Job ID = 2590666 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,208,630 reads read : 72,417,260 reads written : 36,208,630 reads 0-length : 36,208,630 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: 00:14:41 36208630 reads; of these: 36208630 (100.00%) were unpaired; of these: 3523106 (9.73%) aligned 0 times 23941092 (66.12%) aligned exactly 1 time 8744432 (24.15%) aligned >1 times 90.27% overall alignment rate Time searching: 00:14:41 Overall time: 00:14:41 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] 18098409 / 32685524 = 0.5537 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 @ Mon, 12 Aug 2019 23:29:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.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 @ Mon, 12 Aug 2019 23:29:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.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 @ Mon, 12 Aug 2019 23:29:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.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 @ Mon, 12 Aug 2019 23:29:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:29:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:44: 1000000 INFO @ Mon, 12 Aug 2019 23:29:46: 1000000 INFO @ Mon, 12 Aug 2019 23:29:47: 1000000 INFO @ Mon, 12 Aug 2019 23:29:50: 2000000 INFO @ Mon, 12 Aug 2019 23:29:53: 2000000 INFO @ Mon, 12 Aug 2019 23:29:55: 2000000 INFO @ Mon, 12 Aug 2019 23:29:56: 3000000 INFO @ Mon, 12 Aug 2019 23:30:00: 3000000 INFO @ Mon, 12 Aug 2019 23:30:03: 4000000 INFO @ Mon, 12 Aug 2019 23:30:04: 3000000 INFO @ Mon, 12 Aug 2019 23:30:07: 4000000 INFO @ Mon, 12 Aug 2019 23:30:09: 5000000 INFO @ Mon, 12 Aug 2019 23:30:12: 4000000 INFO @ Mon, 12 Aug 2019 23:30:14: 5000000 INFO @ Mon, 12 Aug 2019 23:30:16: 6000000 INFO @ Mon, 12 Aug 2019 23:30:21: 5000000 INFO @ Mon, 12 Aug 2019 23:30:21: 6000000 INFO @ Mon, 12 Aug 2019 23:30:22: 7000000 INFO @ Mon, 12 Aug 2019 23:30:27: 7000000 INFO @ Mon, 12 Aug 2019 23:30:28: 8000000 INFO @ Mon, 12 Aug 2019 23:30:29: 6000000 INFO @ Mon, 12 Aug 2019 23:30:34: 8000000 INFO @ Mon, 12 Aug 2019 23:30:35: 9000000 INFO @ Mon, 12 Aug 2019 23:30:37: 7000000 INFO @ Mon, 12 Aug 2019 23:30:41: 10000000 INFO @ Mon, 12 Aug 2019 23:30:41: 9000000 INFO @ Mon, 12 Aug 2019 23:30:46: 8000000 INFO @ Mon, 12 Aug 2019 23:30:48: 11000000 INFO @ Mon, 12 Aug 2019 23:30:48: 10000000 INFO @ Mon, 12 Aug 2019 23:30:54: 9000000 INFO @ Mon, 12 Aug 2019 23:30:54: 12000000 INFO @ Mon, 12 Aug 2019 23:30:55: 11000000 INFO @ Mon, 12 Aug 2019 23:31:00: 13000000 INFO @ Mon, 12 Aug 2019 23:31:02: 12000000 INFO @ Mon, 12 Aug 2019 23:31:02: 10000000 INFO @ Mon, 12 Aug 2019 23:31:07: 14000000 INFO @ Mon, 12 Aug 2019 23:31:09: 13000000 INFO @ Mon, 12 Aug 2019 23:31:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:31:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:31:11: #1 total tags in treatment: 14587115 INFO @ Mon, 12 Aug 2019 23:31:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:31:11: 11000000 INFO @ Mon, 12 Aug 2019 23:31:11: #1 tags after filtering in treatment: 14587115 INFO @ Mon, 12 Aug 2019 23:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:31:11: #1 finished! INFO @ Mon, 12 Aug 2019 23:31:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:31:12: #2 number of paired peaks: 1376 INFO @ Mon, 12 Aug 2019 23:31:12: start model_add_line... INFO @ Mon, 12 Aug 2019 23:31:12: start X-correlation... INFO @ Mon, 12 Aug 2019 23:31:12: end of X-cor INFO @ Mon, 12 Aug 2019 23:31:12: #2 finished! INFO @ Mon, 12 Aug 2019 23:31:12: #2 predicted fragment length is 94 bps INFO @ Mon, 12 Aug 2019 23:31:12: #2 alternative fragment length(s) may be 94 bps INFO @ Mon, 12 Aug 2019 23:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.05_model.r WARNING @ Mon, 12 Aug 2019 23:31:12: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:31:12: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Mon, 12 Aug 