Job ID = 2590868 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,689,255 reads read : 15,378,510 reads written : 7,689,255 reads 0-length : 7,689,255 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: 00:03:06 7689255 reads; of these: 7689255 (100.00%) were unpaired; of these: 909034 (11.82%) aligned 0 times 5233910 (68.07%) aligned exactly 1 time 1546311 (20.11%) aligned >1 times 88.18% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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_rmdupse_core] 1416827 / 6780221 = 0.2090 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 23:49:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.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 23:49:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.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 23:49:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.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 23:49:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:49:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:49:59: 1000000 INFO @ Mon, 12 Aug 2019 23:50:00: 1000000 INFO @ Mon, 12 Aug 2019 23:50:01: 1000000 INFO @ Mon, 12 Aug 2019 23:50:10: 2000000 INFO @ Mon, 12 Aug 2019 23:50:11: 2000000 INFO @ Mon, 12 Aug 2019 23:50:12: 2000000 INFO @ Mon, 12 Aug 2019 23:50:21: 3000000 INFO @ Mon, 12 Aug 2019 23:50:22: 3000000 INFO @ Mon, 12 Aug 2019 23:50:23: 3000000 INFO @ Mon, 12 Aug 2019 23:50:32: 4000000 INFO @ Mon, 12 Aug 2019 23:50:33: 4000000 INFO @ Mon, 12 Aug 2019 23:50:34: 4000000 INFO @ Mon, 12 Aug 2019 23:50:43: 5000000 INFO @ Mon, 12 Aug 2019 23:50:45: 5000000 INFO @ Mon, 12 Aug 2019 23:50:46: 5000000 INFO @ Mon, 12 Aug 2019 23:50:47: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:50:47: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:50:47: #1 total tags in treatment: 5363394 INFO @ Mon, 12 Aug 2019 23:50:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:47: #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 23:50:47: #1 tags after filtering in treatment: 5363394 INFO @ Mon, 12 Aug 2019 23:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:47: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:48: #2 number of paired peaks: 1236 INFO @ Mon, 12 Aug 2019 23:50:48: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:48: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:48: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:48: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:48: #2 predicted fragment length is 106 bps INFO @ Mon, 12 Aug 2019 23:50:48: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 12 Aug 2019 23:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.05_model.r WARNING @ Mon, 12 Aug 2019 23:50:48: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:50:48: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Mon, 12 Aug 2019 23:50:48: #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 23:50:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:48: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:50:48: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:50:48: #1 total tags in treatment: 5363394 INFO @ Mon, 12 Aug 2019 23:50:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:48: #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 23:50:49: #1 tags after filtering in treatment: 5363394 INFO @ Mon, 12 Aug 2019 23:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:49: #2 number of paired peaks: 1236 INFO @ Mon, 12 Aug 2019 23:50:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:49: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:49: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:49: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:49: #2 predicted fragment length is 106 bps INFO @ Mon, 12 Aug 2019 23:50:49: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 12 Aug 2019 23:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.10_model.r WARNING @ Mon, 12 Aug 2019 23:50:49: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:50:49: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Mon, 12 Aug 2019 23:50:49: #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 23:50:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:49: #1 tag size is determined as 75 bps INFO @ Mon, 12 Aug 2019 23:50:49: #1 tag size = 75 INFO @ Mon, 12 Aug 2019 23:50:49: #1 total tags in treatment: 5363394 INFO @ Mon, 12 Aug 2019 23:50:49: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:50:49: #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 23:50:49: #1 tags after filtering in treatment: 5363394 INFO @ Mon, 12 Aug 2019 23:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:50:49: #1 finished! INFO @ Mon, 12 Aug 2019 23:50:49: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:50:50: #2 number of paired peaks: 1236 INFO @ Mon, 12 Aug 2019 23:50:50: start model_add_line... INFO @ Mon, 12 Aug 2019 23:50:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:50:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:50:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:50:50: #2 predicted fragment length is 106 bps INFO @ Mon, 12 Aug 2019 23:50:50: #2 alternative fragment length(s) may be 106 bps INFO @ Mon, 12 Aug 2019 23:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.20_model.r WARNING @ Mon, 12 Aug 2019 23:50:50: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:50:50: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Mon, 12 Aug 2019 23:50:50: #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 23:50:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:51:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.05_summits.bed INFO @ Mon, 12 Aug 2019 23:51:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2580 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.10_summits.bed INFO @ Mon, 12 Aug 2019 23:51:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1210 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:51:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:51:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:51:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5053151/SRX5053151.20_summits.bed INFO @ Mon, 12 Aug 2019 23:51:15: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。