Job ID = 1293160 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,177,070 reads read : 31,177,070 reads written : 31,177,070 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: 00:07:20 31177070 reads; of these: 31177070 (100.00%) were unpaired; of these: 4842705 (15.53%) aligned 0 times 22643086 (72.63%) aligned exactly 1 time 3691279 (11.84%) aligned >1 times 84.47% overall alignment rate Time searching: 00:07:20 Overall time: 00:07:20 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] 11119205 / 26334365 = 0.4222 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 22:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.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 22:31:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:31:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.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 22:31:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:31:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.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 22:31:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:31:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:31:27: 1000000 INFO @ Sun, 02 Jun 2019 22:31:28: 1000000 INFO @ Sun, 02 Jun 2019 22:31:30: 1000000 INFO @ Sun, 02 Jun 2019 22:31:36: 2000000 INFO @ Sun, 02 Jun 2019 22:31:37: 2000000 INFO @ Sun, 02 Jun 2019 22:31:43: 2000000 INFO @ Sun, 02 Jun 2019 22:31:45: 3000000 INFO @ Sun, 02 Jun 2019 22:31:49: 3000000 INFO @ Sun, 02 Jun 2019 22:31:54: 4000000 INFO @ Sun, 02 Jun 2019 22:31:55: 3000000 INFO @ Sun, 02 Jun 2019 22:31:58: 4000000 INFO @ Sun, 02 Jun 2019 22:32:03: 5000000 INFO @ Sun, 02 Jun 2019 22:32:06: 4000000 INFO @ Sun, 02 Jun 2019 22:32:08: 5000000 INFO @ Sun, 02 Jun 2019 22:32:12: 6000000 INFO @ Sun, 02 Jun 2019 22:32:18: 6000000 INFO @ Sun, 02 Jun 2019 22:32:18: 5000000 INFO @ Sun, 02 Jun 2019 22:32:21: 7000000 INFO @ Sun, 02 Jun 2019 22:32:28: 7000000 INFO @ Sun, 02 Jun 2019 22:32:30: 8000000 INFO @ Sun, 02 Jun 2019 22:32:30: 6000000 INFO @ Sun, 02 Jun 2019 22:32:38: 8000000 INFO @ Sun, 02 Jun 2019 22:32:39: 9000000 INFO @ Sun, 02 Jun 2019 22:32:41: 7000000 INFO @ Sun, 02 Jun 2019 22:32:47: 10000000 INFO @ Sun, 02 Jun 2019 22:32:48: 9000000 INFO @ Sun, 02 Jun 2019 22:32:53: 8000000 INFO @ Sun, 02 Jun 2019 22:32:56: 11000000 INFO @ Sun, 02 Jun 2019 22:32:58: 10000000 INFO @ Sun, 02 Jun 2019 22:33:05: 12000000 INFO @ Sun, 02 Jun 2019 22:33:05: 9000000 INFO @ Sun, 02 Jun 2019 22:33:08: 11000000 INFO @ Sun, 02 Jun 2019 22:33:14: 13000000 INFO @ Sun, 02 Jun 2019 22:33:17: 10000000 INFO @ Sun, 02 Jun 2019 22:33:17: 12000000 INFO @ Sun, 02 Jun 2019 22:33:23: 14000000 INFO @ Sun, 02 Jun 2019 22:33:27: 13000000 INFO @ Sun, 02 Jun 2019 22:33:29: 11000000 INFO @ Sun, 02 Jun 2019 22:33:31: 15000000 INFO @ Sun, 02 Jun 2019 22:33:33: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:33:33: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:33:33: #1 total tags in treatment: 15215160 INFO @ Sun, 02 Jun 2019 22:33:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:33:33: #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 22:33:34: #1 tags after filtering in treatment: 15215160 INFO @ Sun, 02 Jun 2019 22:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:33:34: #1 finished! INFO @ Sun, 02 Jun 2019 22:33:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:33:35: #2 number of paired peaks: 2487 INFO @ Sun, 02 Jun 2019 22:33:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:33:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:33:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:33:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:33:36: #2 predicted fragment length is 130 bps INFO @ Sun, 02 Jun 2019 22:33:36: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 02 Jun 2019 22:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.10_model.r INFO @ Sun, 02 Jun 2019 22:33:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:33:36: 14000000 INFO @ Sun, 02 Jun 2019 22:33:40: 12000000 INFO @ Sun, 02 Jun 2019 22:33:47: 15000000 INFO @ Sun, 02 Jun 2019 22:33:49: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:33:49: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:33:49: #1 total tags in treatment: 15215160 INFO @ Sun, 02 Jun 2019 22:33:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:33:49: #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 22:33:49: #1 tags after filtering in treatment: 15215160 INFO @ Sun, 02 Jun 2019 22:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:33:49: #1 finished! INFO @ Sun, 02 Jun 2019 22:33:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:33:51: 13000000 INFO @ Sun, 02 Jun 2019 22:33:51: #2 number of paired peaks: 2487 INFO @ Sun, 02 Jun 2019 22:33:51: start model_add_line... INFO @ Sun, 02 Jun 2019 22:33:51: start X-correlation... INFO @ Sun, 02 Jun 2019 22:33:51: end of X-cor INFO @ Sun, 02 Jun 2019 22:33:51: #2 finished! INFO @ Sun, 02 Jun 2019 22:33:51: #2 predicted fragment length is 130 bps INFO @ Sun, 02 Jun 2019 22:33:51: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 02 Jun 2019 22:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.20_model.r INFO @ Sun, 02 Jun 2019 22:33:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:02: 14000000 INFO @ Sun, 02 Jun 2019 22:34:14: 15000000 INFO @ Sun, 02 Jun 2019 22:34:17: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:34:17: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:34:17: #1 total tags in treatment: 15215160 INFO @ Sun, 02 Jun 2019 22:34:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:17: #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 22:34:17: #1 tags after filtering in treatment: 15215160 INFO @ Sun, 02 Jun 2019 22:34:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:17: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:34:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:34:18: #2 number of paired peaks: 2487 INFO @ Sun, 02 Jun 2019 22:34:18: start model_add_line... INFO @ Sun, 02 Jun 2019 22:34:19: start X-correlation... INFO @ Sun, 02 Jun 2019 22:34:19: end of X-cor INFO @ Sun, 02 Jun 2019 22:34:19: #2 finished! INFO @ Sun, 02 Jun 2019 22:34:19: #2 predicted fragment length is 130 bps INFO @ Sun, 02 Jun 2019 22:34:19: #2 alternative fragment length(s) may be 130 bps INFO @ Sun, 02 Jun 2019 22:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.05_model.r INFO @ Sun, 02 Jun 2019 22:34:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.10_summits.bed INFO @ Sun, 02 Jun 2019 22:34:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5555 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.20_summits.bed INFO @ Sun, 02 Jun 2019 22:34:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4491 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:35:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:35:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402725/SRX5402725.05_summits.bed INFO @ Sun, 02 Jun 2019 22:35:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6872 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。