2019 23:31:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:31:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:16: 14000000 INFO @ Mon, 12 Aug 2019 23:31:19: 12000000 INFO @ Mon, 12 Aug 2019 23:31:20: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:31:20: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:31:20: #1 total tags in treatment: 14587115 INFO @ Mon, 12 Aug 2019 23:31:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:31:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:31:20: #1 tags after filtering in treatment: 14587115 INFO @ Mon, 12 Aug 2019 23:31:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:31:20: #1 finished! INFO @ Mon, 12 Aug 2019 23:31:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:31:22: #2 number of paired peaks: 1376 INFO @ Mon, 12 Aug 2019 23:31:22: start model_add_line... INFO @ Mon, 12 Aug 2019 23:31:22: start X-correlation... INFO @ Mon, 12 Aug 2019 23:31:22: end of X-cor INFO @ Mon, 12 Aug 2019 23:31:22: #2 finished! INFO @ Mon, 12 Aug 2019 23:31:22: #2 predicted fragment length is 94 bps INFO @ Mon, 12 Aug 2019 23:31:22: #2 alternative fragment length(s) may be 94 bps INFO @ Mon, 12 Aug 2019 23:31:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.20_model.r WARNING @ Mon, 12 Aug 2019 23:31:22: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:31:22: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Mon, 12 Aug 2019 23:31:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:31:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:31:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:27: 13000000 INFO @ Mon, 12 Aug 2019 23:31:35: 14000000 INFO @ Mon, 12 Aug 2019 23:31:40: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:31:40: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:31:40: #1 total tags in treatment: 14587115 INFO @ Mon, 12 Aug 2019 23:31:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:31:41: #1 tags after filtering in treatment: 14587115 INFO @ Mon, 12 Aug 2019 23:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:31:41: #1 finished! INFO @ Mon, 12 Aug 2019 23:31:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:31:42: #2 number of paired peaks: 1376 INFO @ Mon, 12 Aug 2019 23:31:42: start model_add_line... INFO @ Mon, 12 Aug 2019 23:31:42: start X-correlation... INFO @ Mon, 12 Aug 2019 23:31:42: end of X-cor INFO @ Mon, 12 Aug 2019 23:31:42: #2 finished! INFO @ Mon, 12 Aug 2019 23:31:42: #2 predicted fragment length is 94 bps INFO @ Mon, 12 Aug 2019 23:31:42: #2 alternative fragment length(s) may be 94 bps INFO @ Mon, 12 Aug 2019 23:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.10_model.r WARNING @ Mon, 12 Aug 2019 23:31:42: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:31:42: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Mon, 12 Aug 2019 23:31:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:31:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:32:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:32:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:32:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:32:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.05_summits.bed INFO @ Mon, 12 Aug 2019 23:32:14: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (9597 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:32:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:32:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:32:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.20_summits.bed INFO @ Mon, 12 Aug 2019 23:32:23: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2785 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:32:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011015/SRX5011015.10_summits.bed INFO @ Mon, 12 Aug 2019 23:32:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5619 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。