Job ID = 2590865 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,952,245 reads read : 65,904,490 reads written : 32,952,245 reads 0-length : 32,952,245 rm: cannot remove ‘[DSE]RR*’: 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: 00:15:28 32952245 reads; of these: 32952245 (100.00%) were unpaired; of these: 2451085 (7.44%) aligned 0 times 20948743 (63.57%) aligned exactly 1 time 9552417 (28.99%) aligned >1 times 92.56% overall alignment rate Time searching: 00:15:28 Overall time: 00:15:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 12087734 / 30501160 = 0.3963 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 @ Tue, 13 Aug 2019 00:10:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:10:26: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:10:26: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:10:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:10:27: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:10:27: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:10:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 13 Aug 2019 00:10:28: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:10:28: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:10:33: 1000000 INFO @ Tue, 13 Aug 2019 00:10:33: 1000000 INFO @ Tue, 13 Aug 2019 00:10:34: 1000000 INFO @ Tue, 13 Aug 2019 00:10:39: 2000000 INFO @ Tue, 13 Aug 2019 00:10:39: 2000000 INFO @ Tue, 13 Aug 2019 00:10:40: 2000000 INFO @ Tue, 13 Aug 2019 00:10:45: 3000000 INFO @ Tue, 13 Aug 2019 00:10:46: 3000000 INFO @ Tue, 13 Aug 2019 00:10:46: 3000000 INFO @ Tue, 13 Aug 2019 00:10:51: 4000000 INFO @ Tue, 13 Aug 2019 00:10:52: 4000000 INFO @ Tue, 13 Aug 2019 00:10:52: 4000000 INFO @ Tue, 13 Aug 2019 00:10:57: 5000000 INFO @ Tue, 13 Aug 2019 00:10:58: 5000000 INFO @ Tue, 13 Aug 2019 00:10:59: 5000000 INFO @ Tue, 13 Aug 2019 00:11:03: 6000000 INFO @ Tue, 13 Aug 2019 00:11:04: 6000000 INFO @ Tue, 13 Aug 2019 00:11:05: 6000000 INFO @ Tue, 13 Aug 2019 00:11:09: 7000000 INFO @ Tue, 13 Aug 2019 00:11:10: 7000000 INFO @ Tue, 13 Aug 2019 00:11:11: 7000000 INFO @ Tue, 13 Aug 2019 00:11:15: 8000000 INFO @ Tue, 13 Aug 2019 00:11:16: 8000000 INFO @ Tue, 13 Aug 2019 00:11:18: 8000000 INFO @ Tue, 13 Aug 2019 00:11:21: 9000000 INFO @ Tue, 13 Aug 2019 00:11:22: 9000000 INFO @ Tue, 13 Aug 2019 00:11:24: 9000000 INFO @ Tue, 13 Aug 2019 00:11:27: 10000000 INFO @ Tue, 13 Aug 2019 00:11:28: 10000000 INFO @ Tue, 13 Aug 2019 00:11:30: 10000000 INFO @ Tue, 13 Aug 2019 00:11:33: 11000000 INFO @ Tue, 13 Aug 2019 00:11:34: 11000000 INFO @ Tue, 13 Aug 2019 00:11:36: 11000000 INFO @ Tue, 13 Aug 2019 00:11:39: 12000000 INFO @ Tue, 13 Aug 2019 00:11:40: 12000000 INFO @ Tue, 13 Aug 2019 00:11:43: 12000000 INFO @ Tue, 13 Aug 2019 00:11:45: 13000000 INFO @ Tue, 13 Aug 2019 00:11:46: 13000000 INFO @ Tue, 13 Aug 2019 00:11:49: 13000000 INFO @ Tue, 13 Aug 2019 00:11:51: 14000000 INFO @ Tue, 13 Aug 2019 00:11:52: 14000000 INFO @ Tue, 13 Aug 2019 00:11:56: 14000000 INFO @ Tue, 13 Aug 2019 00:11:57: 15000000 INFO @ Tue, 13 Aug 2019 00:11:58: 15000000 INFO @ Tue, 13 Aug 2019 00:12:02: 15000000 INFO @ Tue, 13 Aug 2019 00:12:03: 16000000 INFO @ Tue, 13 Aug 2019 00:12:03: 16000000 INFO @ Tue, 13 Aug 2019 00:12:08: 16000000 INFO @ Tue, 13 Aug 2019 00:12:09: 17000000 INFO @ Tue, 13 Aug 2019 00:12:09: 17000000 INFO @ Tue, 13 Aug 2019 00:12:14: 17000000 INFO @ Tue, 13 Aug 2019 00:12:15: 18000000 INFO @ Tue, 13 Aug 2019 00:12:15: 18000000 INFO @ Tue, 13 Aug 2019 00:12:18: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:12:18: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:12:18: #1 total tags in treatment: 18413426 INFO @ Tue, 13 Aug 2019 00:12:18: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:12:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:12:18: #1 tags after filtering in treatment: 18413426 INFO @ Tue, 13 Aug 2019 00:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:12:18: #1 finished! INFO @ Tue, 13 Aug 2019 00:12:18: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:12:18: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:12:18: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:12:18: #1 total tags in treatment: 18413426 INFO @ Tue, 13 Aug 2019 