Job ID = 2590668 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 41,719,566 reads read : 83,439,132 reads written : 41,719,566 reads 0-length : 41,719,566 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: 00:17:18 41719566 reads; of these: 41719566 (100.00%) were unpaired; of these: 886894 (2.13%) aligned 0 times 28944465 (69.38%) aligned exactly 1 time 11888207 (28.50%) aligned >1 times 97.87% overall alignment rate Time searching: 00:17:18 Overall time: 00:17:18 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 20 files... [bam_rmdupse_core] 19988708 / 40832672 = 0.4895 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 23:35:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.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 23:35:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.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 23:35:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.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 23:35:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:35:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:35:50: 1000000 INFO @ Mon, 12 Aug 2019 23:35:50: 1000000 INFO @ Mon, 12 Aug 2019 23:35:51: 1000000 INFO @ Mon, 12 Aug 2019 23:35:58: 2000000 INFO @ Mon, 12 Aug 2019 23:35:59: 2000000 INFO @ Mon, 12 Aug 2019 23:36:01: 2000000 INFO @ Mon, 12 Aug 2019 23:36:06: 3000000 INFO @ Mon, 12 Aug 2019 23:36:08: 3000000 INFO @ Mon, 12 Aug 2019 23:36:11: 3000000 INFO @ Mon, 12 Aug 2019 23:36:14: 4000000 INFO @ Mon, 12 Aug 2019 23:36:17: 4000000 INFO @ Mon, 12 Aug 2019 23:36:21: 4000000 INFO @ Mon, 12 Aug 2019 23:36:21: 5000000 INFO @ Mon, 12 Aug 2019 23:36:26: 5000000 INFO @ Mon, 12 Aug 2019 23:36:29: 6000000 INFO @ Mon, 12 Aug 2019 23:36:31: 5000000 INFO @ Mon, 12 Aug 2019 23:36:35: 6000000 INFO @ Mon, 12 Aug 2019 23:36:37: 7000000 INFO @ Mon, 12 Aug 2019 23:36:40: 6000000 INFO @ Mon, 12 Aug 2019 23:36:44: 7000000 INFO @ Mon, 12 Aug 2019 23:36:45: 8000000 INFO @ Mon, 12 Aug 2019 23:36:50: 7000000 INFO @ Mon, 12 Aug 2019 23:36:52: 9000000 INFO @ Mon, 12 Aug 2019 23:36:53: 8000000 INFO @ Mon, 12 Aug 2019 23:37:00: 8000000 INFO @ Mon, 12 Aug 2019 23:37:00: 10000000 INFO @ Mon, 12 Aug 2019 23:37:02: 9000000 INFO @ Mon, 12 Aug 2019 23:37:08: 11000000 INFO @ Mon, 12 Aug 2019 23:37:10: 9000000 INFO @ Mon, 12 Aug 2019 23:37:10: 10000000 INFO @ Mon, 12 Aug 2019 23:37:16: 12000000 INFO @ Mon, 12 Aug 2019 23:37:19: 11000000 INFO @ Mon, 12 Aug 2019 23:37:20: 10000000 INFO @ Mon, 12 Aug 2019 23:37:23: 13000000 INFO @ Mon, 12 Aug 2019 23:37:28: 12000000 INFO @ Mon, 12 Aug 2019 23:37:30: 11000000 INFO @ Mon, 12 Aug 2019 23:37:31: 14000000 INFO @ Mon, 12 Aug 2019 23:37:37: 13000000 INFO @ Mon, 12 Aug 2019 23:37:39: 15000000 INFO @ Mon, 12 Aug 2019 23:37:39: 12000000 INFO @ Mon, 12 Aug 2019 23:37:46: 14000000 INFO @ Mon, 12 Aug 2019 23:37:47: 16000000 INFO @ Mon, 12 Aug 2019 23:37:49: 13000000 INFO @ Mon, 12 Aug 2019 23:37:54: 17000000 INFO @ Mon, 12 Aug 2019 23:37:56: 15000000 INFO @ Mon, 12 Aug 2019 23:37:59: 14000000 INFO @ Mon, 12 Aug 2019 23:38:01: 18000000 INFO @ Mon, 12 Aug 2019 23:38:05: 16000000 INFO @ Mon, 12 Aug 2019 23:38:08: 15000000 INFO @ Mon, 12 Aug 2019 23:38:09: 19000000 INFO @ Mon, 12 Aug 2019 23:38:14: 17000000 INFO @ Mon, 12 Aug 2019 23:38:16: 20000000 INFO @ Mon, 12 Aug 2019 23:38:18: 16000000 INFO @ Mon, 12 Aug 2019 23:38:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:38:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:38:22: #1 total tags in treatment: 20843964 INFO @ Mon, 12 Aug 2019 23:38:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:38:22: #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 23:38:22: #1 tags after filtering in treatment: 20843964 INFO @ Mon, 12 Aug 2019 23:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:38:22: #1 finished! INFO @ Mon, 12 Aug 2019 23:38:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:38:23: 18000000 INFO @ Mon, 12 Aug 2019 23:38:24: #2 number of paired peaks: 514 WARNING @ Mon, 12 Aug 2019 23:38:24: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Mon, 12 Aug 2019 23:38:24: start model_add_line... INFO @ Mon, 12 Aug 2019 23:38:24: start X-correlation... INFO @ Mon, 12 Aug 2019 23:38:24: end of X-cor INFO @ Mon, 12 Aug 2019 23:38:24: #2 finished! INFO @ Mon, 12 Aug 2019 23:38:24: #2 predicted fragment length is 68 bps INFO @ Mon, 12 Aug 2019 23:38:24: #2 alternative fragment length(s) may be 3,63,68,586 bps INFO @ Mon, 12 Aug 2019 23:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.20_model.r