Job ID = 1291689 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,514,426 reads read : 7,514,426 reads written : 7,514,426 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: 00:01:32 7514426 reads; of these: 7514426 (100.00%) were unpaired; of these: 1119069 (14.89%) aligned 0 times 5633264 (74.97%) aligned exactly 1 time 762093 (10.14%) aligned >1 times 85.11% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 892564 / 6395357 = 0.1396 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 16:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.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 16:22:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:22:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.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 16:22:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:22:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.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 16:22:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:22:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:22:08: 1000000 INFO @ Sun, 02 Jun 2019 16:22:09: 1000000 INFO @ Sun, 02 Jun 2019 16:22:10: 1000000 INFO @ Sun, 02 Jun 2019 16:22:15: 2000000 INFO @ Sun, 02 Jun 2019 16:22:18: 2000000 INFO @ Sun, 02 Jun 2019 16:22:18: 2000000 INFO @ Sun, 02 Jun 2019 16:22:23: 3000000 INFO @ Sun, 02 Jun 2019 16:22:26: 3000000 INFO @ Sun, 02 Jun 2019 16:22:26: 3000000 INFO @ Sun, 02 Jun 2019 16:22:30: 4000000 INFO @ Sun, 02 Jun 2019 16:22:34: 4000000 INFO @ Sun, 02 Jun 2019 16:22:35: 4000000 INFO @ Sun, 02 Jun 2019 16:22:37: 5000000 INFO @ Sun, 02 Jun 2019 16:22:41: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:22:41: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:22:41: #1 total tags in treatment: 5502793 INFO @ Sun, 02 Jun 2019 16:22:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:22:41: #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 16:22:41: #1 tags after filtering in treatment: 5502793 INFO @ Sun, 02 Jun 2019 16:22:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:22:41: #1 finished! INFO @ Sun, 02 Jun 2019 16:22:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:22:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:22:42: #2 number of paired peaks: 890 WARNING @ Sun, 02 Jun 2019 16:22:42: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Sun, 02 Jun 2019 16:22:42: start model_add_line... INFO @ Sun, 02 Jun 2019 16:22:42: start X-correlation... INFO @ Sun, 02 Jun 2019 16:22:42: end of X-cor INFO @ Sun, 02 Jun 2019 16:22:42: #2 finished! INFO @ Sun, 02 Jun 2019 16:22:42: #2 predicted fragment length is 181 bps INFO @ Sun, 02 Jun 2019 16:22:42: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 02 Jun 2019 16:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.20_model.r INFO @ Sun, 02 Jun 2019 16:22:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:22:42: 5000000 INFO @ Sun, 02 Jun 2019 16:22:43: 5000000 INFO @ Sun, 02 Jun 2019 16:22:46: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:22:46: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:22:46: #1 total tags in treatment: 5502793 INFO @ Sun, 02 Jun 2019 16:22:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:22:46: #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 16:22:46: #1 tags after filtering in treatment: 5502793 INFO @ Sun, 02 Jun 2019 16:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:22:46: #1 finished! INFO @ Sun, 02 Jun 2019 16:22:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:22:47: #2 number of paired peaks: 890 WARNING @ Sun, 02 Jun 2019 16:22:47: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Sun, 02 Jun 2019 16:22:47: start model_add_line... INFO @ Sun, 02 Jun 2019 16:22:47: start X-correlation... INFO @ Sun, 02 Jun 2019 16:22:47: end of X-cor INFO @ Sun, 02 Jun 2019 16:22:47: #2 finished! INFO @ Sun, 02 Jun 2019 16:22:47: #2 predicted fragment length is 181 bps INFO @ Sun, 02 Jun 2019 16:22:47: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 02 Jun 2019 16:22:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.05_model.r INFO @ Sun, 02 Jun 2019 16:22:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:22:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:22:47: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:22:47: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:22:47: #1 total tags in treatment: 5502793 INFO @ Sun, 02 Jun 2019 16:22:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:22:47: #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 16:22:47: #1 tags after filtering in treatment: 5502793 INFO @ Sun, 02 Jun 2019 16:22:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:22:47: #1 finished! INFO @ Sun, 02 Jun 2019 16:22:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:22:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:22:48: #2 number of paired peaks: 890 WARNING @ Sun, 02 Jun 2019 16:22:48: Fewer paired peaks (890) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 890 pairs to build model! INFO @ Sun, 02 Jun 2019 16:22:48: start model_add_line... INFO @ Sun, 02 Jun 2019 16:22:48: start X-correlation... INFO @ Sun, 02 Jun 2019 16:22:48: end of X-cor INFO @ Sun, 02 Jun 2019 16:22:48: #2 finished! INFO @ Sun, 02 Jun 2019 16:22:48: #2 predicted fragment length is 181 bps INFO @ Sun, 02 Jun 2019 16:22:48: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 02 Jun 2019 16:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.10_model.r INFO @ Sun, 02 Jun 2019 16:22:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:22:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:23:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:23:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:23:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.20_summits.bed INFO @ Sun, 02 Jun 2019 16:23:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:23:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:23:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:23:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.05_summits.bed INFO @ Sun, 02 Jun 2019 16:23:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2959 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:23:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:23:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:23:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216759/SRX216759.10_summits.bed INFO @ Sun, 02 Jun 2019 16:23:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1539 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。