Job ID = 2590586 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,108,805 reads read : 40,217,610 reads written : 20,108,805 reads 0-length : 20,108,805 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: 00:11:38 20108805 reads; of these: 20108805 (100.00%) were unpaired; of these: 411537 (2.05%) aligned 0 times 6166234 (30.66%) aligned exactly 1 time 13531034 (67.29%) aligned >1 times 97.95% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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] 6698967 / 19697268 = 0.3401 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 22:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.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 22:50:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:50:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.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 22:50:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:50:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.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 22:50:45: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:50:45: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:50:50: 1000000 INFO @ Mon, 12 Aug 2019 22:50:51: 1000000 INFO @ Mon, 12 Aug 2019 22:50:52: 1000000 INFO @ Mon, 12 Aug 2019 22:50:57: 2000000 INFO @ Mon, 12 Aug 2019 22:50:57: 2000000 INFO @ Mon, 12 Aug 2019 22:50:58: 2000000 INFO @ Mon, 12 Aug 2019 22:51:04: 3000000 INFO @ Mon, 12 Aug 2019 22:51:04: 3000000 INFO @ Mon, 12 Aug 2019 22:51:05: 3000000 INFO @ Mon, 12 Aug 2019 22:51:11: 4000000 INFO @ Mon, 12 Aug 2019 22:51:11: 4000000 INFO @ Mon, 12 Aug 2019 22:51:11: 4000000 INFO @ Mon, 12 Aug 2019 22:51:17: 5000000 INFO @ Mon, 12 Aug 2019 22:51:18: 5000000 INFO @ Mon, 12 Aug 2019 22:51:19: 5000000 INFO @ Mon, 12 Aug 2019 22:51:24: 6000000 INFO @ Mon, 12 Aug 2019 22:51:25: 6000000 INFO @ Mon, 12 Aug 2019 22:51:26: 6000000 INFO @ Mon, 12 Aug 2019 22:51:30: 7000000 INFO @ Mon, 12 Aug 2019 22:51:31: 7000000 INFO @ Mon, 12 Aug 2019 22:51:33: 7000000 INFO @ Mon, 12 Aug 2019 22:51:37: 8000000 INFO @ Mon, 12 Aug 2019 22:51:38: 8000000 INFO @ Mon, 12 Aug 2019 22:51:40: 8000000 INFO @ Mon, 12 Aug 2019 22:51:43: 9000000 INFO @ Mon, 12 Aug 2019 22:51:44: 9000000 INFO @ Mon, 12 Aug 2019 22:51:47: 9000000 INFO @ Mon, 12 Aug 2019 22:51:50: 10000000 INFO @ Mon, 12 Aug 2019 22:51:51: 10000000 INFO @ Mon, 12 Aug 2019 22:51:54: 10000000 INFO @ Mon, 12 Aug 2019 22:51:56: 11000000 INFO @ Mon, 12 Aug 2019 22:51:57: 11000000 INFO @ Mon, 12 Aug 2019 22:52:02: 11000000 INFO @ Mon, 12 Aug 2019 22:52:03: 12000000 INFO @ Mon, 12 Aug 2019 22:52:04: 12000000 INFO @ Mon, 12 Aug 2019 22:52:09: 12000000 INFO @ Mon, 12 Aug 2019 22:52:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:52:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:52:10: #1 total tags in treatment: 12998301 INFO @ Mon, 12 Aug 2019 22:52:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:52:10: #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 22:52:10: #1 tags after filtering in treatment: 12998301 INFO @ Mon, 12 Aug 2019 22:52:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:52:10: #1 finished! INFO @ Mon, 12 Aug 2019 22:52:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:52:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:52:11: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:52:11: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:52:11: #1 total tags in treatment: 12998301 INFO @ Mon, 12 Aug 2019 22:52:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:52:11: #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 22:52:11: #1 tags after filtering in treatment: 12998301 INFO @ Mon, 12 Aug 2019 22:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:52:11: #1 finished! INFO @ Mon, 12 Aug 2019 22:52:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:52:11: #2 number of paired peaks: 3136 INFO @ Mon, 12 Aug 2019 22:52:11: start model_add_line... INFO @ Mon, 12 Aug 2019 22:52:12: start X-correlation... INFO @ Mon, 12 Aug 2019 22:52:12: end of X-cor INFO @ Mon, 12 Aug 2019 22:52:12: #2 finished! INFO @ Mon, 12 Aug 2019 22:52:12: #2 predicted fragment length is 62 bps INFO @ Mon, 12 Aug 2019 22:52:12: #2 alternative fragment length(s) may be 4,62 bps INFO @ Mon, 12 Aug 2019 22:52:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.10_model.r WARNING @ Mon, 12 Aug 2019 22:52:12: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:52:12: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Mon, 12 Aug 2019 22:52:12: #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 22:52:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:52:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:52:12: #2 number of paired peaks: 3136 INFO @ Mon, 12 Aug 2019 22:52:12: start model_add_line... INFO @ Mon, 12 Aug 2019 22:52:13: start X-correlation... INFO @ Mon, 12 Aug 2019 22:52:13: end of X-cor INFO @ Mon, 12 Aug 2019 22:52:13: #2 finished! INFO @ Mon, 12 Aug 2019 22:52:13: #2 predicted fragment length is 62 bps INFO @ Mon, 12 Aug 2019 22:52:13: #2 alternative fragment length(s) may be 4,62 bps INFO @ Mon, 12 Aug 2019 22:52:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.20_model.r WARNING @ Mon, 12 Aug 2019 22:52:13: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:52:13: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Mon, 12 Aug 2019 22:52:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:52:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:52:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:52:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:52:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:52:16: #1 total tags in treatment: 12998301 INFO @ Mon, 12 Aug 2019 22:52:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:52:16: #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 22:52:16: #1 tags after filtering in treatment: 12998301 INFO @ Mon, 12 Aug 2019 22:52:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:52:16: #1 finished! INFO @ Mon, 12 Aug 2019 22:52:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:52:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:52:18: #2 number of paired peaks: 3136 INFO @ Mon, 12 Aug 2019 22:52:18: start model_add_line... INFO @ Mon, 12 Aug 2019 22:52:18: start X-correlation... INFO @ Mon, 12 Aug 2019 22:52:18: end of X-cor INFO @ Mon, 12 Aug 2019 22:52:18: #2 finished! INFO @ Mon, 12 Aug 2019 22:52:18: #2 predicted fragment length is 62 bps INFO @ Mon, 12 Aug 2019 22:52:18: #2 alternative fragment length(s) may be 4,62 bps INFO @ Mon, 12 Aug 2019 22:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.05_model.r WARNING @ Mon, 12 Aug 2019 22:52:18: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:52:18: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Mon, 12 Aug 2019 22:52:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 22:52:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:52:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:52:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:52:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.10_summits.bed INFO @ Mon, 12 Aug 2019 22:53:05: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (6466 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.20_summits.bed INFO @ Mon, 12 Aug 2019 22:53:05: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1806 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:53:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:53:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923179/SRX4923179.05_summits.bed INFO @ Mon, 12 Aug 2019 22:53:12: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (14239 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。