Job ID = 1293034 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,133,712 reads read : 8,133,712 reads written : 8,133,712 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: 00:02:06 8133712 reads; of these: 8133712 (100.00%) were unpaired; of these: 112345 (1.38%) aligned 0 times 6594636 (81.08%) aligned exactly 1 time 1426731 (17.54%) aligned >1 times 98.62% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 497284 / 8021367 = 0.0620 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 21:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.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 21:30:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:30:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.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 21:30:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:30:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:30:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.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 21:30:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:30:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:30:41: 1000000 INFO @ Sun, 02 Jun 2019 21:30:44: 1000000 INFO @ Sun, 02 Jun 2019 21:30:44: 1000000 INFO @ Sun, 02 Jun 2019 21:30:49: 2000000 INFO @ Sun, 02 Jun 2019 21:30:54: 2000000 INFO @ Sun, 02 Jun 2019 21:30:55: 2000000 INFO @ Sun, 02 Jun 2019 21:30:57: 3000000 INFO @ Sun, 02 Jun 2019 21:31:04: 3000000 INFO @ Sun, 02 Jun 2019 21:31:04: 4000000 INFO @ Sun, 02 Jun 2019 21:31:05: 3000000 INFO @ Sun, 02 Jun 2019 21:31:12: 5000000 INFO @ Sun, 02 Jun 2019 21:31:13: 4000000 INFO @ Sun, 02 Jun 2019 21:31:15: 4000000 INFO @ Sun, 02 Jun 2019 21:31:20: 6000000 INFO @ Sun, 02 Jun 2019 21:31:23: 5000000 INFO @ Sun, 02 Jun 2019 21:31:25: 5000000 INFO @ Sun, 02 Jun 2019 21:31:28: 7000000 INFO @ Sun, 02 Jun 2019 21:31:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:31:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:31:32: #1 total tags in treatment: 7524083 INFO @ Sun, 02 Jun 2019 21:31:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:31:32: #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 21:31:32: #1 tags after filtering in treatment: 7524083 INFO @ Sun, 02 Jun 2019 21:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:31:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:31:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:31:33: #2 number of paired peaks: 397 WARNING @ Sun, 02 Jun 2019 21:31:33: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sun, 02 Jun 2019 21:31:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:31:33: 6000000 INFO @ Sun, 02 Jun 2019 21:31:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:31:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:31:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:31:33: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 21:31:33: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 02 Jun 2019 21:31:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.20_model.r WARNING @ Sun, 02 Jun 2019 21:31:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:31:33: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 02 Jun 2019 21:31:33: #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 21:31:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:31:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:35: 6000000 INFO @ Sun, 02 Jun 2019 21:31:42: 7000000 INFO @ Sun, 02 Jun 2019 21:31:45: 7000000 INFO @ Sun, 02 Jun 2019 21:31:47: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:31:47: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:31:47: #1 total tags in treatment: 7524083 INFO @ Sun, 02 Jun 2019 21:31:47: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:31:47: #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 21:31:47: #1 tags after filtering in treatment: 7524083 INFO @ Sun, 02 Jun 2019 21:31:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:31:47: #1 finished! INFO @ Sun, 02 Jun 2019 21:31:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:31:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:31:48: #2 number of paired peaks: 397 WARNING @ Sun, 02 Jun 2019 21:31:48: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sun, 02 Jun 2019 21:31:48: start model_add_line... INFO @ Sun, 02 Jun 2019 21:31:48: start X-correlation... INFO @ Sun, 02 Jun 2019 21:31:48: end of X-cor INFO @ Sun, 02 Jun 2019 21:31:48: #2 finished! INFO @ Sun, 02 Jun 2019 21:31:48: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 21:31:48: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 02 Jun 2019 21:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.05_model.r WARNING @ Sun, 02 Jun 2019 21:31:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:31:48: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 02 Jun 2019 21:31:48: #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 21:31:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:49: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:31:49: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:31:49: #1 total tags in treatment: 7524083 INFO @ Sun, 02 Jun 2019 21:31:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:31:49: #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 21:31:50: #1 tags after filtering in treatment: 7524083 INFO @ Sun, 02 Jun 2019 21:31:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:31:50: #1 finished! INFO @ Sun, 02 Jun 2019 21:31:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:31:50: #2 number of paired peaks: 397 WARNING @ Sun, 02 Jun 2019 21:31:50: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sun, 02 Jun 2019 21:31:50: start model_add_line... INFO @ Sun, 02 Jun 2019 21:31:50: start X-correlation... INFO @ Sun, 02 Jun 2019 21:31:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:31:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:31:50: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 21:31:50: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 02 Jun 2019 21:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.10_model.r WARNING @ Sun, 02 Jun 2019 21:31:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:31:50: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 02 Jun 2019 21:31:50: #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 21:31:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.20_summits.bed INFO @ Sun, 02 Jun 2019 21:32:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (157 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:32:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.05_summits.bed INFO @ Sun, 02 Jun 2019 21:32:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020800/SRX5020800.10_summits.bed INFO @ Sun, 02 Jun 2019 21:32:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 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。