Job ID = 1293056 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,174,985 reads read : 9,174,985 reads written : 9,174,985 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: 00:02:25 9174985 reads; of these: 9174985 (100.00%) were unpaired; of these: 97478 (1.06%) aligned 0 times 7581870 (82.64%) aligned exactly 1 time 1495637 (16.30%) aligned >1 times 98.94% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 477528 / 9077507 = 0.0526 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 21:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.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 21:38:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:38:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.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 21:38:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:38:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:38:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.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 21:38:24: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:38:24: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:38:32: 1000000 INFO @ Sun, 02 Jun 2019 21:38:34: 1000000 INFO @ Sun, 02 Jun 2019 21:38:35: 1000000 INFO @ Sun, 02 Jun 2019 21:38:40: 2000000 INFO @ Sun, 02 Jun 2019 21:38:44: 2000000 INFO @ Sun, 02 Jun 2019 21:38:45: 2000000 INFO @ Sun, 02 Jun 2019 21:38:48: 3000000 INFO @ Sun, 02 Jun 2019 21:38:53: 3000000 INFO @ Sun, 02 Jun 2019 21:38:54: 3000000 INFO @ Sun, 02 Jun 2019 21:38:56: 4000000 INFO @ Sun, 02 Jun 2019 21:39:01: 4000000 INFO @ Sun, 02 Jun 2019 21:39:03: 4000000 INFO @ Sun, 02 Jun 2019 21:39:04: 5000000 INFO @ Sun, 02 Jun 2019 21:39:10: 5000000 INFO @ Sun, 02 Jun 2019 21:39:12: 6000000 INFO @ Sun, 02 Jun 2019 21:39:12: 5000000 INFO @ Sun, 02 Jun 2019 21:39:18: 6000000 INFO @ Sun, 02 Jun 2019 21:39:20: 7000000 INFO @ Sun, 02 Jun 2019 21:39:21: 6000000 INFO @ Sun, 02 Jun 2019 21:39:27: 7000000 INFO @ Sun, 02 Jun 2019 21:39:27: 8000000 INFO @ Sun, 02 Jun 2019 21:39:29: 7000000 INFO @ Sun, 02 Jun 2019 21:39:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:39:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:39:32: #1 total tags in treatment: 8599979 INFO @ Sun, 02 Jun 2019 21:39:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:32: #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 21:39:32: #1 tags after filtering in treatment: 8599979 INFO @ Sun, 02 Jun 2019 21:39:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:39:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:33: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 21:39:33: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:33: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:39:33: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 02 Jun 2019 21:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.10_model.r WARNING @ Sun, 02 Jun 2019 21:39:33: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:39:33: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 02 Jun 2019 21:39:33: #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 21:39:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:37: 8000000 INFO @ Sun, 02 Jun 2019 21:39:38: 8000000 INFO @ Sun, 02 Jun 2019 21:39:42: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:39:42: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:39:42: #1 total tags in treatment: 8599979 INFO @ Sun, 02 Jun 2019 21:39:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:42: #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 21:39:43: #1 tags after filtering in treatment: 8599979 INFO @ Sun, 02 Jun 2019 21:39:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:39:43: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:43: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 21:39:43: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:43: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:43: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:43: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:43: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:43: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:39:43: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 02 Jun 2019 21:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.20_model.r WARNING @ Sun, 02 Jun 2019 21:39:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:39:44: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 02 Jun 2019 21:39:44: #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 21:39:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:44: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:39:44: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:39:44: #1 total tags in treatment: 8599979 INFO @ Sun, 02 Jun 2019 21:39:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:39:44: #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 21:39:44: #1 tags after filtering in treatment: 8599979 INFO @ Sun, 02 Jun 2019 21:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:39:44: #1 finished! INFO @ Sun, 02 Jun 2019 21:39:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:39:45: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 21:39:45: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 21:39:45: start model_add_line... INFO @ Sun, 02 Jun 2019 21:39:45: start X-correlation... INFO @ Sun, 02 Jun 2019 21:39:45: end of X-cor INFO @ Sun, 02 Jun 2019 21:39:45: #2 finished! INFO @ Sun, 02 Jun 2019 21:39:45: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:39:45: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 02 Jun 2019 21:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.05_model.r WARNING @ Sun, 02 Jun 2019 21:39:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:39:45: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 02 Jun 2019 21:39:45: #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 21:39:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:39:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.10_summits.bed INFO @ Sun, 02 Jun 2019 21:40:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:40:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.20_summits.bed INFO @ Sun, 02 Jun 2019 21:40:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:40:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:40:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:40:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020820/SRX5020820.05_summits.bed INFO @ Sun, 02 Jun 2019 21:40:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (556 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。