Job ID = 1300125 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,840,198 reads read : 21,840,198 reads written : 21,840,198 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:00:01 Multiseed full-index search: 00:11:34 21840198 reads; of these: 21840198 (100.00%) were unpaired; of these: 476831 (2.18%) aligned 0 times 14184032 (64.94%) aligned exactly 1 time 7179335 (32.87%) aligned >1 times 97.82% overall alignment rate Time searching: 00:11:35 Overall time: 00:11:35 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] 2082790 / 21363367 = 0.0975 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, 03 Jun 2019 19:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.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, 03 Jun 2019 19:26:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:26:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.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, 03 Jun 2019 19:26:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:26:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.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, 03 Jun 2019 19:26:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:26:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:26:18: 1000000 INFO @ Mon, 03 Jun 2019 19:26:18: 1000000 INFO @ Mon, 03 Jun 2019 19:26:20: 1000000 INFO @ Mon, 03 Jun 2019 19:26:28: 2000000 INFO @ Mon, 03 Jun 2019 19:26:28: 2000000 INFO @ Mon, 03 Jun 2019 19:26:31: 2000000 INFO @ Mon, 03 Jun 2019 19:26:38: 3000000 INFO @ Mon, 03 Jun 2019 19:26:38: 3000000 INFO @ Mon, 03 Jun 2019 19:26:42: 3000000 INFO @ Mon, 03 Jun 2019 19:26:47: 4000000 INFO @ Mon, 03 Jun 2019 19:26:49: 4000000 INFO @ Mon, 03 Jun 2019 19:26:53: 4000000 INFO @ Mon, 03 Jun 2019 19:26:57: 5000000 INFO @ Mon, 03 Jun 2019 19:27:00: 5000000 INFO @ Mon, 03 Jun 2019 19:27:05: 5000000 INFO @ Mon, 03 Jun 2019 19:27:07: 6000000 INFO @ Mon, 03 Jun 2019 19:27:11: 6000000 INFO @ Mon, 03 Jun 2019 19:27:17: 6000000 INFO @ Mon, 03 Jun 2019 19:27:18: 7000000 INFO @ Mon, 03 Jun 2019 19:27:23: 7000000 INFO @ Mon, 03 Jun 2019 19:27:29: 7000000 INFO @ Mon, 03 Jun 2019 19:27:31: 8000000 INFO @ Mon, 03 Jun 2019 19:27:36: 8000000 INFO @ Mon, 03 Jun 2019 19:27:41: 8000000 INFO @ Mon, 03 Jun 2019 19:27:44: 9000000 INFO @ Mon, 03 Jun 2019 19:27:49: 9000000 INFO @ Mon, 03 Jun 2019 19:27:53: 9000000 INFO @ Mon, 03 Jun 2019 19:27:58: 10000000 INFO @ Mon, 03 Jun 2019 19:28:02: 10000000 INFO @ Mon, 03 Jun 2019 19:28:05: 10000000 INFO @ Mon, 03 Jun 2019 19:28:10: 11000000 INFO @ Mon, 03 Jun 2019 19:28:15: 11000000 INFO @ Mon, 03 Jun 2019 19:28:16: 11000000 INFO @ Mon, 03 Jun 2019 19:28:22: 12000000 INFO @ Mon, 03 Jun 2019 19:28:27: 12000000 INFO @ Mon, 03 Jun 2019 19:28:27: 12000000 INFO @ Mon, 03 Jun 2019 19:28:35: 13000000 INFO @ Mon, 03 Jun 2019 19:28:38: 13000000 INFO @ Mon, 03 Jun 2019 19:28:40: 13000000 INFO @ Mon, 03 Jun 2019 19:28:47: 14000000 INFO @ Mon, 03 Jun 2019 19:28:49: 14000000 INFO @ Mon, 03 Jun 2019 19:28:52: 14000000 INFO @ Mon, 03 Jun 2019 19:29:00: 15000000 INFO @ Mon, 03 Jun 2019 19:29:00: 15000000 INFO @ Mon, 03 Jun 2019 19:29:05: 15000000 INFO @ Mon, 03 Jun 2019 19:29:12: 16000000 INFO @ Mon, 03 Jun 2019 19:29:12: 16000000 INFO @ Mon, 03 Jun 2019 19:29:17: 16000000 INFO @ Mon, 03 Jun 2019 19:29:23: 17000000 INFO @ Mon, 03 Jun 2019 19:29:25: 17000000 INFO @ Mon, 03 Jun 2019 19:29:29: 17000000 INFO @ Mon, 03 Jun 2019 19:29:34: 18000000 INFO @ Mon, 03 Jun 2019 19:29:37: 18000000 INFO @ Mon, 03 Jun 2019 19:29:41: 18000000 INFO @ Mon, 03 Jun 2019 19:29:44: 19000000 INFO @ Mon, 03 Jun 2019 19:29:46: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:29:46: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:29:46: #1 total tags in treatment: 19280577 INFO @ Mon, 03 Jun 2019 19:29:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:29:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:29:46: #1 tags after filtering in treatment: 19280577 INFO @ Mon, 03 Jun 2019 19:29:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:29:46: #1 finished! INFO @ Mon, 03 Jun 2019 19:29:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:29:48: #2 number of paired peaks: 733 WARNING @ Mon, 03 Jun 2019 19:29:48: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Mon, 03 Jun 2019 19:29:48: start model_add_line... INFO @ Mon, 03 Jun 2019 19:29:48: 19000000 INFO @ Mon, 03 Jun 2019 19:29:49: start X-correlation... INFO @ Mon, 03 Jun 2019 19:29:49: end of X-cor INFO @ Mon, 03 Jun 2019 19:29:49: #2 