Job ID = 2590804 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,656,390 reads read : 63,312,780 reads written : 31,656,390 reads 0-length : 31,656,390 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: 00:12:02 31656390 reads; of these: 31656390 (100.00%) were unpaired; of these: 3950983 (12.48%) aligned 0 times 20133761 (63.60%) aligned exactly 1 time 7571646 (23.92%) aligned >1 times 87.52% overall alignment rate Time searching: 00:12:02 Overall time: 00:12:02 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 12 files... [bam_rmdupse_core] 14638847 / 27705407 = 0.5284 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 23:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.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 23:39:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:39:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:39:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.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 23:39:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:39:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.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 23:39:09: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:39:09: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:39:15: 1000000 INFO @ Mon, 12 Aug 2019 23:39:16: 1000000 INFO @ Mon, 12 Aug 2019 23:39:16: 1000000 INFO @ Mon, 12 Aug 2019 23:39:23: 2000000 INFO @ Mon, 12 Aug 2019 23:39:23: 2000000 INFO @ Mon, 12 Aug 2019 23:39:24: 2000000 INFO @ Mon, 12 Aug 2019 23:39:31: 3000000 INFO @ Mon, 12 Aug 2019 23:39:31: 3000000 INFO @ Mon, 12 Aug 2019 23:39:31: 3000000 INFO @ Mon, 12 Aug 2019 23:39:37: 4000000 INFO @ Mon, 12 Aug 2019 23:39:38: 4000000 INFO @ Mon, 12 Aug 2019 23:39:39: 4000000 INFO @ Mon, 12 Aug 2019 23:39:44: 5000000 INFO @ Mon, 12 Aug 2019 23:39:46: 5000000 INFO @ Mon, 12 Aug 2019 23:39:46: 5000000 INFO @ Mon, 12 Aug 2019 23:39:51: 6000000 INFO @ Mon, 12 Aug 2019 23:39:53: 6000000 INFO @ Mon, 12 Aug 2019 23:39:54: 6000000 INFO @ Mon, 12 Aug 2019 23:39:58: 7000000 INFO @ Mon, 12 Aug 2019 23:40:01: 7000000 INFO @ Mon, 12 Aug 2019 23:40:02: 7000000 INFO @ Mon, 12 Aug 2019 23:40:05: 8000000 INFO @ Mon, 12 Aug 2019 23:40:08: 8000000 INFO @ Mon, 12 Aug 2019 23:40:09: 8000000 INFO @ Mon, 12 Aug 2019 23:40:13: 9000000 INFO @ Mon, 12 Aug 2019 23:40:16: 9000000 INFO @ Mon, 12 Aug 2019 23:40:17: 9000000 INFO @ Mon, 12 Aug 2019 23:40:20: 10000000 INFO @ Mon, 12 Aug 2019 23:40:23: 10000000 INFO @ Mon, 12 Aug 2019 23:40:24: 10000000 INFO @ Mon, 12 Aug 2019 23:40:27: 11000000 INFO @ Mon, 12 Aug 2019 23:40:31: 11000000 INFO @ Mon, 12 Aug 2019 23:40:32: 11000000 INFO @ Mon, 12 Aug 2019 23:40:34: 12000000 INFO @ Mon, 12 Aug 2019 23:40:38: 12000000 INFO @ Mon, 12 Aug 2019 23:40:39: 12000000 INFO @ Mon, 12 Aug 2019 23:40:41: 13000000 INFO @ Mon, 12 Aug 2019 23:40:41: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:40:41: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:40:41: #1 total tags in treatment: 13066560 INFO @ Mon, 12 Aug 2019 23:40:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:40:41: #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 23:40:41: #1 tags after filtering in treatment: 13066560 INFO @ Mon, 12 Aug 2019 23:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:40:41: #1 finished! INFO @ Mon, 12 Aug 2019 23:40:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:40:43: #2 number of paired peaks: 1511 INFO @ Mon, 12 Aug 2019 23:40:43: start model_add_line... INFO @ Mon, 12 Aug 2019 23:40:43: start X-correlation... INFO @ Mon, 12 Aug 2019 23:40:43: end of X-cor INFO @ Mon, 12 Aug 2019 23:40:43: #2 finished! INFO @ Mon, 12 Aug 2019 23:40:43: #2 predicted fragment length is 96 bps INFO @ Mon, 12 Aug 2019 23:40:43: #2 alternative fragment length(s) may be 96 bps INFO @ Mon, 12 Aug 2019 23:40:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.20_model.r WARNING @ Mon, 12 Aug 2019 23:40:43: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:40:43: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Mon, 