ Sun, 02 Jun 2019 18:16:04: 4000000 INFO @ Sun, 02 Jun 2019 18:16:07: 4000000 INFO @ Sun, 02 Jun 2019 18:16:09: 5000000 INFO @ Sun, 02 Jun 2019 18:16:12: 5000000 INFO @ Sun, 02 Jun 2019 18:16:15: 5000000 INFO @ Sun, 02 Jun 2019 18:16:16: 6000000 INFO @ Sun, 02 Jun 2019 18:16:20: 6000000 INFO @ Sun, 02 Jun 2019 18:16:24: 6000000 INFO @ Sun, 02 Jun 2019 18:16:24: 7000000 INFO @ Sun, 02 Jun 2019 18:16:27: 7000000 INFO @ Sun, 02 Jun 2019 18:16:31: 8000000 INFO @ Sun, 02 Jun 2019 18:16:32: 7000000 INFO @ Sun, 02 Jun 2019 18:16:34: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:16:34: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:16:34: #1 total tags in treatment: 8357836 INFO @ Sun, 02 Jun 2019 18:16:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:16:34: #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 18:16:34: #1 tags after filtering in treatment: 8357836 INFO @ Sun, 02 Jun 2019 18:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:16:34: #1 finished! INFO @ Sun, 02 Jun 2019 18:16:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:16:35: 8000000 INFO @ Sun, 02 Jun 2019 18:16:35: #2 number of paired peaks: 2462 INFO @ Sun, 02 Jun 2019 18:16:35: start model_add_line... INFO @ Sun, 02 Jun 2019 18:16:35: start X-correlation... INFO @ Sun, 02 Jun 2019 18:16:35: end of X-cor INFO @ Sun, 02 Jun 2019 18:16:35: #2 finished! INFO @ Sun, 02 Jun 2019 18:16:35: #2 predicted fragment length is 270 bps INFO @ Sun, 02 Jun 2019 18:16:35: #2 alternative fragment length(s) may be 270 bps INFO @ Sun, 02 Jun 2019 18:16:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.10_model.r INFO @ Sun, 02 Jun 2019 18:16:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:16:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:16:38: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:16:38: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:16:38: #1 total tags in treatment: 8357836 INFO @ Sun, 02 Jun 2019 18:16:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:16:38: #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 18:16:38: #1 tags after filtering in treatment: 8357836 INFO @ Sun, 02 Jun 2019 18:16:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:16:38: #1 finished! INFO @ Sun, 02 Jun 2019 18:16:38: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:16:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:16:39: #2 number of paired peaks: 2462 INFO @ Sun, 02 Jun 2019 18:16:39: start model_add_line... INFO @ Sun, 02 Jun 2019 18:16:39: start X-correlation... INFO @ Sun, 02 Jun 2019 18:16:39: end of X-cor INFO @ Sun, 02 Jun 2019 18:16:39: #2 finished! INFO @ Sun, 02 Jun 2019 18:16:39: #2 predicted fragment length is 270 bps INFO @ Sun, 02 Jun 2019 18:16:39: #2 alternative fragment length(s) may be 270 bps INFO @ Sun, 02 Jun 2019 18:16:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.05_model.r INFO @ Sun, 02 Jun 2019 18:16:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:16:40: 8000000 INFO @ Sun, 02 Jun 2019 18:16:44: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:16:44: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:16:44: #1 total tags in treatment: 8357836 INFO @ Sun, 02 Jun 2019 18:16:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:16:44: #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 18:16:44: #1 tags after filtering in treatment: 8357836 INFO @ Sun, 02 Jun 2019 18:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:16:44: #1 finished! INFO @ Sun, 02 Jun 2019 18:16:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:16:45: #2 number of paired peaks: 2462 INFO @ Sun, 02 Jun 2019 18:16:45: start model_add_line... INFO @ Sun, 02 Jun 2019 18:16:45: start X-correlation... INFO @ Sun, 02 Jun 2019 18:16:45: end of X-cor INFO @ Sun, 02 Jun 2019 18:16:45: #2 finished! INFO @ Sun, 02 Jun 2019 18:16:45: #2 predicted fragment length is 270 bps INFO @ Sun, 02 Jun 2019 18:16:45: #2 alternative fragment length(s) may be 270 bps INFO @ Sun, 02 Jun 2019 18:16:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.20_model.r INFO @ Sun, 02 Jun 2019 18:16:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:17:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:17:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:17:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:17:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:17:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:17:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.10_summits.bed INFO @ Sun, 02 Jun 2019 18:17:16: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4166 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:17:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:17:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:17:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.05_summits.bed INFO @ Sun, 02 Jun 2019 18:17:20: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5483 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:17:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:17:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:17:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341788/SRX341788.20_summits.bed INFO @ Sun, 02 Jun 2019 18:17:25: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2845 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。