Job ID = 1295616 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,739,672 reads read : 41,739,672 reads written : 41,739,672 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: 00:18:08 41739672 reads; of these: 41739672 (100.00%) were unpaired; of these: 17670991 (42.34%) aligned 0 times 13677951 (32.77%) aligned exactly 1 time 10390730 (24.89%) aligned >1 times 57.66% overall alignment rate Time searching: 00:18:08 Overall time: 00:18:08 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] 14389862 / 24068681 = 0.5979 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, 03 Jun 2019 15:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.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, 03 Jun 2019 15:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.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, 03 Jun 2019 15:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.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, 03 Jun 2019 15:22:02: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:22:02: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:22:10: 1000000 INFO @ Mon, 03 Jun 2019 15:22:10: 1000000 INFO @ Mon, 03 Jun 2019 15:22:11: 1000000 INFO @ Mon, 03 Jun 2019 15:22:17: 2000000 INFO @ Mon, 03 Jun 2019 15:22:18: 2000000 INFO @ Mon, 03 Jun 2019 15:22:20: 2000000 INFO @ Mon, 03 Jun 2019 15:22:25: 3000000 INFO @ Mon, 03 Jun 2019 15:22:26: 3000000 INFO @ Mon, 03 Jun 2019 15:22:29: 3000000 INFO @ Mon, 03 Jun 2019 15:22:32: 4000000 INFO @ Mon, 03 Jun 2019 15:22:32: 4000000 INFO @ Mon, 03 Jun 2019 15:22:37: 4000000 INFO @ Mon, 03 Jun 2019 15:22:39: 5000000 INFO @ Mon, 03 Jun 2019 15:22:40: 5000000 INFO @ Mon, 03 Jun 2019 15:22:46: 6000000 INFO @ Mon, 03 Jun 2019 15:22:47: 5000000 INFO @ Mon, 03 Jun 2019 15:22:50: 6000000 INFO @ Mon, 03 Jun 2019 15:22:53: 7000000 INFO @ Mon, 03 Jun 2019 15:22:56: 6000000 INFO @ Mon, 03 Jun 2019 15:22:57: 7000000 INFO @ Mon, 03 Jun 2019 15:23:00: 8000000 INFO @ Mon, 03 Jun 2019 15:23:05: 8000000 INFO @ Mon, 03 Jun 2019 15:23:05: 7000000 INFO @ Mon, 03 Jun 2019 15:23:06: 9000000 INFO @ Mon, 03 Jun 2019 15:23:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 15:23:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 15:23:11: #1 total tags in treatment: 9678819 INFO @ Mon, 03 Jun 2019 15:23:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:23:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:23:11: #1 tags after filtering in treatment: 9678819 INFO @ Mon, 03 Jun 2019 15:23:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:23:11: #1 finished! INFO @ Mon, 03 Jun 2019 15:23:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:23:12: 9000000 INFO @ Mon, 03 Jun 2019 15:23:12: #2 number of paired peaks: 1149 INFO @ Mon, 03 Jun 2019 15:23:12: start model_add_line... INFO @ Mon, 03 Jun 2019 15:23:13: start X-correlation... INFO @ Mon, 03 Jun 2019 15:23:13: end of X-cor INFO @ Mon, 03 Jun 2019 15:23:13: #2 finished! INFO @ Mon, 03 Jun 2019 15:23:13: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 15:23:13: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 15:23:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.20_model.r WARNING @ Mon, 03 Jun 2019 15:23:13: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:23:13: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 15:23:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:23:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:23:14: 8000000 INFO @ Mon, 03 Jun 2019 15:23:17: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 15:23:17: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 15:23:17: #1 total tags in treatment: 9678819 INFO @ Mon, 03 Jun 2019 15:23:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:23:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:23:17: #1 tags after filtering in treatment: 9678819 INFO @ Mon, 03 Jun 2019 15:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:23:17: #1 finished! INFO @ Mon, 03 Jun 2019 15:23:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:23:18: #2 number of paired peaks: 1149 INFO @ Mon, 03 Jun 2019 15:23:18: start model_add_line... INFO @ Mon, 03 Jun 2019 15:23:18: start X-correlation... INFO @ Mon, 03 Jun 2019 15:23:18: end of X-cor INFO @ Mon, 03 Jun 2019 15:23:18: #2 finished! INFO @ Mon, 03 Jun 2019 15:23:18: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 15:23:18: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 15:23:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.05_model.r WARNING @ Mon, 03 Jun 2019 15:23:18: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:23:18: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 15:23:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:23:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:23:22: 9000000 INFO @ Mon, 03 Jun 2019 15:23:27: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 15:23:27: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 15:23:27: #1 total tags in treatment: 9678819 INFO @ Mon, 03 Jun 2019 15:23:27: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:23:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:23:28: #1 tags after filtering in treatment: 9678819 INFO @ Mon, 03 Jun 2019 15:23:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 15:23:28: #1 finished! INFO @ Mon, 03 Jun 2019 15:23:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:23:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:23:29: #2 number of paired peaks: 1149 INFO @ Mon, 03 Jun 2019 15:23:29: start model_add_line... INFO @ Mon, 03 Jun 2019 15:23:29: start X-correlation... INFO @ Mon, 03 Jun 2019 15:23:29: end of X-cor INFO @ Mon, 03 Jun 2019 15:23:29: #2 finished! INFO @ Mon, 03 Jun 2019 15:23:29: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 15:23:29: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 15:23:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.10_model.r WARNING @ Mon, 03 Jun 2019 15:23:29: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 15:23:29: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 15:23:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 15:23:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:23:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:23:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.20_summits.bed INFO @ Mon, 03 Jun 2019 15:23:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2248 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:23:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:24:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:24:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:24:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.05_summits.bed INFO @ Mon, 03 Jun 2019 15:24:00: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4413 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:24:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:24:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX375353/SRX375353.10_summits.bed INFO @ Mon, 03 Jun 2019 15:24:11: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3238 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。