Job ID = 1290616 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,406,714 reads read : 18,406,714 reads written : 18,406,714 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: 00:02:43 18406714 reads; of these: 18406714 (100.00%) were unpaired; of these: 5529557 (30.04%) aligned 0 times 11480415 (62.37%) aligned exactly 1 time 1396742 (7.59%) aligned >1 times 69.96% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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_rmdupse_core] 3103611 / 12877157 = 0.2410 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 @ Sat, 01 Jun 2019 21:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.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 @ Sat, 01 Jun 2019 21:50:37: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:37: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.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 @ Sat, 01 Jun 2019 21:50:37: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:37: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.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 @ Sat, 01 Jun 2019 21:50:37: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:37: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:44: 1000000 INFO @ Sat, 01 Jun 2019 21:50:46: 1000000 INFO @ Sat, 01 Jun 2019 21:50:46: 1000000 INFO @ Sat, 01 Jun 2019 21:50:50: 2000000 INFO @ Sat, 01 Jun 2019 21:50:53: 2000000 INFO @ Sat, 01 Jun 2019 21:50:54: 2000000 INFO @ Sat, 01 Jun 2019 21:50:56: 3000000 INFO @ Sat, 01 Jun 2019 21:51:01: 3000000 INFO @ Sat, 01 Jun 2019 21:51:02: 3000000 INFO @ Sat, 01 Jun 2019 21:51:02: 4000000 INFO @ Sat, 01 Jun 2019 21:51:08: 5000000 INFO @ Sat, 01 Jun 2019 21:51:08: 4000000 INFO @ Sat, 01 Jun 2019 21:51:09: 4000000 INFO @ Sat, 01 Jun 2019 21:51:15: 6000000 INFO @ Sat, 01 Jun 2019 21:51:16: 5000000 INFO @ Sat, 01 Jun 2019 21:51:17: 5000000 INFO @ Sat, 01 Jun 2019 21:51:21: 7000000 INFO @ Sat, 01 Jun 2019 21:51:24: 6000000 INFO @ Sat, 01 Jun 2019 21:51:24: 6000000 INFO @ Sat, 01 Jun 2019 21:51:27: 8000000 INFO @ Sat, 01 Jun 2019 21:51:31: 7000000 INFO @ Sat, 01 Jun 2019 21:51:31: 7000000 INFO @ Sat, 01 Jun 2019 21:51:33: 9000000 INFO @ Sat, 01 Jun 2019 21:51:38: #1 tag size is determined as 35 bps INFO @ Sat, 01 Jun 2019 21:51:38: #1 tag size = 35 INFO @ Sat, 01 Jun 2019 21:51:38: #1 total tags in treatment: 9773546 INFO @ Sat, 01 Jun 2019 21:51:38: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:38: #1 tags after filtering in treatment: 9773546 INFO @ Sat, 01 Jun 2019 21:51:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:38: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:38: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:39: 8000000 INFO @ Sat, 01 Jun 2019 21:51:39: 8000000 INFO @ Sat, 01 Jun 2019 21:51:39: #2 number of paired peaks: 3956 INFO @ Sat, 01 Jun 2019 21:51:39: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:39: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:39: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:39: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:39: #2 predicted fragment length is 233 bps INFO @ Sat, 01 Jun 2019 21:51:39: #2 alternative fragment length(s) may be 233 bps INFO @ Sat, 01 Jun 2019 21:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.05_model.r INFO @ Sat, 01 Jun 2019 21:51:39: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:46: 9000000 INFO @ Sat, 01 Jun 2019 21:51:47: 9000000 INFO @ Sat, 01 Jun 2019 21:51:52: #1 tag size is determined as 35 bps INFO @ Sat, 01 Jun 2019 21:51:52: #1 tag size = 35 INFO @ Sat, 01 Jun 2019 21:51:52: #1 total tags in treatment: 9773546 INFO @ Sat, 01 Jun 2019 21:51:52: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:52: #1 tags after filtering in treatment: 9773546 INFO @ Sat, 01 Jun 2019 21:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:52: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:52: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:52: #1 tag size is determined as 35 bps INFO @ Sat, 01 Jun 2019 21:51:52: #1 tag size = 35 INFO @ Sat, 01 Jun 2019 21:51:52: #1 total tags in treatment: 9773546 INFO @ Sat, 01 Jun 2019 21:51:52: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:53: #1 tags after filtering in treatment: 9773546 INFO @ Sat, 01 Jun 2019 21:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:53: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:53: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:53: #2 number of paired peaks: 3956 INFO @ Sat, 01 Jun 2019 21:51:53: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:53: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:53: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:53: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:53: #2 predicted fragment length is 233 bps INFO @ Sat, 01 Jun 2019 21:51:53: #2 alternative fragment length(s) may be 233 bps INFO @ Sat, 01 Jun 2019 21:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.20_model.r INFO @ Sat, 01 Jun 2019 21:51:53: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:54: #2 number of paired peaks: 3956 INFO @ Sat, 01 Jun 2019 21:51:54: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:54: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:54: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:54: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:54: #2 predicted fragment length is 233 bps INFO @ Sat, 01 Jun 2019 21:51:54: #2 alternative fragment length(s) may be 233 bps INFO @ Sat, 01 Jun 2019 21:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.10_model.r INFO @ Sat, 01 Jun 2019 21:51:54: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:14: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.05_summits.bed INFO @ Sat, 01 Jun 2019 21:52:28: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5153 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:28: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:29: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.20_summits.bed INFO @ Sat, 01 Jun 2019 21:52:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3458 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2228866/SRX2228866.10_summits.bed INFO @ Sat, 01 Jun 2019 21:52:43: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4260 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。