00:12:18: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:12:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:12:18: #1 tags after filtering in treatment: 18413426 INFO @ Tue, 13 Aug 2019 00:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:12:18: #1 finished! INFO @ Tue, 13 Aug 2019 00:12:18: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:12:20: #2 number of paired peaks: 518 WARNING @ Tue, 13 Aug 2019 00:12:20: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 13 Aug 2019 00:12:20: start model_add_line... INFO @ Tue, 13 Aug 2019 00:12:20: start X-correlation... INFO @ Tue, 13 Aug 2019 00:12:20: end of X-cor INFO @ Tue, 13 Aug 2019 00:12:20: #2 finished! INFO @ Tue, 13 Aug 2019 00:12:20: #2 predicted fragment length is 46 bps INFO @ Tue, 13 Aug 2019 00:12:20: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 13 Aug 2019 00:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.10_model.r WARNING @ Tue, 13 Aug 2019 00:12:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:12:20: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 13 Aug 2019 00:12:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:12:20: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:12:20: #2 number of paired peaks: 518 WARNING @ Tue, 13 Aug 2019 00:12:20: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 13 Aug 2019 00:12:20: start model_add_line... INFO @ Tue, 13 Aug 2019 00:12:20: start X-correlation... INFO @ Tue, 13 Aug 2019 00:12:20: end of X-cor INFO @ Tue, 13 Aug 2019 00:12:20: #2 finished! INFO @ Tue, 13 Aug 2019 00:12:20: #2 predicted fragment length is 46 bps INFO @ Tue, 13 Aug 2019 00:12:20: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 13 Aug 2019 00:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.20_model.r WARNING @ Tue, 13 Aug 2019 00:12:20: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:12:20: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 13 Aug 2019 00:12:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:12:20: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:12:21: 18000000 INFO @ Tue, 13 Aug 2019 00:12:24: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:12:24: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:12:24: #1 total tags in treatment: 18413426 INFO @ Tue, 13 Aug 2019 00:12:24: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:12:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:12:24: #1 tags after filtering in treatment: 18413426 INFO @ Tue, 13 Aug 2019 00:12:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:12:24: #1 finished! INFO @ Tue, 13 Aug 2019 00:12:24: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:12:26: #2 number of paired peaks: 518 WARNING @ Tue, 13 Aug 2019 00:12:26: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Tue, 13 Aug 2019 00:12:26: start model_add_line... INFO @ Tue, 13 Aug 2019 00:12:26: start X-correlation... INFO @ Tue, 13 Aug 2019 00:12:26: end of X-cor INFO @ Tue, 13 Aug 2019 00:12:26: #2 finished! INFO @ Tue, 13 Aug 2019 00:12:26: #2 predicted fragment length is 46 bps INFO @ Tue, 13 Aug 2019 00:12:26: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 13 Aug 2019 00:12:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.05_model.r WARNING @ Tue, 13 Aug 2019 00:12:26: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:12:26: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 13 Aug 2019 00:12:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:12:26: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:12:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:13:07: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:08: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:13: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.10_summits.bed INFO @ Tue, 13 Aug 2019 00:13:30: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3296 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.20_summits.bed INFO @ Tue, 13 Aug 2019 00:13:30: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (1710 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011098/SRX5011098.05_summits.bed INFO @ Tue, 13 Aug 2019 00:13:36: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4604 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。