WARNING @ Mon, 12 Aug 2019 23:38:24: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:38:24: #2 You may need to consider one of the other alternative d(s): 3,63,68,586 WARNING @ Mon, 12 Aug 2019 23:38:24: #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 23:38:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:38:27: 17000000 INFO @ Mon, 12 Aug 2019 23:38:32: 19000000 INFO @ Mon, 12 Aug 2019 23:38:36: 18000000 INFO @ Mon, 12 Aug 2019 23:38:40: 20000000 INFO @ Mon, 12 Aug 2019 23:38:45: 19000000 INFO @ Mon, 12 Aug 2019 23:38:48: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:38:48: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:38:48: #1 total tags in treatment: 20843964 INFO @ Mon, 12 Aug 2019 23:38:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:38:48: #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 23:38:48: #1 tags after filtering in treatment: 20843964 INFO @ Mon, 12 Aug 2019 23:38:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:38:48: #1 finished! INFO @ Mon, 12 Aug 2019 23:38:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:38:50: #2 number of paired peaks: 514 WARNING @ Mon, 12 Aug 2019 23:38:50: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Mon, 12 Aug 2019 23:38:50: start model_add_line... INFO @ Mon, 12 Aug 2019 23:38:50: start X-correlation... INFO @ Mon, 12 Aug 2019 23:38:50: end of X-cor INFO @ Mon, 12 Aug 2019 23:38:50: #2 finished! INFO @ Mon, 12 Aug 2019 23:38:50: #2 predicted fragment length is 68 bps INFO @ Mon, 12 Aug 2019 23:38:50: #2 alternative fragment length(s) may be 3,63,68,586 bps INFO @ Mon, 12 Aug 2019 23:38:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.05_model.r WARNING @ Mon, 12 Aug 2019 23:38:50: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:38:50: #2 You may need to consider one of the other alternative d(s): 3,63,68,586 WARNING @ Mon, 12 Aug 2019 23:38:50: #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 23:38:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:38:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:38:54: 20000000 INFO @ Mon, 12 Aug 2019 23:39:01: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:39:01: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:39:01: #1 total tags in treatment: 20843964 INFO @ Mon, 12 Aug 2019 23:39:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:39:01: #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 23:39:01: #1 tags after filtering in treatment: 20843964 INFO @ Mon, 12 Aug 2019 23:39:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:39:01: #1 finished! INFO @ Mon, 12 Aug 2019 23:39:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:39:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:39:03: #2 number of paired peaks: 514 WARNING @ Mon, 12 Aug 2019 23:39:03: Fewer paired peaks (514) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 514 pairs to build model! INFO @ Mon, 12 Aug 2019 23:39:03: start model_add_line... INFO @ Mon, 12 Aug 2019 23:39:04: start X-correlation... INFO @ Mon, 12 Aug 2019 23:39:04: end of X-cor INFO @ Mon, 12 Aug 2019 23:39:04: #2 finished! INFO @ Mon, 12 Aug 2019 23:39:04: #2 predicted fragment length is 68 bps INFO @ Mon, 12 Aug 2019 23:39:04: #2 alternative fragment length(s) may be 3,63,68,586 bps INFO @ Mon, 12 Aug 2019 23:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.10_model.r WARNING @ Mon, 12 Aug 2019 23:39:04: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:39:04: #2 You may need to consider one of the other alternative d(s): 3,63,68,586 WARNING @ Mon, 12 Aug 2019 23:39:04: #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 23:39:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:39:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:39:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.20_summits.bed INFO @ Mon, 12 Aug 2019 23:39:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1240 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:39:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.05_summits.bed INFO @ Mon, 12 Aug 2019 23:40:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5265 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:40:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:40:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:40:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011017/SRX5011017.10_summits.bed INFO @ Mon, 12 Aug 2019 23:40:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2494 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。