Job ID = 1292989 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,513,693 reads read : 15,513,693 reads written : 15,513,693 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: 00:07:00 15513693 reads; of these: 15513693 (100.00%) were unpaired; of these: 1929561 (12.44%) aligned 0 times 11353684 (73.18%) aligned exactly 1 time 2230448 (14.38%) aligned >1 times 87.56% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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 8 files... [bam_rmdupse_core] 7477419 / 13584132 = 0.5505 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 21:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.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 21:29:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.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 21:29:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.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 21:29:01: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:01: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:16: 1000000 INFO @ Sun, 02 Jun 2019 21:29:16: 1000000 INFO @ Sun, 02 Jun 2019 21:29:17: 1000000 INFO @ Sun, 02 Jun 2019 21:29:32: 2000000 INFO @ Sun, 02 Jun 2019 21:29:33: 2000000 INFO @ Sun, 02 Jun 2019 21:29:33: 2000000 INFO @ Sun, 02 Jun 2019 21:29:46: 3000000 INFO @ Sun, 02 Jun 2019 21:29:47: 3000000 INFO @ Sun, 02 Jun 2019 21:29:48: 3000000 INFO @ Sun, 02 Jun 2019 21:30:02: 4000000 INFO @ Sun, 02 Jun 2019 21:30:02: 4000000 INFO @ Sun, 02 Jun 2019 21:30:04: 4000000 INFO @ Sun, 02 Jun 2019 21:30:16: 5000000 INFO @ Sun, 02 Jun 2019 21:30:18: 5000000 INFO @ Sun, 02 Jun 2019 21:30:19: 5000000 INFO @ Sun, 02 Jun 2019 21:30:31: 6000000 INFO @ Sun, 02 Jun 2019 21:30:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:30:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:30:32: #1 total tags in treatment: 6106713 INFO @ Sun, 02 Jun 2019 21:30:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:30:32: #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 21:30:32: #1 tags after filtering in treatment: 6106713 INFO @ Sun, 02 Jun 2019 21:30:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:30:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:30:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:30:33: #2 number of paired peaks: 629 WARNING @ Sun, 02 Jun 2019 21:30:33: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Sun, 02 Jun 2019 21:30:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:30:33: 6000000 INFO @ Sun, 02 Jun 2019 21:30:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:30:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:30:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:30:33: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 21:30:33: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 02 Jun 2019 21:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.05_model.r WARNING @ Sun, 02 Jun 2019 21:30:33: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:30:33: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 02 Jun 2019 21:30:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:30:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:30:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:30:35: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:30:35: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:30:35: #1 total tags in treatment: 6106713 INFO @ Sun, 02 Jun 2019 21:30:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:30:35: #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 21:30:35: #1 tags after filtering in treatment: 6106713 INFO @ Sun, 02 Jun 2019 21:30:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:30:35: #1 finished! INFO @ Sun, 02 Jun 2019 21:30:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:30:35: 6000000 INFO @ Sun, 02 Jun 2019 21:30:36: #2 number of paired peaks: 629 WARNING @ Sun, 02 Jun 2019 21:30:36: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Sun, 02 Jun 2019 21:30:36: start model_add_line... INFO @ Sun, 02 Jun 2019 21:30:36: start X-correlation... INFO @ Sun, 02 Jun 2019 21:30:36: end of X-cor INFO @ Sun, 02 Jun 2019 21:30:36: #2 finished! INFO @ Sun, 02 Jun 2019 21:30:36: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 21:30:36: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 02 Jun 2019 21:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.10_model.r WARNING @ Sun, 02 Jun 2019 21:30:36: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:30:36: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 02 Jun 2019 21:30:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:30:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:30:36: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:30:36: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:30:36: #1 total tags in treatment: 6106713 INFO @ Sun, 02 Jun 2019 21:30:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:30:36: #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 21:30:37: #1 tags after filtering in treatment: 6106713 INFO @ Sun, 02 Jun 2019 21:30:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:30:37: #1 finished! INFO @ Sun, 02 Jun 2019 21:30:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:30:38: #2 number of paired peaks: 629 WARNING @ Sun, 02 Jun 2019 21:30:38: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Sun, 02 Jun 2019 21:30:38: start model_add_line... INFO @ Sun, 02 Jun 2019 21:30:38: start X-correlation... INFO @ Sun, 02 Jun 2019 21:30:38: end of X-cor INFO @ Sun, 02 Jun 2019 21:30:38: #2 finished! INFO @ Sun, 02 Jun 2019 21:30:38: #2 predicted fragment length is 61 bps INFO @ Sun, 02 Jun 2019 21:30:38: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sun, 02 Jun 2019 21:30:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.20_model.r WARNING @ Sun, 02 Jun 2019 21:30:38: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:30:38: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sun, 02 Jun 2019 21:30:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:30:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:30:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:31:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:31:06: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:31:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:31:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:31:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.05_summits.bed INFO @ Sun, 02 Jun 2019 21:31:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (780 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.10_summits.bed INFO @ Sun, 02 Jun 2019 21:31:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:31:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:31:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:31:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020765/SRX5020765.20_summits.bed INFO @ Sun, 02 Jun 2019 21:31:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。