Job ID = 1293172 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,553,583 reads read : 22,553,583 reads written : 22,553,583 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: 00:05:14 22553583 reads; of these: 22553583 (100.00%) were unpaired; of these: 2521556 (11.18%) aligned 0 times 17167848 (76.12%) aligned exactly 1 time 2864179 (12.70%) aligned >1 times 88.82% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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 12 files... [bam_rmdupse_core] 5679117 / 20032027 = 0.2835 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 22:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.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 22:28:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:28:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.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 22:29:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.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 22:29:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:29:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:29:13: 1000000 INFO @ Sun, 02 Jun 2019 22:29:14: 1000000 INFO @ Sun, 02 Jun 2019 22:29:14: 1000000 INFO @ Sun, 02 Jun 2019 22:29:24: 2000000 INFO @ Sun, 02 Jun 2019 22:29:26: 2000000 INFO @ Sun, 02 Jun 2019 22:29:27: 2000000 INFO @ Sun, 02 Jun 2019 22:29:37: 3000000 INFO @ Sun, 02 Jun 2019 22:29:39: 3000000 INFO @ Sun, 02 Jun 2019 22:29:39: 3000000 INFO @ Sun, 02 Jun 2019 22:29:49: 4000000 INFO @ Sun, 02 Jun 2019 22:29:51: 4000000 INFO @ Sun, 02 Jun 2019 22:29:51: 4000000 INFO @ Sun, 02 Jun 2019 22:30:01: 5000000 INFO @ Sun, 02 Jun 2019 22:30:02: 5000000 INFO @ Sun, 02 Jun 2019 22:30:03: 5000000 INFO @ Sun, 02 Jun 2019 22:30:13: 6000000 INFO @ Sun, 02 Jun 2019 22:30:14: 6000000 INFO @ Sun, 02 Jun 2019 22:30:16: 6000000 INFO @ Sun, 02 Jun 2019 22:30:25: 7000000 INFO @ Sun, 02 Jun 2019 22:30:26: 7000000 INFO @ Sun, 02 Jun 2019 22:30:28: 7000000 INFO @ Sun, 02 Jun 2019 22:30:38: 8000000 INFO @ Sun, 02 Jun 2019 22:30:38: 8000000 INFO @ Sun, 02 Jun 2019 22:30:40: 8000000 INFO @ Sun, 02 Jun 2019 22:30:50: 9000000 INFO @ Sun, 02 Jun 2019 22:30:50: 9000000 INFO @ Sun, 02 Jun 2019 22:30:53: 9000000 INFO @ Sun, 02 Jun 2019 22:31:02: 10000000 INFO @ Sun, 02 Jun 2019 22:31:03: 10000000 INFO @ Sun, 02 Jun 2019 22:31:06: 10000000 INFO @ Sun, 02 Jun 2019 22:31:14: 11000000 INFO @ Sun, 02 Jun 2019 22:31:17: 11000000 INFO @ Sun, 02 Jun 2019 22:31:19: 11000000 INFO @ Sun, 02 Jun 2019 22:31:26: 12000000 INFO @ Sun, 02 Jun 2019 22:31:28: 12000000 INFO @ Sun, 02 Jun 2019 22:31:29: 12000000 INFO @ Sun, 02 Jun 2019 22:31:38: 13000000 INFO @ Sun, 02 Jun 2019 22:31:41: 13000000 INFO @ Sun, 02 Jun 2019 22:31:42: 13000000 INFO @ Sun, 02 Jun 2019 22:31:50: 14000000 INFO @ Sun, 02 Jun 2019 22:31:54: 14000000 INFO @ Sun, 02 Jun 2019 22:31:54: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:31:54: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:31:54: #1 total tags in treatment: 14352910 INFO @ Sun, 02 Jun 2019 22:31:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:31:54: #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 22:31:55: #1 tags after filtering in treatment: 14352910 INFO @ Sun, 02 Jun 2019 22:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:31:55: #1 finished! INFO @ Sun, 02 Jun 2019 22:31:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:31:55: 14000000 INFO @ Sun, 02 Jun 2019 22:31:56: #2 number of paired peaks: 1793 INFO @ Sun, 02 Jun 2019 22:31:56: start model_add_line... INFO @ Sun, 02 Jun 2019 22:31:56: start X-correlation... INFO @ Sun, 02 Jun 2019 22:31:56: end of X-cor INFO @ Sun, 02 Jun 2019 22:31:56: #2 finished! INFO @ Sun, 02 Jun 2019 22:31:56: #2 predicted fragment length is 153 bps INFO @ Sun, 02 Jun 2019 22:31:56: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 02 Jun 2019 22:31:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.05_model.r INFO @ Sun, 02 Jun 2019 22:31:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:31:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:31:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:31:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:31:58: #1 total tags in treatment: 14352910 INFO @ Sun, 02 Jun 2019 22:31:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:31:58: #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 22:31:58: #1 tags after filtering in treatment: 14352910 INFO @ Sun, 02 Jun 2019 22:31:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:31:58: #1 finished! INFO @ Sun, 02 Jun 2019 22:31:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:31:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:31:59: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:31:59: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:31:59: #1 total tags in treatment: 14352910 INFO @ Sun, 02 Jun 2019 22:31:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:31:59: #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 22:31:59: #1 tags after filtering in treatment: 14352910 INFO @ Sun, 02 Jun 2019 22:31:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:31:59: #1 finished! INFO @ Sun, 02 Jun 2019 22:31:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:31:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:32:00: #2 number of paired peaks: 1793 INFO @ Sun, 02 Jun 2019 22:32:00: start model_add_line... INFO @ Sun, 02 Jun 2019 22:32:00: start X-correlation... INFO @ Sun, 02 Jun 2019 22:32:00: end of X-cor INFO @ Sun, 02 Jun 2019 22:32:00: #2 finished! INFO @ Sun, 02 Jun 2019 22:32:00: #2 predicted fragment length is 153 bps INFO @ Sun, 02 Jun 2019 22:32:00: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 02 Jun 2019 22:32:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.20_model.r INFO @ Sun, 02 Jun 2019 22:32:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:32:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:32:01: #2 number of paired peaks: 1793 INFO @ Sun, 02 Jun 2019 22:32:01: start model_add_line... INFO @ Sun, 02 Jun 2019 22:32:01: start X-correlation... INFO @ Sun, 02 Jun 2019 22:32:01: end of X-cor INFO @ Sun, 02 Jun 2019 22:32:01: #2 finished! INFO @ Sun, 02 Jun 2019 22:32:01: #2 predicted fragment length is 153 bps INFO @ Sun, 02 Jun 2019 22:32:01: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 02 Jun 2019 22:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.10_model.r INFO @ Sun, 02 Jun 2019 22:32:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:32:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:32:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:32:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.05_summits.bed INFO @ Sun, 02 Jun 2019 22:32:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5366 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.20_summits.bed INFO @ Sun, 02 Jun 2019 22:33:01: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3641 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:33:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:33:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:33:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402736/SRX5402736.10_summits.bed INFO @ Sun, 02 Jun 2019 22:33:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4422 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。