Job ID = 1292943 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,566,894 reads read : 11,566,894 reads written : 11,566,894 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:43 11566894 reads; of these: 11566894 (100.00%) were unpaired; of these: 820556 (7.09%) aligned 0 times 8983363 (77.66%) aligned exactly 1 time 1762975 (15.24%) aligned >1 times 92.91% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 819482 / 10746338 = 0.0763 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 21:14:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.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 21:14:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:14:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:14:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.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 21:14:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.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 21:14:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:14:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:14:14: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:14:14: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:14:22: 1000000 INFO @ Sun, 02 Jun 2019 21:14:24: 1000000 INFO @ Sun, 02 Jun 2019 21:14:24: 1000000 INFO @ Sun, 02 Jun 2019 21:14:30: 2000000 INFO @ Sun, 02 Jun 2019 21:14:34: 2000000 INFO @ Sun, 02 Jun 2019 21:14:34: 2000000 INFO @ Sun, 02 Jun 2019 21:14:38: 3000000 INFO @ Sun, 02 Jun 2019 21:14:43: 3000000 INFO @ Sun, 02 Jun 2019 21:14:43: 3000000 INFO @ Sun, 02 Jun 2019 21:14:46: 4000000 INFO @ Sun, 02 Jun 2019 21:14:54: 4000000 INFO @ Sun, 02 Jun 2019 21:14:54: 4000000 INFO @ Sun, 02 Jun 2019 21:14:54: 5000000 INFO @ Sun, 02 Jun 2019 21:15:02: 6000000 INFO @ Sun, 02 Jun 2019 21:15:04: 5000000 INFO @ Sun, 02 Jun 2019 21:15:04: 5000000 INFO @ Sun, 02 Jun 2019 21:15:10: 7000000 INFO @ Sun, 02 Jun 2019 21:15:13: 6000000 INFO @ Sun, 02 Jun 2019 21:15:14: 6000000 INFO @ Sun, 02 Jun 2019 21:15:18: 8000000 INFO @ Sun, 02 Jun 2019 21:15:23: 7000000 INFO @ Sun, 02 Jun 2019 21:15:23: 7000000 INFO @ Sun, 02 Jun 2019 21:15:25: 9000000 INFO @ Sun, 02 Jun 2019 21:15:33: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:15:33: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:15:33: #1 total tags in treatment: 9926856 INFO @ Sun, 02 Jun 2019 21:15:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:15:33: #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 21:15:33: #1 tags after filtering in treatment: 9926856 INFO @ Sun, 02 Jun 2019 21:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:15:33: #1 finished! INFO @ Sun, 02 Jun 2019 21:15:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:15:33: 8000000 INFO @ Sun, 02 Jun 2019 21:15:33: 8000000 INFO @ Sun, 02 Jun 2019 21:15:34: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 21:15:34: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 21:15:34: start model_add_line... INFO @ Sun, 02 Jun 2019 21:15:34: start X-correlation... INFO @ Sun, 02 Jun 2019 21:15:34: end of X-cor INFO @ Sun, 02 Jun 2019 21:15:34: #2 finished! INFO @ Sun, 02 Jun 2019 21:15:34: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 21:15:34: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sun, 02 Jun 2019 21:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.10_model.r WARNING @ Sun, 02 Jun 2019 21:15:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:15:34: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sun, 02 Jun 2019 21:15:34: #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 21:15:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:15:42: 9000000 INFO @ Sun, 02 Jun 2019 21:15:43: 9000000 INFO @ Sun, 02 Jun 2019 21:15:52: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:15:52: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:15:52: #1 total tags in treatment: 9926856 INFO @ Sun, 02 Jun 2019 21:15:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:15:52: #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 21:15:52: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:15:52: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:15:52: #1 total tags in treatment: 9926856 INFO @ Sun, 02 Jun 2019 21:15:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:15:52: #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 21:15:52: #1 tags after filtering in treatment: 9926856 INFO @ Sun, 02 Jun 2019 21:15:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:15:52: #1 finished! INFO @ Sun, 02 Jun 2019 21:15:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:15:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:15:52: #1 tags after filtering in treatment: 9926856 INFO @ Sun, 02 Jun 2019 21:15:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:15:52: #1 finished! INFO @ Sun, 02 Jun 2019 21:15:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:15:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:15:53: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 21:15:53: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 21:15:53: start model_add_line... INFO @ Sun, 02 Jun 2019 21:15:53: start X-correlation... INFO @ Sun, 02 Jun 2019 21:15:53: end of X-cor INFO @ Sun, 02 Jun 2019 21:15:53: #2 finished! INFO @ Sun, 02 Jun 2019 21:15:53: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 21:15:53: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sun, 02 Jun 2019 21:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.20_model.r WARNING @ Sun, 02 Jun 2019 21:15:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:15:53: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sun, 02 Jun 2019 21:15:53: #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 21:15:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:15:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:15:53: #2 number of paired peaks: 309 WARNING @ Sun, 02 Jun 2019 21:15:53: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Sun, 02 Jun 2019 21:15:53: start model_add_line... INFO @ Sun, 02 Jun 2019 21:15:53: start X-correlation... INFO @ Sun, 02 Jun 2019 21:15:53: end of X-cor INFO @ Sun, 02 Jun 2019 21:15:53: #2 finished! INFO @ Sun, 02 Jun 2019 21:15:53: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 21:15:53: #2 alternative fragment length(s) may be 3,50 bps INFO @ Sun, 02 Jun 2019 21:15:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.05_model.r WARNING @ Sun, 02 Jun 2019 21:15:53: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:15:53: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Sun, 02 Jun 2019 21:15:53: #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 21:15:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:15:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:16:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.10_summits.bed INFO @ Sun, 02 Jun 2019 21:16:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (357 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:16:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:16:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.20_summits.bed INFO @ Sun, 02 Jun 2019 21:16:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:16:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:16:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:16:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020730/SRX5020730.05_summits.bed INFO @ Sun, 02 Jun 2019 21:16:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。