Job ID = 2590793 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,184,024 reads read : 74,368,048 reads written : 37,184,024 reads 0-length : 37,184,024 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: 00:14:50 37184024 reads; of these: 37184024 (100.00%) were unpaired; of these: 762571 (2.05%) aligned 0 times 25871938 (69.58%) aligned exactly 1 time 10549515 (28.37%) aligned >1 times 97.95% overall alignment rate Time searching: 00:14:50 Overall time: 00:14:50 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 16 files... [bam_rmdupse_core] 17152050 / 36421453 = 0.4709 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 23:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.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 23:41:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.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 23:41:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.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 23:41:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:41:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:41:27: 1000000 INFO @ Mon, 12 Aug 2019 23:41:27: 1000000 INFO @ Mon, 12 Aug 2019 23:41:28: 1000000 INFO @ Mon, 12 Aug 2019 23:41:34: 2000000 INFO @ Mon, 12 Aug 2019 23:41:35: 2000000 INFO @ Mon, 12 Aug 2019 23:41:36: 2000000 INFO @ Mon, 12 Aug 2019 23:41:42: 3000000 INFO @ Mon, 12 Aug 2019 23:41:43: 3000000 INFO @ Mon, 12 Aug 2019 23:41:44: 3000000 INFO @ Mon, 12 Aug 2019 23:41:49: 4000000 INFO @ Mon, 12 Aug 2019 23:41:50: 4000000 INFO @ Mon, 12 Aug 2019 23:41:51: 4000000 INFO @ Mon, 12 Aug 2019 23:41:56: 5000000 INFO @ Mon, 12 Aug 2019 23:41:58: 5000000 INFO @ Mon, 12 Aug 2019 23:41:58: 5000000 INFO @ Mon, 12 Aug 2019 23:42:03: 6000000 INFO @ Mon, 12 Aug 2019 23:42:05: 6000000 INFO @ Mon, 12 Aug 2019 23:42:06: 6000000 INFO @ Mon, 12 Aug 2019 23:42:10: 7000000 INFO @ Mon, 12 Aug 2019 23:42:12: 7000000 INFO @ Mon, 12 Aug 2019 23:42:14: 7000000 INFO @ Mon, 12 Aug 2019 23:42:17: 8000000 INFO @ Mon, 12 Aug 2019 23:42:19: 8000000 INFO @ Mon, 12 Aug 2019 23:42:21: 8000000 INFO @ Mon, 12 Aug 2019 23:42:24: 9000000 INFO @ Mon, 12 Aug 2019 23:42:26: 9000000 INFO @ Mon, 12 Aug 2019 23:42:29: 9000000 INFO @ Mon, 12 Aug 2019 23:42:31: 10000000 INFO @ Mon, 12 Aug 2019 23:42:33: 10000000 INFO @ Mon, 12 Aug 2019 23:42:37: 10000000 INFO @ Mon, 12 Aug 2019 23:42:38: 11000000 INFO @ Mon, 12 Aug 2019 23:42:40: 11000000 INFO @ Mon, 12 Aug 2019 23:42:44: 11000000 INFO @ Mon, 12 Aug 2019 23:42:45: 12000000 INFO @ Mon, 12 Aug 2019 23:42:47: 12000000 INFO @ Mon, 12 Aug 2019 23:42:52: 13000000 INFO @ Mon, 12 Aug 2019 23:42:52: 12000000 INFO @ Mon, 12 Aug 2019 23:42:54: 13000000 INFO @ Mon, 12 Aug 2019 23:42:59: 14000000 INFO @ Mon, 12 Aug 2019 23:42:59: 13000000 INFO @ Mon, 12 Aug 2019 23:43:01: 14000000 INFO @ Mon, 12 Aug 2019 23:43:06: 15000000 INFO @ Mon, 12 Aug 2019 23:43:07: 14000000 INFO @ Mon, 12 Aug 2019 23:43:08: 15000000 INFO @ Mon, 12 Aug 2019 23:43:13: 16000000 INFO @ Mon, 12 Aug 2019 23:43:15: 15000000 INFO @ Mon, 12 Aug 2019 23:43:16: 16000000 INFO @ Mon, 12 Aug 2019 23:43:20: 17000000 INFO @ Mon, 12 Aug 2019 23:43:23: 17000000 INFO @ Mon, 12 Aug 2019 23:43:23: 16000000 INFO @ Mon, 12 Aug 2019 23:43:27: 18000000 INFO @ Mon, 12 Aug 2019 23:43:29: 18000000 INFO @ Mon, 12 Aug 2019 23:43:31: 17000000 INFO @ Mon, 12 Aug 2019 23:43:34: 19000000 INFO @ Mon, 12 Aug 2019 23:43:36: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:36: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:36: #1 total tags in treatment: 19269403 INFO @ Mon, 12 Aug 2019 23:43:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:36: #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 23:43:36: #1 tags after filtering in treatment: 19269403 INFO @ Mon, 12 Aug 2019 23:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:36: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:36: 19000000 INFO @ Mon, 12 Aug 2019 23:43:38: #2 number of paired peaks: 502 WARNING @ Mon, 12 Aug 2019 23:43:38: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 12 Aug 2019 23:43:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:38: 18000000 INFO @ Mon, 12 Aug 2019 23:43:38: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:38: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:38: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:38: #2 predicted fragment length is 68 bps INFO @ Mon, 12 Aug 2019 23:43:38: #2 alternative fragment length(s) may be 4,68 bps INFO @ Mon, 12 Aug 2019 23:43:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.10_model.r WARNING @ Mon, 12 Aug 2019 23:43:38: #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 23:43:38: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Mon, 12 Aug 2019 23:43:38: #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 23:43:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:43:38: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:38: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:38: #1 total tags in treatment: 19269403 INFO @ Mon, 12 Aug 2019 23:43:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:38: #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 23:43:39: #1 tags after filtering in treatment: 19269403 INFO @ Mon, 12 Aug 2019 23:43:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:39: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:40: #2 number of paired peaks: 502 WARNING @ Mon, 12 Aug 2019 23:43:40: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 12 Aug 2019 23:43:40: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:40: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:41: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:41: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:41: #2 predicted fragment length is 68 bps INFO @ Mon, 12 Aug 2019 23:43:41: #2 alternative fragment length(s) may be 4,68 bps INFO @ Mon, 12 Aug 2019 23:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.20_model.r WARNING @ Mon, 12 Aug 2019 23:43:41: #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 23:43:41: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Mon, 12 Aug 2019 23:43:41: #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 23:43:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:43:45: 19000000 INFO @ Mon, 12 Aug 2019 23:43:47: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:43:47: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:43:47: #1 total tags in treatment: 19269403 INFO @ Mon, 12 Aug 2019 23:43:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:43:47: #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 23:43:47: #1 tags after filtering in treatment: 19269403 INFO @ Mon, 12 Aug 2019 23:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:43:47: #1 finished! INFO @ Mon, 12 Aug 2019 23:43:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:43:49: #2 number of paired peaks: 502 WARNING @ Mon, 12 Aug 2019 23:43:49: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Mon, 12 Aug 2019 23:43:49: start model_add_line... INFO @ Mon, 12 Aug 2019 23:43:49: start X-correlation... INFO @ Mon, 12 Aug 2019 23:43:49: end of X-cor INFO @ Mon, 12 Aug 2019 23:43:49: #2 finished! INFO @ Mon, 12 Aug 2019 23:43:49: #2 predicted fragment length is 68 bps INFO @ Mon, 12 Aug 2019 23:43:49: #2 alternative fragment length(s) may be 4,68 bps INFO @ Mon, 12 Aug 2019 23:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.05_model.r WARNING @ Mon, 12 Aug 2019 23:43:49: #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 23:43:49: #2 You may need to consider one of the other alternative d(s): 4,68 WARNING @ Mon, 12 Aug 2019 23:43:49: #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 23:43:49: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:44:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:38: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:44:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:44:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:44:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.10_summits.bed INFO @ Mon, 12 Aug 2019 23:44:52: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2269 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:44:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:44:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.20_summits.bed INFO @ Mon, 12 Aug 2019 23:44:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (912 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011035/SRX5011035.05_summits.bed INFO @ Mon, 12 Aug 2019 23:45:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5201 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。