Job ID = 2590970 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 18,877,884 reads read : 37,755,768 reads written : 37,755,768 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: 00:46:18 18877884 reads; of these: 18877884 (100.00%) were paired; of these: 4459044 (23.62%) aligned concordantly 0 times 9694381 (51.35%) aligned concordantly exactly 1 time 4724459 (25.03%) aligned concordantly >1 times ---- 4459044 pairs aligned concordantly 0 times; of these: 485209 (10.88%) aligned discordantly 1 time ---- 3973835 pairs aligned 0 times concordantly or discordantly; of these: 7947670 mates make up the pairs; of these: 6952447 (87.48%) aligned 0 times 484464 (6.10%) aligned exactly 1 time 510759 (6.43%) aligned >1 times 81.59% overall alignment rate Time searching: 00:46:18 Overall time: 00:46:18 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1685754 / 14815116 = 0.1138 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 @ Tue, 13 Aug 2019 01:22:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.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 @ Tue, 13 Aug 2019 01:22:11: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:22:11: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.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 @ Tue, 13 Aug 2019 01:22:12: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:22:12: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.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 @ Tue, 13 Aug 2019 01:22:13: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:22:13: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:22:19: 1000000 INFO @ Tue, 13 Aug 2019 01:22:19: 1000000 INFO @ Tue, 13 Aug 2019 01:22:22: 1000000 INFO @ Tue, 13 Aug 2019 01:22:26: 2000000 INFO @ Tue, 13 Aug 2019 01:22:26: 2000000 INFO @ Tue, 13 Aug 2019 01:22:31: 2000000 INFO @ Tue, 13 Aug 2019 01:22:33: 3000000 INFO @ Tue, 13 Aug 2019 01:22:34: 3000000 INFO @ Tue, 13 Aug 2019 01:22:39: 3000000 INFO @ Tue, 13 Aug 2019 01:22:39: 4000000 INFO @ Tue, 13 Aug 2019 01:22:41: 4000000 INFO @ Tue, 13 Aug 2019 01:22:46: 5000000 INFO @ Tue, 13 Aug 2019 01:22:48: 4000000 INFO @ Tue, 13 Aug 2019 01:22:48: 5000000 INFO @ Tue, 13 Aug 2019 01:22:53: 6000000 INFO @ Tue, 13 Aug 2019 01:22:56: 6000000 INFO @ Tue, 13 Aug 2019 01:22:57: 5000000 INFO @ Tue, 13 Aug 2019 01:23:00: 7000000 INFO @ Tue, 13 Aug 2019 01:23:03: 7000000 INFO @ Tue, 13 Aug 2019 01:23:05: 6000000 INFO @ Tue, 13 Aug 2019 01:23:06: 8000000 INFO @ Tue, 13 Aug 2019 01:23:10: 8000000 INFO @ Tue, 13 Aug 2019 01:23:13: 9000000 INFO @ Tue, 13 Aug 2019 01:23:14: 7000000 INFO @ Tue, 13 Aug 2019 01:23:18: 9000000 INFO @ Tue, 13 Aug 2019 01:23:20: 10000000 INFO @ Tue, 13 Aug 2019 01:23:23: 8000000 INFO @ Tue, 13 Aug 2019 01:23:25: 10000000 INFO @ Tue, 13 Aug 2019 01:23:26: 11000000 INFO @ Tue, 13 Aug 2019 01:23:31: 9000000 INFO @ Tue, 13 Aug 2019 01:23:33: 11000000 INFO @ Tue, 13 Aug 2019 01:23:33: 12000000 INFO @ Tue, 13 Aug 2019 01:23:40: 13000000 INFO @ Tue, 13 Aug 2019 01:23:40: 12000000 INFO @ Tue, 13 Aug 2019 01:23:40: 10000000 INFO @ Tue, 13 Aug 2019 01:23:46: 14000000 INFO @ Tue, 13 Aug 2019 01:23:47: 13000000 INFO @ Tue, 13 Aug 2019 01:23:49: 11000000 INFO @ Tue, 13 Aug 2019 01:23:53: 15000000 INFO @ Tue, 13 Aug 2019 01:23:55: 14000000 INFO @ Tue, 13 Aug 2019 01:23:57: 12000000 INFO @ Tue, 13 Aug 2019 01:23:59: 16000000 INFO @ Tue, 13 Aug 2019 01:24:02: 15000000 INFO @ Tue, 13 Aug 2019 01:24:06: 13000000 INFO @ Tue, 13 Aug 2019 01:24:06: 17000000 INFO @ Tue, 13 Aug 2019 01:24:09: 16000000 INFO @ Tue, 13 Aug 2019 01:24:13: 18000000 INFO @ Tue, 13 Aug 2019 01:24:15: 14000000 INFO @ Tue, 13 Aug 2019 01:24:17: 17000000 INFO @ Tue, 13 Aug 2019 01:24:19: 19000000 INFO @ Tue, 13 Aug 2019 01:24:23: 15000000 INFO @ Tue, 13 Aug 2019 01:24:24: 18000000 INFO @ Tue, 13 Aug 2019 01:24:26: 20000000 INFO @ Tue, 13 Aug 2019 01:24:31: 19000000 INFO @ Tue, 13 Aug 2019 01:24:32: 16000000 INFO @ Tue, 13 Aug 2019 01:24:33: 21000000 INFO @ Tue, 13 Aug 2019 01:24:38: 20000000 INFO @ Tue, 13 Aug 2019 01:24:39: 22000000 INFO @ Tue, 13 Aug 2019 01:24:41: 17000000 INFO @ Tue, 13 Aug 2019 01:24:45: 23000000 INFO @ Tue, 13 Aug 2019 01:24:46: 21000000 INFO @ Tue, 13 Aug 2019 01:24:50: 18000000 INFO @ Tue, 13 Aug 2019 01:24:52: 24000000 INFO @ Tue, 13 Aug 2019 01:24:53: 22000000 INFO @ Tue, 13 Aug 2019 01:24:58: 19000000 INFO @ Tue, 13 Aug 2019 01:24:58: 25000000 INFO @ Tue, 13 Aug 2019 01:25:00: 23000000 INFO @ Tue, 13 Aug 2019 01:25:05: 26000000 INFO @ Tue, 13 Aug 2019 01:25:07: 24000000 INFO @ Tue, 13 Aug 2019 01:25:07: 20000000 INFO @ Tue, 13 Aug 2019 01:25:12: 27000000 INFO @ Tue, 13 Aug 2019 01:25:14: 25000000 INFO @ Tue, 13 Aug 2019 01:25:15: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:25:15: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:25:15: #1 total tags in treatment: 12757734 INFO @ Tue, 13 Aug 2019 01:25:15: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:25:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:25:15: #1 tags after filtering in treatment: 11166522 INFO @ Tue, 13 Aug 2019 01:25:15: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 13 Aug 2019 01:25:15: #1 finished! INFO @ Tue, 13 Aug 2019 01:25:15: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:25:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:25:15: 21000000 INFO @ Tue, 13 Aug 2019 01:25:16: #2 number of paired peaks: 112 WARNING @ Tue, 13 Aug 2019 01:25:16: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 13 Aug 2019 01:25:16: start model_add_line... INFO @ Tue, 13 Aug 2019 01:25:16: start X-correlation... INFO @ Tue, 13 Aug 2019 01:25:16: end of X-cor INFO @ Tue, 13 Aug 2019 01:25:16: #2 finished! INFO @ Tue, 13 Aug 2019 01:25:16: #2 predicted fragment length is 89 bps INFO @ Tue, 13 Aug 2019 01:25:16: #2 alternative fragment length(s) may be 89,536 bps INFO @ Tue, 13 Aug 2019 01:25:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.10_model.r WARNING @ Tue, 13 Aug 2019 01:25:16: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:25:16: #2 You may need to consider one of the other alternative d(s): 89,536 WARNING @ Tue, 13 Aug 2019 01:25:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:25:16: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:25:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:25:21: 26000000 INFO @ Tue, 13 Aug 2019 01:25:24: 22000000 INFO @ Tue, 13 Aug 2019 01:25:29: 27000000 INFO @ Tue, 13 Aug 2019 01:25:32: 23000000 INFO @ Tue, 13 Aug 2019 01:25:32: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:25:32: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:25:32: #1 total tags in treatment: 12757734 INFO @ Tue, 13 Aug 2019 01:25:32: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:25:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:25:32: #1 tags after filtering in treatment: 11166522 INFO @ Tue, 13 Aug 2019 01:25:32: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 