Job ID = 2590679 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,843,880 reads read : 53,687,760 reads written : 26,843,880 reads 0-length : 26,843,880 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: 00:12:03 26843880 reads; of these: 26843880 (100.00%) were unpaired; of these: 554112 (2.06%) aligned 0 times 18491947 (68.89%) aligned exactly 1 time 7797821 (29.05%) aligned >1 times 97.94% overall alignment rate Time searching: 00:12:03 Overall time: 00:12:03 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] 13517922 / 26289768 = 0.5142 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 23:28:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.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 23:28:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:28:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.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 23:28:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:28:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:28:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.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 23:28:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:28:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:29:00: 1000000 INFO @ Mon, 12 Aug 2019 23:29:01: 1000000 INFO @ Mon, 12 Aug 2019 23:29:01: 1000000 INFO @ Mon, 12 Aug 2019 23:29:08: 2000000 INFO @ Mon, 12 Aug 2019 23:29:09: 2000000 INFO @ Mon, 12 Aug 2019 23:29:09: 2000000 INFO @ Mon, 12 Aug 2019 23:29:16: 3000000 INFO @ Mon, 12 Aug 2019 23:29:16: 3000000 INFO @ Mon, 12 Aug 2019 23:29:17: 3000000 INFO @ Mon, 12 Aug 2019 23:29:24: 4000000 INFO @ Mon, 12 Aug 2019 23:29:24: 4000000 INFO @ Mon, 12 Aug 2019 23:29:25: 4000000 INFO @ Mon, 12 Aug 2019 23:29:31: 5000000 INFO @ Mon, 12 Aug 2019 23:29:31: 5000000 INFO @ Mon, 12 Aug 2019 23:29:33: 5000000 INFO @ Mon, 12 Aug 2019 23:29:38: 6000000 INFO @ Mon, 12 Aug 2019 23:29:39: 6000000 INFO @ Mon, 12 Aug 2019 23:29:40: 6000000 INFO @ Mon, 12 Aug 2019 23:29:44: 7000000 INFO @ Mon, 12 Aug 2019 23:29:47: 7000000 INFO @ Mon, 12 Aug 2019 23:29:48: 7000000 INFO @ Mon, 12 Aug 2019 23:29:51: 8000000 INFO @ Mon, 12 Aug 2019 23:29:55: 8000000 INFO @ Mon, 12 Aug 2019 23:29:56: 8000000 INFO @ Mon, 12 Aug 2019 23:29:58: 9000000 INFO @ Mon, 12 Aug 2019 23:30:03: 9000000 INFO @ Mon, 12 Aug 2019 23:30:04: 9000000 INFO @ Mon, 12 Aug 2019 23:30:04: 10000000 INFO @ Mon, 12 Aug 2019 23:30:11: 10000000 INFO @ Mon, 12 Aug 2019 23:30:11: 11000000 INFO @ Mon, 12 Aug 2019 23:30:11: 10000000 INFO @ Mon, 12 Aug 2019 23:30:18: 12000000 INFO @ Mon, 12 Aug 2019 23:30:19: 11000000 INFO @ Mon, 12 Aug 2019 23:30:19: 11000000 INFO @ Mon, 12 Aug 2019 23:30:23: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:30:23: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:30:23: #1 total tags in treatment: 12771846 INFO @ Mon, 12 Aug 2019 23:30:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:30:23: #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 23:30:24: #1 tags after filtering in treatment: 12771846 INFO @ Mon, 12 Aug 2019 23:30:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:30:24: #1 finished! INFO @ Mon, 12 Aug 2019 23:30:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:30:25: #2 number of paired peaks: 943 WARNING @ Mon, 12 Aug 2019 23:30:25: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Mon, 12 Aug 2019 23:30:25: start model_add_line... INFO @ Mon, 12 Aug 2019 23:30:25: start X-correlation... INFO @ Mon, 12 Aug 2019 23:30:25: end of X-cor INFO @ Mon, 12 Aug 2019 23:30:25: #2 finished! INFO @ Mon, 12 Aug 2019 23:30:25: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:30:25: #2 alternative fragment length(s) may be 4,59 bps INFO @ Mon, 12 Aug 2019 23:30:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.10_model.r WARNING @ Mon, 12 Aug 2019 23:30:25: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:30:25: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Mon, 12 Aug 2019 23:30:25: #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 23:30:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:30:27: 12000000 INFO @ Mon, 12 Aug 2019 23:30:27: 12000000 INFO @ Mon, 12 Aug 2019 23:30:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:30:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:30:33: #1 total tags in treatment: 12771846 INFO @ Mon, 12 Aug 2019 23:30:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:30:33: #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 23:30:33: #1 tags after filtering in treatment: 12771846 INFO @ Mon, 12 Aug 2019 23:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:30:33: #1 finished! INFO @ Mon, 12 Aug 2019 23:30:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:30:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:30:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:30:33: #1 total tags in treatment: 12771846 INFO @ Mon, 12 Aug 2019 23:30:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:30:33: #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 23:30:33: #1 tags after filtering in treatment: 12771846 INFO @ Mon, 12 Aug 2019 23:30:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:30:33: #1 finished! INFO @ Mon, 12 Aug 2019 23:30:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:30:34: #2 number of paired peaks: 943 WARNING @ Mon, 12 Aug 2019 23:30:34: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Mon, 12 Aug 2019 23:30:34: start model_add_line... INFO @ Mon, 12 Aug 2019 23:30:34: start X-correlation... INFO @ Mon, 12 Aug 2019 23:30:34: end of X-cor INFO @ Mon, 12 Aug 2019 23:30:34: #2 finished! INFO @ Mon, 12 Aug 2019 23:30:34: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:30:34: #2 alternative fragment length(s) may be 4,59 bps INFO @ Mon, 12 Aug 2019 23:30:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.05_model.r WARNING @ Mon, 12 Aug 2019 23:30:34: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:30:34: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Mon, 12 Aug 2019 23:30:34: #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 23:30:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:30:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:30:35: #2 number of paired peaks: 943 WARNING @ Mon, 12 Aug 2019 23:30:35: Fewer paired peaks (943) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 943 pairs to build model! INFO @ Mon, 12 Aug 2019 23:30:35: start model_add_line... INFO @ Mon, 12 Aug 2019 23:30:35: start X-correlation... INFO @ Mon, 12 Aug 2019 23:30:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:30:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:30:35: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 23:30:35: #2 alternative fragment length(s) may be 4,59 bps INFO @ Mon, 12 Aug 2019 23:30:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.20_model.r WARNING @ Mon, 12 Aug 2019 23:30:35: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:30:35: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Mon, 12 Aug 2019 23:30:35: #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 23:30:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:30:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:31:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:31:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:31:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.10_summits.bed INFO @ Mon, 12 Aug 2019 23:31:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2060 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:31:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:31:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:31:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.05_summits.bed INFO @ Mon, 12 Aug 2019 23:31:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3567 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:31:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:31:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:31:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011026/SRX5011026.20_summits.bed INFO @ Mon, 12 Aug 2019 23:31:28: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1065 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。