finished! INFO @ Mon, 03 Jun 2019 19:29:49: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 19:29:49: #2 alternative fragment length(s) may be 2,65 bps INFO @ Mon, 03 Jun 2019 19:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.10_model.r WARNING @ Mon, 03 Jun 2019 19:29:49: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:29:49: #2 You may need to consider one of the other alternative d(s): 2,65 WARNING @ Mon, 03 Jun 2019 19:29:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:29:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:29:52: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:29:52: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:29:52: #1 total tags in treatment: 19280577 INFO @ Mon, 03 Jun 2019 19:29:52: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:29:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:29:52: #1 tags after filtering in treatment: 19280577 INFO @ Mon, 03 Jun 2019 19:29:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:29:52: #1 finished! INFO @ Mon, 03 Jun 2019 19:29:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:29:53: 19000000 INFO @ Mon, 03 Jun 2019 19:29:54: #2 number of paired peaks: 733 WARNING @ Mon, 03 Jun 2019 19:29:54: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Mon, 03 Jun 2019 19:29:54: start model_add_line... INFO @ Mon, 03 Jun 2019 19:29:54: start X-correlation... INFO @ Mon, 03 Jun 2019 19:29:54: end of X-cor INFO @ Mon, 03 Jun 2019 19:29:54: #2 finished! INFO @ Mon, 03 Jun 2019 19:29:54: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 19:29:54: #2 alternative fragment length(s) may be 2,65 bps INFO @ Mon, 03 Jun 2019 19:29:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.20_model.r WARNING @ Mon, 03 Jun 2019 19:29:54: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:29:54: #2 You may need to consider one of the other alternative d(s): 2,65 WARNING @ Mon, 03 Jun 2019 19:29:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:29:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:29:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:29:56: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 19:29:56: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 19:29:56: #1 total tags in treatment: 19280577 INFO @ Mon, 03 Jun 2019 19:29:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:29:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 19:29:56: #1 tags after filtering in treatment: 19280577 INFO @ Mon, 03 Jun 2019 19:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 19:29:56: #1 finished! INFO @ Mon, 03 Jun 2019 19:29:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:29:58: #2 number of paired peaks: 733 WARNING @ Mon, 03 Jun 2019 19:29:58: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Mon, 03 Jun 2019 19:29:58: start model_add_line... INFO @ Mon, 03 Jun 2019 19:29:58: start X-correlation... INFO @ Mon, 03 Jun 2019 19:29:58: end of X-cor INFO @ Mon, 03 Jun 2019 19:29:58: #2 finished! INFO @ Mon, 03 Jun 2019 19:29:58: #2 predicted fragment length is 65 bps INFO @ Mon, 03 Jun 2019 19:29:58: #2 alternative fragment length(s) may be 2,65 bps INFO @ Mon, 03 Jun 2019 19:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.05_model.r WARNING @ Mon, 03 Jun 2019 19:29:58: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 19:29:58: #2 You may need to consider one of the other alternative d(s): 2,65 WARNING @ Mon, 03 Jun 2019 19:29:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 19:29:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:30:40: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:30:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:30:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:31:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:31:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:31:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.10_summits.bed INFO @ Mon, 03 Jun 2019 19:31:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2333 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:31:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:31:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.20_summits.bed INFO @ Mon, 03 Jun 2019 19:31:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1085 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4801809/SRX4801809.05_summits.bed INFO @ Mon, 03 Jun 2019 19:31:14: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4184 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。