Job ID = 1292936 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,323,763 reads read : 18,323,763 reads written : 18,323,763 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: 00:04:38 18323763 reads; of these: 18323763 (100.00%) were unpaired; of these: 326149 (1.78%) aligned 0 times 14634861 (79.87%) aligned exactly 1 time 3362753 (18.35%) aligned >1 times 98.22% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 2154789 / 17997614 = 0.1197 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 21:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.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 21:17:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:17:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.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 21:17:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:17:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:17:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.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 21:17:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:17:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:17:35: 1000000 INFO @ Sun, 02 Jun 2019 21:17:35: 1000000 INFO @ Sun, 02 Jun 2019 21:17:36: 1000000 INFO @ Sun, 02 Jun 2019 21:17:44: 2000000 INFO @ Sun, 02 Jun 2019 21:17:44: 2000000 INFO @ Sun, 02 Jun 2019 21:17:45: 2000000 INFO @ Sun, 02 Jun 2019 21:17:53: 3000000 INFO @ Sun, 02 Jun 2019 21:17:53: 3000000 INFO @ Sun, 02 Jun 2019 21:17:54: 3000000 INFO @ Sun, 02 Jun 2019 21:18:01: 4000000 INFO @ Sun, 02 Jun 2019 21:18:03: 4000000 INFO @ Sun, 02 Jun 2019 21:18:03: 4000000 INFO @ Sun, 02 Jun 2019 21:18:09: 5000000 INFO @ Sun, 02 Jun 2019 21:18:12: 5000000 INFO @ Sun, 02 Jun 2019 21:18:12: 5000000 INFO @ Sun, 02 Jun 2019 21:18:18: 6000000 INFO @ Sun, 02 Jun 2019 21:18:20: 6000000 INFO @ Sun, 02 Jun 2019 21:18:21: 6000000 INFO @ Sun, 02 Jun 2019 21:18:26: 7000000 INFO @ Sun, 02 Jun 2019 21:18:29: 7000000 INFO @ Sun, 02 Jun 2019 21:18:30: 7000000 INFO @ Sun, 02 Jun 2019 21:18:35: 8000000 INFO @ Sun, 02 Jun 2019 21:18:38: 8000000 INFO @ Sun, 02 Jun 2019 21:18:39: 8000000 INFO @ Sun, 02 Jun 2019 21:18:43: 9000000 INFO @ Sun, 02 Jun 2019 21:18:47: 9000000 INFO @ Sun, 02 Jun 2019 21:18:48: 9000000 INFO @ Sun, 02 Jun 2019 21:18:52: 10000000 INFO @ Sun, 02 Jun 2019 21:18:55: 10000000 INFO @ Sun, 02 Jun 2019 21:18:57: 10000000 INFO @ Sun, 02 Jun 2019 21:19:00: 11000000 INFO @ Sun, 02 Jun 2019 21:19:04: 11000000 INFO @ Sun, 02 Jun 2019 21:19:06: 11000000 INFO @ Sun, 02 Jun 2019 21:19:08: 12000000 INFO @ Sun, 02 Jun 2019 21:19:12: 12000000 INFO @ Sun, 02 Jun 2019 21:19:14: 12000000 INFO @ Sun, 02 Jun 2019 21:19:16: 13000000 INFO @ Sun, 02 Jun 2019 21:19:21: 13000000 INFO @ Sun, 02 Jun 2019 21:19:23: 13000000 INFO @ Sun, 02 Jun 2019 21:19:24: 14000000 INFO @ Sun, 02 Jun 2019 21:19:30: 14000000 INFO @ Sun, 02 Jun 2019 21:19:32: 14000000 INFO @ Sun, 02 Jun 2019 21:19:33: 15000000 INFO @ Sun, 02 Jun 2019 21:19:38: 15000000 INFO @ Sun, 02 Jun 2019 21:19:40: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:40: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:40: #1 total tags in treatment: 15842825 INFO @ Sun, 02 Jun 2019 21:19:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:40: #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 21:19:40: #1 tags after filtering in treatment: 15842825 INFO @ Sun, 02 Jun 2019 21:19:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:40: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:41: 15000000 INFO @ Sun, 02 Jun 2019 21:19:41: #2 number of paired peaks: 258 WARNING @ Sun, 02 Jun 2019 21:19:41: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:41: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:42: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:42: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:42: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:42: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:19:42: #2 alternative fragment length(s) may be 2,52,559,583,591 bps INFO @ Sun, 02 Jun 2019 21:19:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.20_model.r WARNING @ Sun, 02 Jun 2019 21:19:42: #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 21:19:42: #2 You may need to consider one of the other alternative d(s): 2,52,559,583,591 WARNING @ Sun, 02 Jun 2019 21:19:42: #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 21:19:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:19:46: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:46: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:46: #1 total tags in treatment: 15842825 INFO @ Sun, 02 Jun 2019 21:19:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:46: #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 21:19:46: #1 tags after filtering in treatment: 15842825 INFO @ Sun, 02 Jun 2019 21:19:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:46: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:47: #2 number of paired peaks: 258 WARNING @ Sun, 02 Jun 2019 21:19:47: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:47: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:47: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:47: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:47: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:47: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:19:47: #2 alternative fragment length(s) may be 2,52,559,583,591 bps INFO @ Sun, 02 Jun 2019 21:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.05_model.r WARNING @ Sun, 02 Jun 2019 21:19:47: #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 21:19:47: #2 You may need to consider one of the other alternative d(s): 2,52,559,583,591 WARNING @ Sun, 02 Jun 2019 21:19:47: #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 21:19:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:19:48: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:19:48: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:19:48: #1 total tags in treatment: 15842825 INFO @ Sun, 02 Jun 2019 21:19:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:19:48: #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 21:19:48: #1 tags after filtering in treatment: 15842825 INFO @ Sun, 02 Jun 2019 21:19:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:19:48: #1 finished! INFO @ Sun, 02 Jun 2019 21:19:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:19:50: #2 number of paired peaks: 258 WARNING @ Sun, 02 Jun 2019 21:19:50: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 02 Jun 2019 21:19:50: start model_add_line... INFO @ Sun, 02 Jun 2019 21:19:50: start X-correlation... INFO @ Sun, 02 Jun 2019 21:19:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:19:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:19:50: #2 predicted fragment length is 52 bps INFO @ Sun, 02 Jun 2019 21:19:50: #2 alternative fragment length(s) may be 2,52,559,583,591 bps INFO @ Sun, 02 Jun 2019 21:19:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.10_model.r WARNING @ Sun, 02 Jun 2019 21:19:50: #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 21:19:50: #2 You may need to consider one of the other alternative d(s): 2,52,559,583,591 WARNING @ Sun, 02 Jun 2019 21:19:50: #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 21:19:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:20:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:20:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:20:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:20:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.20_summits.bed INFO @ Sun, 02 Jun 2019 21:20:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.05_summits.bed INFO @ Sun, 02 Jun 2019 21:20:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1288 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:20:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:20:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:20:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020725/SRX5020725.10_summits.bed INFO @ Sun, 02 Jun 2019 21:20:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (471 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。