Job ID = 1291879 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,309,990 reads read : 56,619,980 reads written : 28,309,990 reads 0-length : 28,309,990 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: 00:06:01 28309990 reads; of these: 28309990 (100.00%) were unpaired; of these: 3692929 (13.04%) aligned 0 times 21412229 (75.63%) aligned exactly 1 time 3204832 (11.32%) aligned >1 times 86.96% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 9725242 / 24617061 = 0.3951 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 17:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.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 17:08:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:08:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.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 17:08:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:08:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.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 17:08:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:08:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:08:52: 1000000 INFO @ Sun, 02 Jun 2019 17:08:52: 1000000 INFO @ Sun, 02 Jun 2019 17:08:52: 1000000 INFO @ Sun, 02 Jun 2019 17:08:59: 2000000 INFO @ Sun, 02 Jun 2019 17:08:59: 2000000 INFO @ Sun, 02 Jun 2019 17:09:00: 2000000 INFO @ Sun, 02 Jun 2019 17:09:07: 3000000 INFO @ Sun, 02 Jun 2019 17:09:07: 3000000 INFO @ Sun, 02 Jun 2019 17:09:07: 3000000 INFO @ Sun, 02 Jun 2019 17:09:14: 4000000 INFO @ Sun, 02 Jun 2019 17:09:15: 4000000 INFO @ Sun, 02 Jun 2019 17:09:15: 4000000 INFO @ Sun, 02 Jun 2019 17:09:22: 5000000 INFO @ Sun, 02 Jun 2019 17:09:22: 5000000 INFO @ Sun, 02 Jun 2019 17:09:22: 5000000 INFO @ Sun, 02 Jun 2019 17:09:29: 6000000 INFO @ Sun, 02 Jun 2019 17:09:30: 6000000 INFO @ Sun, 02 Jun 2019 17:09:30: 6000000 INFO @ Sun, 02 Jun 2019 17:09:37: 7000000 INFO @ Sun, 02 Jun 2019 17:09:37: 7000000 INFO @ Sun, 02 Jun 2019 17:09:38: 7000000 INFO @ Sun, 02 Jun 2019 17:09:44: 8000000 INFO @ Sun, 02 Jun 2019 17:09:45: 8000000 INFO @ Sun, 02 Jun 2019 17:09:45: 8000000 INFO @ Sun, 02 Jun 2019 17:09:52: 9000000 INFO @ Sun, 02 Jun 2019 17:09:52: 9000000 INFO @ Sun, 02 Jun 2019 17:09:53: 9000000 INFO @ Sun, 02 Jun 2019 17:09:59: 10000000 INFO @ Sun, 02 Jun 2019 17:10:00: 10000000 INFO @ Sun, 02 Jun 2019 17:10:00: 10000000 INFO @ Sun, 02 Jun 2019 17:10:07: 11000000 INFO @ Sun, 02 Jun 2019 17:10:08: 11000000 INFO @ Sun, 02 Jun 2019 17:10:08: 11000000 INFO @ Sun, 02 Jun 2019 17:10:14: 12000000 INFO @ Sun, 02 Jun 2019 17:10:15: 12000000 INFO @ Sun, 02 Jun 2019 17:10:17: 12000000 INFO @ Sun, 02 Jun 2019 17:10:22: 13000000 INFO @ Sun, 02 Jun 2019 17:10:23: 13000000 INFO @ Sun, 02 Jun 2019 17:10:25: 13000000 INFO @ Sun, 02 Jun 2019 17:10:29: 14000000 INFO @ Sun, 02 Jun 2019 17:10:30: 14000000 INFO @ Sun, 02 Jun 2019 17:10:34: 14000000 INFO @ Sun, 02 Jun 2019 17:10:35: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:10:35: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:10:35: #1 total tags in treatment: 14891819 INFO @ Sun, 02 Jun 2019 17:10:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:10:35: #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 17:10:36: #1 tags after filtering in treatment: 14891819 INFO @ Sun, 02 Jun 2019 17:10:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:10:36: #1 finished! INFO @ Sun, 02 Jun 2019 17:10:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:10:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:10:37: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:10:37: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:10:37: #1 total tags in treatment: 14891819 INFO @ Sun, 02 Jun 2019 17:10:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:10:37: #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 17:10:37: #1 tags after filtering in treatment: 14891819 INFO @ Sun, 02 Jun 2019 17:10:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:10:37: #1 finished! INFO @ Sun, 02 Jun 2019 17:10:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:10:37: #2 number of paired peaks: 2048 INFO @ Sun, 02 Jun 2019 17:10:37: start model_add_line... INFO @ Sun, 02 Jun 2019 17:10:37: start X-correlation... INFO @ Sun, 02 Jun 2019 17:10:38: end of X-cor INFO @ Sun, 02 Jun 2019 17:10:38: #2 finished! INFO @ Sun, 02 Jun 2019 17:10:38: #2 predicted fragment length is 155 bps INFO @ Sun, 02 Jun 2019 17:10:38: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 02 Jun 2019 17:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.05_model.r INFO @ Sun, 02 Jun 2019 17:10:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:10:39: #2 number of paired peaks: 2048 INFO @ Sun, 02 Jun 2019 17:10:39: start model_add_line... INFO @ Sun, 02 Jun 2019 17:10:39: start X-correlation... INFO @ Sun, 02 Jun 2019 17:10:39: end of X-cor INFO @ Sun, 02 Jun 2019 17:10:39: #2 finished! INFO @ Sun, 02 Jun 2019 17:10:39: #2 predicted fragment length is 155 bps INFO @ Sun, 02 Jun 2019 17:10:39: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 02 Jun 2019 17:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.20_model.r INFO @ Sun, 02 Jun 2019 17:10:39: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:10:42: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:10:42: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:10:42: #1 total tags in treatment: 14891819 INFO @ Sun, 02 Jun 2019 17:10:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:10:42: #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 17:10:42: #1 tags after filtering in treatment: 14891819 INFO @ Sun, 02 Jun 2019 17:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:10:42: #1 finished! INFO @ Sun, 02 Jun 2019 17:10:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:10:44: #2 number of paired peaks: 2048 INFO @ Sun, 02 Jun 2019 17:10:44: start model_add_line... INFO @ Sun, 02 Jun 2019 17:10:44: start X-correlation... INFO @ Sun, 02 Jun 2019 17:10:44: end of X-cor INFO @ Sun, 02 Jun 2019 17:10:44: #2 finished! INFO @ Sun, 02 Jun 2019 17:10:44: #2 predicted fragment length is 155 bps INFO @ Sun, 02 Jun 2019 17:10:44: #2 alternative fragment length(s) may be 4,155 bps INFO @ Sun, 02 Jun 2019 17:10:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.10_model.r INFO @ Sun, 02 Jun 2019 17:10:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:10:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:11:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:11:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:11:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:11:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:11:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.05_summits.bed INFO @ Sun, 02 Jun 2019 17:11:43: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7647 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.20_summits.bed INFO @ Sun, 02 Jun 2019 17:11:44: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2318 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737090/SRX2737090.10_summits.bed INFO @ Sun, 02 Jun 2019 17:11:49: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4811 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。