12 Aug 2019 23:40:43: #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 23:40:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:40:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:40:46: 13000000 INFO @ Mon, 12 Aug 2019 23:40:46: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:40:46: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:40:46: #1 total tags in treatment: 13066560 INFO @ Mon, 12 Aug 2019 23:40:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:40:46: #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 23:40:47: #1 tags after filtering in treatment: 13066560 INFO @ Mon, 12 Aug 2019 23:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:40:47: #1 finished! INFO @ Mon, 12 Aug 2019 23:40:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:40:47: 13000000 INFO @ Mon, 12 Aug 2019 23:40:47: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:40:47: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:40:47: #1 total tags in treatment: 13066560 INFO @ Mon, 12 Aug 2019 23:40:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:40:47: #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 23:40:47: #1 tags after filtering in treatment: 13066560 INFO @ Mon, 12 Aug 2019 23:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:40:47: #1 finished! INFO @ Mon, 12 Aug 2019 23:40:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:40:48: #2 number of paired peaks: 1511 INFO @ Mon, 12 Aug 2019 23:40:48: start model_add_line... INFO @ Mon, 12 Aug 2019 23:40:48: start X-correlation... INFO @ Mon, 12 Aug 2019 23:40:48: end of X-cor INFO @ Mon, 12 Aug 2019 23:40:48: #2 finished! INFO @ Mon, 12 Aug 2019 23:40:48: #2 predicted fragment length is 96 bps INFO @ Mon, 12 Aug 2019 23:40:48: #2 alternative fragment length(s) may be 96 bps INFO @ Mon, 12 Aug 2019 23:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.05_model.r WARNING @ Mon, 12 Aug 2019 23:40:48: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:40:48: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Mon, 12 Aug 2019 23:40:48: #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 23:40:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:40:49: #2 number of paired peaks: 1511 INFO @ Mon, 12 Aug 2019 23:40:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:40:49: start X-correlation... INFO @ Mon, 12 Aug 2019 23:40:49: end of X-cor INFO @ Mon, 12 Aug 2019 23:40:49: #2 finished! INFO @ Mon, 12 Aug 2019 23:40:49: #2 predicted fragment length is 96 bps INFO @ Mon, 12 Aug 2019 23:40:49: #2 alternative fragment length(s) may be 96 bps INFO @ Mon, 12 Aug 2019 23:40:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.10_model.r WARNING @ Mon, 12 Aug 2019 23:40:49: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:40:49: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Mon, 12 Aug 2019 23:40:49: #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 23:40:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:40:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:41:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:41:25: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:41:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.20_summits.bed INFO @ Mon, 12 Aug 2019 23:41:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2662 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.05_summits.bed INFO @ Mon, 12 Aug 2019 23:41:44: Done! pass1 - making usageList (15 chroms): 4 millis INFO @ Mon, 12 Aug 2019 23:41:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.10_peaks.xls pass2 - checking and writing primary data (7309 records, 4 fields): 12 millis INFO @ Mon, 12 Aug 2019 23:41:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.10_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:41:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011046/SRX5011046.10_summits.bed INFO @ Mon, 12 Aug 2019 23:41:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4779 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。