Job ID = 1293163 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,847,839 reads read : 23,847,839 reads written : 23,847,839 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: 00:05:38 23847839 reads; of these: 23847839 (100.00%) were unpaired; of these: 2876962 (12.06%) aligned 0 times 18799273 (78.83%) aligned exactly 1 time 2171604 (9.11%) aligned >1 times 87.94% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 9003528 / 20970877 = 0.4293 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 22:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.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 22:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.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 22:25:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.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 22:25:41: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:41: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:49: 1000000 INFO @ Sun, 02 Jun 2019 22:25:49: 1000000 INFO @ Sun, 02 Jun 2019 22:25:51: 1000000 INFO @ Sun, 02 Jun 2019 22:25:57: 2000000 INFO @ Sun, 02 Jun 2019 22:25:57: 2000000 INFO @ Sun, 02 Jun 2019 22:26:01: 2000000 INFO @ Sun, 02 Jun 2019 22:26:05: 3000000 INFO @ Sun, 02 Jun 2019 22:26:05: 3000000 INFO @ Sun, 02 Jun 2019 22:26:11: 3000000 INFO @ Sun, 02 Jun 2019 22:26:12: 4000000 INFO @ Sun, 02 Jun 2019 22:26:13: 4000000 INFO @ Sun, 02 Jun 2019 22:26:20: 5000000 INFO @ Sun, 02 Jun 2019 22:26:20: 4000000 INFO @ Sun, 02 Jun 2019 22:26:21: 5000000 INFO @ Sun, 02 Jun 2019 22:26:27: 6000000 INFO @ Sun, 02 Jun 2019 22:26:28: 6000000 INFO @ Sun, 02 Jun 2019 22:26:30: 5000000 INFO @ Sun, 02 Jun 2019 22:26:35: 7000000 INFO @ Sun, 02 Jun 2019 22:26:36: 7000000 INFO @ Sun, 02 Jun 2019 22:26:40: 6000000 INFO @ Sun, 02 Jun 2019 22:26:42: 8000000 INFO @ Sun, 02 Jun 2019 22:26:44: 8000000 INFO @ Sun, 02 Jun 2019 22:26:49: 7000000 INFO @ Sun, 02 Jun 2019 22:26:51: 9000000 INFO @ Sun, 02 Jun 2019 22:26:52: 9000000 INFO @ Sun, 02 Jun 2019 22:26:59: 8000000 INFO @ Sun, 02 Jun 2019 22:26:59: 10000000 INFO @ Sun, 02 Jun 2019 22:27:00: 10000000 INFO @ Sun, 02 Jun 2019 22:27:07: 11000000 INFO @ Sun, 02 Jun 2019 22:27:08: 9000000 INFO @ Sun, 02 Jun 2019 22:27:09: 11000000 INFO @ Sun, 02 Jun 2019 22:27:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:14: #1 total tags in treatment: 11967349 INFO @ Sun, 02 Jun 2019 22:27:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:14: #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 22:27:14: #1 tags after filtering in treatment: 11967349 INFO @ Sun, 02 Jun 2019 22:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:27:14: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:16: #2 number of paired peaks: 5030 INFO @ Sun, 02 Jun 2019 22:27:16: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:16: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:16: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:16: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:16: #2 predicted fragment length is 169 bps INFO @ Sun, 02 Jun 2019 22:27:16: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 02 Jun 2019 22:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.10_model.r INFO @ Sun, 02 Jun 2019 22:27:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:27:17: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:17: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:17: #1 total tags in treatment: 11967349 INFO @ Sun, 02 Jun 2019 22:27:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:17: #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 22:27:17: 10000000 INFO @ Sun, 02 Jun 2019 22:27:17: #1 tags after filtering in treatment: 11967349 INFO @ Sun, 02 Jun 2019 22:27:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:27:17: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:19: #2 number of paired peaks: 5030 INFO @ Sun, 02 Jun 2019 22:27:19: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:19: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:19: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:19: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:19: #2 predicted fragment length is 169 bps INFO @ Sun, 02 Jun 2019 22:27:19: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 02 Jun 2019 22:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.05_model.r INFO @ Sun, 02 Jun 2019 22:27:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:27:27: 11000000 INFO @ Sun, 02 Jun 2019 22:27:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:36: #1 total tags in treatment: 11967349 INFO @ Sun, 02 Jun 2019 22:27:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:36: #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 22:27:36: #1 tags after filtering in treatment: 11967349 INFO @ Sun, 02 Jun 2019 22:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:27:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:38: #2 number of paired peaks: 5030 INFO @ Sun, 02 Jun 2019 22:27:38: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:38: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:38: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:38: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:38: #2 predicted fragment length is 169 bps INFO @ Sun, 02 Jun 2019 22:27:38: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 02 Jun 2019 22:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.20_model.r INFO @ Sun, 02 Jun 2019 22:27:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:27:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.10_summits.bed INFO @ Sun, 02 Jun 2019 22:28:12: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6423 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:28:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.05_summits.bed INFO @ Sun, 02 Jun 2019 22:28:14: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (7970 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:28:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402728/SRX5402728.20_summits.bed INFO @ Sun, 02 Jun 2019 22:28:33: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (5033 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。