Job ID = 2590829 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,207,186 reads read : 62,414,372 reads written : 31,207,186 reads 0-length : 31,207,186 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: 00:12:15 31207186 reads; of these: 31207186 (100.00%) were unpaired; of these: 2288646 (7.33%) aligned 0 times 21553332 (69.07%) aligned exactly 1 time 7365208 (23.60%) aligned >1 times 92.67% overall alignment rate Time searching: 00:12:15 Overall time: 00:12:15 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] 11080973 / 28918540 = 0.3832 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 23:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.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 23:50:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.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 23:50:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.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 23:50:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:50:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:04: 1000000 INFO @ Mon, 12 Aug 2019 23:51:05: 1000000 INFO @ Mon, 12 Aug 2019 23:51:05: 1000000 INFO @ Mon, 12 Aug 2019 23:51:11: 2000000 INFO @ Mon, 12 Aug 2019 23:51:11: 2000000 INFO @ Mon, 12 Aug 2019 23:51:12: 2000000 INFO @ Mon, 12 Aug 2019 23:51:18: 3000000 INFO @ Mon, 12 Aug 2019 23:51:18: 3000000 INFO @ Mon, 12 Aug 2019 23:51:19: 3000000 INFO @ Mon, 12 Aug 2019 23:51:25: 4000000 INFO @ Mon, 12 Aug 2019 23:51:26: 4000000 INFO @ Mon, 12 Aug 2019 23:51:26: 4000000 INFO @ Mon, 12 Aug 2019 23:51:32: 5000000 INFO @ Mon, 12 Aug 2019 23:51:33: 5000000 INFO @ Mon, 12 Aug 2019 23:51:35: 5000000 INFO @ Mon, 12 Aug 2019 23:51:39: 6000000 INFO @ Mon, 12 Aug 2019 23:51:40: 6000000 INFO @ Mon, 12 Aug 2019 23:51:42: 6000000 INFO @ Mon, 12 Aug 2019 23:51:46: 7000000 INFO @ Mon, 12 Aug 2019 23:51:47: 7000000 INFO @ Mon, 12 Aug 2019 23:51:50: 7000000 INFO @ Mon, 12 Aug 2019 23:51:53: 8000000 INFO @ Mon, 12 Aug 2019 23:51:54: 8000000 INFO @ Mon, 12 Aug 2019 23:51:58: 8000000 INFO @ Mon, 12 Aug 2019 23:52:00: 9000000 INFO @ Mon, 12 Aug 2019 23:52:01: 9000000 INFO @ Mon, 12 Aug 2019 23:52:06: 9000000 INFO @ Mon, 12 Aug 2019 23:52:07: 10000000 INFO @ Mon, 12 Aug 2019 23:52:08: 10000000 INFO @ Mon, 12 Aug 2019 23:52:13: 11000000 INFO @ Mon, 12 Aug 2019 23:52:14: 10000000 INFO @ Mon, 12 Aug 2019 23:52:15: 11000000 INFO @ Mon, 12 Aug 2019 23:52:20: 12000000 INFO @ Mon, 12 Aug 2019 23:52:22: 11000000 INFO @ Mon, 12 Aug 2019 23:52:22: 12000000 INFO @ Mon, 12 Aug 2019 23:52:28: 13000000 INFO @ Mon, 12 Aug 2019 23:52:29: 13000000 INFO @ Mon, 12 Aug 2019 23:52:30: 12000000 INFO @ Mon, 12 Aug 2019 23:52:35: 14000000 INFO @ Mon, 12 Aug 2019 23:52:36: 14000000 INFO @ Mon, 12 Aug 2019 23:52:38: 13000000 INFO @ Mon, 12 Aug 2019 23:52:42: 15000000 INFO @ Mon, 12 Aug 2019 23:52:43: 15000000 INFO @ Mon, 12 Aug 2019 23:52:46: 14000000 INFO @ Mon, 12 Aug 2019 23:52:48: 16000000 INFO @ Mon, 12 Aug 2019 23:52:50: 16000000 INFO @ Mon, 12 Aug 2019 23:52:54: 15000000 INFO @ Mon, 12 Aug 2019 23:52:55: 17000000 INFO @ Mon, 12 Aug 2019 23:52:57: 17000000 INFO @ Mon, 12 Aug 2019 23:53:01: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:53:01: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:53:01: #1 total tags in treatment: 17837567 INFO @ Mon, 12 Aug 2019 23:53:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:53:01: #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 23:53:01: 16000000 INFO @ Mon, 12 Aug 2019 23:53:02: #1 tags after filtering in treatment: 17837567 INFO @ Mon, 12 Aug 2019 23:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:53:02: #1 finished! INFO @ Mon, 12 Aug 2019 23:53:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:53:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:53:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:53:03: #1 total tags in treatment: 17837567 INFO @ Mon, 12 Aug 2019 23:53:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:53:03: #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 23:53:03: #1 tags after filtering in treatment: 17837567 