Job ID = 2590653 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,371,239 reads read : 17,371,239 reads written : 17,371,239 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: 00:04:43 17371239 reads; of these: 17371239 (100.00%) were unpaired; of these: 9561629 (55.04%) aligned 0 times 4847630 (27.91%) aligned exactly 1 time 2961980 (17.05%) aligned >1 times 44.96% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 1464039 / 7809610 = 0.1875 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 23:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.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 23:10:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.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 23:10:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.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 23:10:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:10:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:10:48: 1000000 INFO @ Mon, 12 Aug 2019 23:10:49: 1000000 INFO @ Mon, 12 Aug 2019 23:10:50: 1000000 INFO @ Mon, 12 Aug 2019 23:10:58: 2000000 INFO @ Mon, 12 Aug 2019 23:10:59: 2000000 INFO @ Mon, 12 Aug 2019 23:11:01: 2000000 INFO @ Mon, 12 Aug 2019 23:11:08: 3000000 INFO @ Mon, 12 Aug 2019 23:11:10: 3000000 INFO @ Mon, 12 Aug 2019 23:11:11: 3000000 INFO @ Mon, 12 Aug 2019 23:11:19: 4000000 INFO @ Mon, 12 Aug 2019 23:11:20: 4000000 INFO @ Mon, 12 Aug 2019 23:11:22: 4000000 INFO @ Mon, 12 Aug 2019 23:11:29: 5000000 INFO @ Mon, 12 Aug 2019 23:11:31: 5000000 INFO @ Mon, 12 Aug 2019 23:11:33: 5000000 INFO @ Mon, 12 Aug 2019 23:11:40: 6000000 INFO @ Mon, 12 Aug 2019 23:11:41: 6000000 INFO @ Mon, 12 Aug 2019 23:11:43: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:43: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:43: #1 total tags in treatment: 6345571 INFO @ Mon, 12 Aug 2019 23:11:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:43: #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 23:11:43: #1 tags after filtering in treatment: 6345571 INFO @ Mon, 12 Aug 2019 23:11:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:11:43: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:43: 6000000 INFO @ Mon, 12 Aug 2019 23:11:44: #2 number of paired peaks: 1259 INFO @ Mon, 12 Aug 2019 23:11:44: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:44: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:44: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:44: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:44: #1 total tags in treatment: 6345571 INFO @ Mon, 12 Aug 2019 23:11:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:44: #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 23:11:44: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:44: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:44: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:11:44: #2 alternative fragment length(s) may be 3,47,562 bps INFO @ Mon, 12 Aug 2019 23:11:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.05_model.r WARNING @ Mon, 12 Aug 2019 23:11:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:11:44: #2 You may need to consider one of the other alternative d(s): 3,47,562 WARNING @ Mon, 12 Aug 2019 23:11:44: #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 23:11:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:44: #1 tags after filtering in treatment: 6345571 INFO @ Mon, 12 Aug 2019 23:11:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:11:44: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:45: #2 number of paired peaks: 1259 INFO @ Mon, 12 Aug 2019 23:11:45: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:45: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:45: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:45: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:45: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:11:45: #2 alternative fragment length(s) may be 3,47,562 bps INFO @ Mon, 12 Aug 2019 23:11:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.10_model.r WARNING @ Mon, 12 Aug 2019 23:11:45: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:11:45: #2 You may need to consider one of the other alternative d(s): 3,47,562 WARNING @ Mon, 12 Aug 2019 23:11:45: #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 23:11:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:46: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:11:46: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:11:46: #1 total tags in treatment: 6345571 INFO @ Mon, 12 Aug 2019 23:11:46: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:11:46: #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 23:11:47: #1 tags after filtering in treatment: 6345571 INFO @ Mon, 12 Aug 2019 23:11:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:11:47: #1 finished! INFO @ Mon, 12 Aug 2019 23:11:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:11:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:11:47: #2 number of paired peaks: 1259 INFO @ Mon, 12 Aug 2019 23:11:47: start model_add_line... INFO @ Mon, 12 Aug 2019 23:11:47: start X-correlation... INFO @ Mon, 12 Aug 2019 23:11:47: end of X-cor INFO @ Mon, 12 Aug 2019 23:11:47: #2 finished! INFO @ Mon, 12 Aug 2019 23:11:47: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:11:47: #2 alternative fragment length(s) may be 3,47,562 bps INFO @ Mon, 12 Aug 2019 23:11:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.20_model.r WARNING @ Mon, 12 Aug 2019 23:11:47: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:11:47: #2 You may need to consider one of the other alternative d(s): 3,47,562 WARNING @ Mon, 12 Aug 2019 23:11:47: #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 23:11:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:11:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:12:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:12:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:12:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.05_summits.bed INFO @ Mon, 12 Aug 2019 23:12:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2490 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.10_summits.bed INFO @ Mon, 12 Aug 2019 23:12:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1286 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:12:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:12:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:12:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495790/SRX495790.20_summits.bed INFO @ Mon, 12 Aug 2019 23:12:16: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。