Job ID = 1294444 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,682,016 reads read : 15,682,016 reads written : 15,682,016 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: 00:06:50 15682016 reads; of these: 15682016 (100.00%) were unpaired; of these: 700178 (4.46%) aligned 0 times 11328979 (72.24%) aligned exactly 1 time 3652859 (23.29%) aligned >1 times 95.54% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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 8 files... [bam_rmdupse_core] 1745739 / 14981838 = 0.1165 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 08:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.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 08:14:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:14:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.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 08:14:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:14:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.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 08:14:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:14:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:14:18: 1000000 INFO @ Mon, 03 Jun 2019 08:14:18: 1000000 INFO @ Mon, 03 Jun 2019 08:14:21: 1000000 INFO @ Mon, 03 Jun 2019 08:14:27: 2000000 INFO @ Mon, 03 Jun 2019 08:14:27: 2000000 INFO @ Mon, 03 Jun 2019 08:14:32: 2000000 INFO @ Mon, 03 Jun 2019 08:14:35: 3000000 INFO @ Mon, 03 Jun 2019 08:14:35: 3000000 INFO @ Mon, 03 Jun 2019 08:14:42: 3000000 INFO @ Mon, 03 Jun 2019 08:14:44: 4000000 INFO @ Mon, 03 Jun 2019 08:14:44: 4000000 INFO @ Mon, 03 Jun 2019 08:14:52: 5000000 INFO @ Mon, 03 Jun 2019 08:14:52: 5000000 INFO @ Mon, 03 Jun 2019 08:14:53: 4000000 INFO @ Mon, 03 Jun 2019 08:15:00: 6000000 INFO @ Mon, 03 Jun 2019 08:15:00: 6000000 INFO @ Mon, 03 Jun 2019 08:15:03: 5000000 INFO @ Mon, 03 Jun 2019 08:15:07: 7000000 INFO @ Mon, 03 Jun 2019 08:15:08: 7000000 INFO @ Mon, 03 Jun 2019 08:15:13: 6000000 INFO @ Mon, 03 Jun 2019 08:15:15: 8000000 INFO @ Mon, 03 Jun 2019 08:15:15: 8000000 INFO @ Mon, 03 Jun 2019 08:15:23: 9000000 INFO @ Mon, 03 Jun 2019 08:15:24: 7000000 INFO @ Mon, 03 Jun 2019 08:15:24: 9000000 INFO @ Mon, 03 Jun 2019 08:15:30: 10000000 INFO @ Mon, 03 Jun 2019 08:15:33: 10000000 INFO @ Mon, 03 Jun 2019 08:15:34: 8000000 INFO @ Mon, 03 Jun 2019 08:15:38: 11000000 INFO @ Mon, 03 Jun 2019 08:15:41: 11000000 INFO @ Mon, 03 Jun 2019 08:15:44: 9000000 INFO @ Mon, 03 Jun 2019 08:15:46: 12000000 INFO @ Mon, 03 Jun 2019 08:15:49: 12000000 INFO @ Mon, 03 Jun 2019 08:15:53: 13000000 INFO @ Mon, 03 Jun 2019 08:15:54: 10000000 INFO @ Mon, 03 Jun 2019 08:15:55: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:15:55: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:15:55: #1 total tags in treatment: 13236099 INFO @ Mon, 03 Jun 2019 08:15:55: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:15:55: #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 08:15:55: #1 tags after filtering in treatment: 13236099 INFO @ Mon, 03 Jun 2019 08:15:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:15:55: #1 finished! INFO @ Mon, 03 Jun 2019 08:15:55: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:15:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:15:56: 13000000 INFO @ Mon, 03 Jun 2019 08:15:57: #2 number of paired peaks: 212 WARNING @ Mon, 03 Jun 2019 08:15:57: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Mon, 03 Jun 2019 08:15:57: start model_add_line... INFO @ Mon, 03 Jun 2019 08:15:57: start X-correlation... INFO @ Mon, 03 Jun 2019 08:15:57: end of X-cor INFO @ Mon, 03 Jun 2019 08:15:57: #2 finished! INFO @ Mon, 03 Jun 2019 08:15:57: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:15:57: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:15:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.05_model.r WARNING @ Mon, 03 Jun 2019 08:15:57: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:15:57: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:15:57: #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 08:15:57: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:15:58: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:15:58: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:15:58: #1 total tags in treatment: 13236099 INFO @ Mon, 03 Jun 2019 08:15:58: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:15:58: #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 08:15:58: #1 tags after filtering in treatment: 13236099 INFO @ Mon, 03 Jun 2019 08:15:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:15:58: #1 finished! INFO @ Mon, 03 Jun 2019 08:15:58: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:16:00: #2 number of paired peaks: 212 WARNING @ Mon, 03 Jun 2019 08:16:00: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Mon, 03 Jun 2019 08:16:00: start model_add_line... INFO @ Mon, 03 Jun 2019 08:16:00: start X-correlation... INFO @ Mon, 03 Jun 2019 08:16:00: end of X-cor INFO @ Mon, 03 Jun 2019 08:16:00: #2 finished! INFO @ Mon, 03 Jun 2019 08:16:00: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:16:00: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.10_model.r WARNING @ Mon, 03 Jun 2019 08:16:00: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:16:00: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:16:00: #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 08:16:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:16:04: 11000000 INFO @ Mon, 03 Jun 2019 08:16:15: 12000000 INFO @ Mon, 03 Jun 2019 08:16:25: 13000000 INFO @ Mon, 03 Jun 2019 08:16:28: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:16:28: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:16:28: #1 total tags in treatment: 13236099 INFO @ Mon, 03 Jun 2019 08:16:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:16:28: #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 08:16:28: #1 tags after filtering in treatment: 13236099 INFO @ Mon, 03 Jun 2019 08:16:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 08:16:28: #1 finished! INFO @ Mon, 03 Jun 2019 08:16:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:16:29: #2 number of paired peaks: 212 WARNING @ Mon, 03 Jun 2019 08:16:29: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Mon, 03 Jun 2019 08:16:29: start model_add_line... INFO @ Mon, 03 Jun 2019 08:16:29: start X-correlation... INFO @ Mon, 03 Jun 2019 08:16:29: end of X-cor INFO @ Mon, 03 Jun 2019 08:16:29: #2 finished! INFO @ Mon, 03 Jun 2019 08:16:29: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 08:16:29: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 08:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.20_model.r WARNING @ Mon, 03 Jun 2019 08:16:29: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 08:16:29: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 08:16:29: #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 08:16:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:16:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:16:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:16:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:16:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:16:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.05_summits.bed INFO @ Mon, 03 Jun 2019 08:16:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2010 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.10_summits.bed INFO @ Mon, 03 Jun 2019 08:16:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1539 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:17:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:17:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:17:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:17:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287652/SRX287652.20_summits.bed INFO @ Mon, 03 Jun 2019 08:17:24: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1024 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。