INFO @ Mon, 12 Aug 2019 23:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:53:03: #1 finished! INFO @ Mon, 12 Aug 2019 23:53:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:53:03: #2 number of paired peaks: 416 WARNING @ Mon, 12 Aug 2019 23:53:03: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 12 Aug 2019 23:53:03: start model_add_line... INFO @ Mon, 12 Aug 2019 23:53:03: start X-correlation... INFO @ Mon, 12 Aug 2019 23:53:03: end of X-cor INFO @ Mon, 12 Aug 2019 23:53:03: #2 finished! INFO @ Mon, 12 Aug 2019 23:53:03: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:53:03: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 23:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.05_model.r WARNING @ Mon, 12 Aug 2019 23:53:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:53:04: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 23:53:04: #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 23:53:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:53:05: #2 number of paired peaks: 416 WARNING @ Mon, 12 Aug 2019 23:53:05: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 12 Aug 2019 23:53:05: start model_add_line... INFO @ Mon, 12 Aug 2019 23:53:05: start X-correlation... INFO @ Mon, 12 Aug 2019 23:53:05: end of X-cor INFO @ Mon, 12 Aug 2019 23:53:05: #2 finished! INFO @ Mon, 12 Aug 2019 23:53:05: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:53:05: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 23:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.10_model.r WARNING @ Mon, 12 Aug 2019 23:53:05: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:53:05: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 23:53:05: #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 23:53:05: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:53:09: 17000000 INFO @ Mon, 12 Aug 2019 23:53:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:53:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:53:16: #1 total tags in treatment: 17837567 INFO @ Mon, 12 Aug 2019 23:53:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:53:16: #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 23:53:16: #1 tags after filtering in treatment: 17837567 INFO @ Mon, 12 Aug 2019 23:53:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:53:16: #1 finished! INFO @ Mon, 12 Aug 2019 23:53:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:53:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:53:18: #2 number of paired peaks: 416 WARNING @ Mon, 12 Aug 2019 23:53:18: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Mon, 12 Aug 2019 23:53:18: start model_add_line... INFO @ Mon, 12 Aug 2019 23:53:18: start X-correlation... INFO @ Mon, 12 Aug 2019 23:53:18: end of X-cor INFO @ Mon, 12 Aug 2019 23:53:18: #2 finished! INFO @ Mon, 12 Aug 2019 23:53:18: #2 predicted fragment length is 49 bps INFO @ Mon, 12 Aug 2019 23:53:18: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 12 Aug 2019 23:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.20_model.r WARNING @ Mon, 12 Aug 2019 23:53:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:53:18: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 12 Aug 2019 23:53:18: #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 23:53:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:53:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:53:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.05_summits.bed INFO @ Mon, 12 Aug 2019 23:54:10: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5563 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.10_summits.bed INFO @ Mon, 12 Aug 2019 23:54:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3390 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:54:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:54:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:54:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011068/SRX5011068.20_summits.bed INFO @ Mon, 12 Aug 2019 23:54:24: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1932 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。