13 Aug 2019 01:25:32: #1 finished! INFO @ Tue, 13 Aug 2019 01:25:32: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:25:33: #2 number of paired peaks: 112 WARNING @ Tue, 13 Aug 2019 01:25:33: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 13 Aug 2019 01:25:33: start model_add_line... INFO @ Tue, 13 Aug 2019 01:25:33: start X-correlation... INFO @ Tue, 13 Aug 2019 01:25:33: end of X-cor INFO @ Tue, 13 Aug 2019 01:25:33: #2 finished! INFO @ Tue, 13 Aug 2019 01:25:33: #2 predicted fragment length is 89 bps INFO @ Tue, 13 Aug 2019 01:25:33: #2 alternative fragment length(s) may be 89,536 bps INFO @ Tue, 13 Aug 2019 01:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.05_model.r WARNING @ Tue, 13 Aug 2019 01:25:33: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:25:33: #2 You may need to consider one of the other alternative d(s): 89,536 WARNING @ Tue, 13 Aug 2019 01:25:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:25:33: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:25:40: 24000000 INFO @ Tue, 13 Aug 2019 01:25:47: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:25:49: 25000000 INFO @ Tue, 13 Aug 2019 01:25:57: 26000000 INFO @ Tue, 13 Aug 2019 01:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:26:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.10_summits.bed INFO @ Tue, 13 Aug 2019 01:26:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:26:04: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:26:06: 27000000 INFO @ Tue, 13 Aug 2019 01:26:09: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:26:09: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:26:09: #1 total tags in treatment: 12757734 INFO @ Tue, 13 Aug 2019 01:26:09: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:26:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:26:10: #1 tags after filtering in treatment: 11166522 INFO @ Tue, 13 Aug 2019 01:26:10: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 13 Aug 2019 01:26:10: #1 finished! INFO @ Tue, 13 Aug 2019 01:26:10: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:26:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:26:11: #2 number of paired peaks: 112 WARNING @ Tue, 13 Aug 2019 01:26:11: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Tue, 13 Aug 2019 01:26:11: start model_add_line... INFO @ Tue, 13 Aug 2019 01:26:11: start X-correlation... INFO @ Tue, 13 Aug 2019 01:26:11: end of X-cor INFO @ Tue, 13 Aug 2019 01:26:11: #2 finished! INFO @ Tue, 13 Aug 2019 01:26:11: #2 predicted fragment length is 89 bps INFO @ Tue, 13 Aug 2019 01:26:11: #2 alternative fragment length(s) may be 89,536 bps INFO @ Tue, 13 Aug 2019 01:26:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.20_model.r WARNING @ Tue, 13 Aug 2019 01:26:11: #2 Since the d (89) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 01:26:11: #2 You may need to consider one of the other alternative d(s): 89,536 WARNING @ Tue, 13 Aug 2019 01:26:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 01:26:11: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:26:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.05_summits.bed INFO @ Tue, 13 Aug 2019 01:26:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1740 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:26:41: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865785/SRX5865785.20_summits.bed INFO @ Tue, 13 Aug 2019 01:26:56: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。