Job ID = 2590855 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,996,208 reads read : 21,996,208 reads written : 21,996,208 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: 00:09:23 21996208 reads; of these: 21996208 (100.00%) were unpaired; of these: 1737536 (7.90%) aligned 0 times 14473340 (65.80%) aligned exactly 1 time 5785332 (26.30%) aligned >1 times 92.10% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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] 5666506 / 20258672 = 0.2797 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 23:58:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.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 23:58:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:58:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:58:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.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 23:58:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:58:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.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 23:58:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:58:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:58:55: 1000000 INFO @ Mon, 12 Aug 2019 23:58:58: 1000000 INFO @ Mon, 12 Aug 2019 23:58:59: 1000000 INFO @ Mon, 12 Aug 2019 23:59:01: 2000000 INFO @ Mon, 12 Aug 2019 23:59:07: 2000000 INFO @ Mon, 12 Aug 2019 23:59:07: 2000000 INFO @ Mon, 12 Aug 2019 23:59:08: 3000000 INFO @ Mon, 12 Aug 2019 23:59:14: 4000000 INFO @ Mon, 12 Aug 2019 23:59:15: 3000000 INFO @ Mon, 12 Aug 2019 23:59:16: 3000000 INFO @ Mon, 12 Aug 2019 23:59:21: 5000000 INFO @ Mon, 12 Aug 2019 23:59:24: 4000000 INFO @ Mon, 12 Aug 2019 23:59:24: 4000000 INFO @ Mon, 12 Aug 2019 23:59:28: 6000000 INFO @ Mon, 12 Aug 2019 23:59:32: 5000000 INFO @ Mon, 12 Aug 2019 23:59:33: 5000000 INFO @ Mon, 12 Aug 2019 23:59:34: 7000000 INFO @ Mon, 12 Aug 2019 23:59:41: 6000000 INFO @ Mon, 12 Aug 2019 23:59:41: 8000000 INFO @ Mon, 12 Aug 2019 23:59:41: 6000000 INFO @ Mon, 12 Aug 2019 23:59:48: 9000000 INFO @ Mon, 12 Aug 2019 23:59:49: 7000000 INFO @ Mon, 12 Aug 2019 23:59:50: 7000000 INFO @ Mon, 12 Aug 2019 23:59:54: 10000000 INFO @ Mon, 12 Aug 2019 23:59:57: 8000000 INFO @ Mon, 12 Aug 2019 23:59:58: 8000000 INFO @ Tue, 13 Aug 2019 00:00:01: 11000000 INFO @ Tue, 13 Aug 2019 00:00:06: 9000000 INFO @ Tue, 13 Aug 2019 00:00:06: 9000000 INFO @ Tue, 13 Aug 2019 00:00:08: 12000000 INFO @ Tue, 13 Aug 2019 00:00:14: 10000000 INFO @ Tue, 13 Aug 2019 00:00:14: 13000000 INFO @ Tue, 13 Aug 2019 00:00:15: 10000000 INFO @ Tue, 13 Aug 2019 00:00:21: 14000000 INFO @ Tue, 13 Aug 2019 00:00:22: 11000000 INFO @ Tue, 13 Aug 2019 00:00:23: 11000000 INFO @ Tue, 13 Aug 2019 00:00:25: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:25: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:25: #1 total tags in treatment: 14592166 INFO @ Tue, 13 Aug 2019 00:00:25: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:25: #1 tags after filtering in treatment: 14592166 INFO @ Tue, 13 Aug 2019 00:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:25: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:25: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:27: #2 number of paired peaks: 789 WARNING @ Tue, 13 Aug 2019 00:00:27: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:27: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:27: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:27: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:27: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:27: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:00:27: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 13 Aug 2019 00:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.05_model.r WARNING @ Tue, 13 Aug 2019 00:00:27: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:27: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 13 Aug 2019 00:00:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:27: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:30: 12000000 INFO @ Tue, 13 Aug 2019 00:00:31: 12000000 INFO @ Tue, 13 Aug 2019 00:00:38: 13000000 INFO @ Tue, 13 Aug 2019 00:00:39: 13000000 INFO @ Tue, 13 Aug 2019 00:00:45: 14000000 INFO @ Tue, 13 Aug 2019 00:00:47: 14000000 INFO @ Tue, 13 Aug 2019 00:00:50: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:50: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:50: #1 total tags in treatment: 14592166 INFO @ Tue, 13 Aug 2019 00:00:50: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:51: #1 tags after filtering in treatment: 14592166 INFO @ Tue, 13 Aug 2019 00:00:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:51: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:51: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:52: #2 number of paired peaks: 789 WARNING @ Tue, 13 Aug 2019 00:00:52: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:52: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:52: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:00:52: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:00:52: #1 total tags in treatment: 14592166 INFO @ Tue, 13 Aug 2019 00:00:52: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:00:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:00:52: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:52: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:52: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:52: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:00:52: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 13 Aug 2019 00:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.10_model.r WARNING @ Tue, 13 Aug 2019 00:00:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:52: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 13 Aug 2019 00:00:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:52: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:00:52: #1 tags after filtering in treatment: 14592166 INFO @ Tue, 13 Aug 2019 00:00:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:00:52: #1 finished! INFO @ Tue, 13 Aug 2019 00:00:52: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:00:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:00:54: #2 number of paired peaks: 789 WARNING @ Tue, 13 Aug 2019 00:00:54: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Tue, 13 Aug 2019 00:00:54: start model_add_line... INFO @ Tue, 13 Aug 2019 00:00:54: start X-correlation... INFO @ Tue, 13 Aug 2019 00:00:54: end of X-cor INFO @ Tue, 13 Aug 2019 00:00:54: #2 finished! INFO @ Tue, 13 Aug 2019 00:00:54: #2 predicted fragment length is 49 bps INFO @ Tue, 13 Aug 2019 00:00:54: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 13 Aug 2019 00:00:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.20_model.r WARNING @ Tue, 13 Aug 2019 00:00:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:00:54: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 13 Aug 2019 00:00:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:00:54: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:00:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:01:06: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.05_summits.bed INFO @ Tue, 13 Aug 2019 00:01:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4700 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:01:31: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:32: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:01:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.10_summits.bed INFO @ Tue, 13 Aug 2019 00:01:50: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3223 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:01:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011089/SRX5011089.20_summits.bed INFO @ Tue, 13 Aug 2019 00:01:52: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2252 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。