Job ID = 2590845 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,155,474 reads read : 25,155,474 reads written : 25,155,474 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: 00:10:45 25155474 reads; of these: 25155474 (100.00%) were unpaired; of these: 2099446 (8.35%) aligned 0 times 16609142 (66.03%) aligned exactly 1 time 6446886 (25.63%) aligned >1 times 91.65% overall alignment rate Time searching: 00:10:45 Overall time: 00:10:45 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] 7871953 / 23056028 = 0.3414 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 23:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.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 23:56:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.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 23:56:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.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 23:56:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:56:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:57:04: 1000000 INFO @ Mon, 12 Aug 2019 23:57:06: 1000000 INFO @ Mon, 12 Aug 2019 23:57:06: 1000000 INFO @ Mon, 12 Aug 2019 23:57:11: 2000000 INFO @ Mon, 12 Aug 2019 23:57:14: 2000000 INFO @ Mon, 12 Aug 2019 23:57:16: 2000000 INFO @ Mon, 12 Aug 2019 23:57:19: 3000000 INFO @ Mon, 12 Aug 2019 23:57:22: 3000000 INFO @ Mon, 12 Aug 2019 23:57:26: 3000000 INFO @ Mon, 12 Aug 2019 23:57:26: 4000000 INFO @ Mon, 12 Aug 2019 23:57:31: 4000000 INFO @ Mon, 12 Aug 2019 23:57:33: 5000000 INFO @ Mon, 12 Aug 2019 23:57:36: 4000000 INFO @ Mon, 12 Aug 2019 23:57:39: 5000000 INFO @ Mon, 12 Aug 2019 23:57:41: 6000000 INFO @ Mon, 12 Aug 2019 23:57:46: 5000000 INFO @ Mon, 12 Aug 2019 23:57:47: 6000000 INFO @ Mon, 12 Aug 2019 23:57:48: 7000000 INFO @ Mon, 12 Aug 2019 23:57:55: 7000000 INFO @ Mon, 12 Aug 2019 23:57:55: 8000000 INFO @ Mon, 12 Aug 2019 23:57:56: 6000000 INFO @ Mon, 12 Aug 2019 23:58:03: 9000000 INFO @ Mon, 12 Aug 2019 23:58:04: 8000000 INFO @ Mon, 12 Aug 2019 23:58:06: 7000000 INFO @ Mon, 12 Aug 2019 23:58:10: 10000000 INFO @ Mon, 12 Aug 2019 23:58:12: 9000000 INFO @ Mon, 12 Aug 2019 23:58:15: 8000000 INFO @ Mon, 12 Aug 2019 23:58:17: 11000000 INFO @ Mon, 12 Aug 2019 23:58:20: 10000000 INFO @ Mon, 12 Aug 2019 23:58:25: 12000000 INFO @ Mon, 12 Aug 2019 23:58:25: 9000000 INFO @ Mon, 12 Aug 2019 23:58:28: 11000000 INFO @ Mon, 12 Aug 2019 23:58:32: 13000000 INFO @ Mon, 12 Aug 2019 23:58:35: 10000000 INFO @ Mon, 12 Aug 2019 23:58:37: 12000000 INFO @ Mon, 12 Aug 2019 23:58:39: 14000000 INFO @ Mon, 12 Aug 2019 23:58:45: 13000000 INFO @ Mon, 12 Aug 2019 23:58:45: 11000000 INFO @ Mon, 12 Aug 2019 23:58:46: 15000000 INFO @ Mon, 12 Aug 2019 23:58:48: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:58:48: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:58:48: #1 total tags in treatment: 15184075 INFO @ Mon, 12 Aug 2019 23:58:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:58:48: #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 23:58:48: #1 tags after filtering in treatment: 15184075 INFO @ Mon, 12 Aug 2019 23:58:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:58:48: #1 finished! INFO @ Mon, 12 Aug 2019 23:58:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:58:49: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 23:58:49: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 23:58:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:58:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:58:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:58:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:58:50: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:58:50: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 23:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.10_model.r WARNING @ Mon, 12 Aug 2019 23:58:50: #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 23:58:50: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 23:58:50: #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 23:58:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:58:53: 14000000 INFO @ Mon, 12 Aug 2019 23:58:55: 12000000 INFO @ Mon, 12 Aug 2019 23:59:01: 15000000 INFO @ Mon, 12 Aug 2019 23:59:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:02: #1 total tags in treatment: 15184075 INFO @ Mon, 12 Aug 2019 23:59:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:02: #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 23:59:02: #1 tags after filtering in treatment: 15184075 INFO @ Mon, 12 Aug 2019 23:59:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:02: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:04: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 23:59:04: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 23:59:04: start model_add_line... INFO @ Mon, 12 Aug 2019 23:59:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:59:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:59:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:59:04: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:59:04: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 23:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.20_model.r WARNING @ Mon, 12 Aug 2019 23:59:04: #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 23:59:04: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 23:59:04: #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 23:59:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:59:05: 13000000 INFO @ Mon, 12 Aug 2019 23:59:14: 14000000 INFO @ Mon, 12 Aug 2019 23:59:23: 15000000 INFO @ Mon, 12 Aug 2019 23:59:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:59:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:59:25: #1 total tags in treatment: 15184075 INFO @ Mon, 12 Aug 2019 23:59:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:59:25: #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 23:59:25: #1 tags after filtering in treatment: 15184075 INFO @ Mon, 12 Aug 2019 23:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:59:25: #1 finished! INFO @ Mon, 12 Aug 2019 23:59:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:59:26: #2 number of paired peaks: 794 WARNING @ Mon, 12 Aug 2019 23:59:26: Fewer paired peaks (794) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 794 pairs to build model! INFO @ Mon, 12 Aug 2019 23:59:26: start model_add_line... INFO @ Mon, 12 Aug 2019 23:59:26: start X-correlation... INFO @ Mon, 12 Aug 2019 23:59:26: end of X-cor INFO @ Mon, 12 Aug 2019 23:59:26: #2 finished! INFO @ Mon, 12 Aug 2019 23:59:26: #2 predicted fragment length is 47 bps INFO @ Mon, 12 Aug 2019 23:59:26: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 12 Aug 2019 23:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.05_model.r WARNING @ Mon, 12 Aug 2019 23:59:26: #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 23:59:26: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 12 Aug 2019 23:59:26: #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 23:59:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:59:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:59:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:59:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:59:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:59:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.10_summits.bed INFO @ Mon, 12 Aug 2019 23:59:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3291 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.20_summits.bed INFO @ Tue, 13 Aug 2019 00:00:04: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (2299 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:00:07: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:00:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:00:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:00:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011080/SRX5011080.05_summits.bed INFO @ Tue, 13 Aug 2019 00:00:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4963 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。