Job ID = 4303087 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 28,159,995 reads read : 56,319,990 reads written : 56,319,990 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1151099.sra.cache’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:20:42 28159995 reads; of these: 28159995 (100.00%) were paired; of these: 2521893 (8.96%) aligned concordantly 0 times 17314420 (61.49%) aligned concordantly exactly 1 time 8323682 (29.56%) aligned concordantly >1 times ---- 2521893 pairs aligned concordantly 0 times; of these: 14807 (0.59%) aligned discordantly 1 time ---- 2507086 pairs aligned 0 times concordantly or discordantly; of these: 5014172 mates make up the pairs; of these: 4286595 (85.49%) aligned 0 times 509465 (10.16%) aligned exactly 1 time 218112 (4.35%) aligned >1 times 92.39% overall alignment rate Time searching: 01:20:43 Overall time: 01:20:43 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 24 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] 5591078 / 25618926 = 0.2182 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 02:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.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 @ Thu, 12 Dec 2019 02:21:07: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:21:07: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:21:15: 1000000 INFO @ Thu, 12 Dec 2019 02:21:22: 2000000 INFO @ Thu, 12 Dec 2019 02:21:30: 3000000 INFO @ Thu, 12 Dec 2019 02:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.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 @ Thu, 12 Dec 2019 02:21:36: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:21:36: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:21:37: 4000000 INFO @ Thu, 12 Dec 2019 02:21:45: 1000000 INFO @ Thu, 12 Dec 2019 02:21:45: 5000000 INFO @ Thu, 12 Dec 2019 02:21:52: 6000000 INFO @ Thu, 12 Dec 2019 02:21:53: 2000000 INFO @ Thu, 12 Dec 2019 02:22:00: 7000000 INFO @ Thu, 12 Dec 2019 02:22:02: 3000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 02:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.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 @ Thu, 12 Dec 2019 02:22:06: #1 read tag files... INFO @ Thu, 12 Dec 2019 02:22:06: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 02:22:07: 8000000 INFO @ Thu, 12 Dec 2019 02:22:11: 4000000 INFO @ Thu, 12 Dec 2019 02:22:14: 1000000 INFO @ Thu, 12 Dec 2019 02:22:15: 9000000 INFO @ Thu, 12 Dec 2019 02:22:20: 5000000 INFO @ Thu, 12 Dec 2019 02:22:23: 10000000 INFO @ Thu, 12 Dec 2019 02:22:23: 2000000 INFO @ Thu, 12 Dec 2019 02:22:29: 6000000 INFO @ Thu, 12 Dec 2019 02:22:30: 11000000 INFO @ Thu, 12 Dec 2019 02:22:32: 3000000 INFO @ Thu, 12 Dec 2019 02:22:38: 12000000 INFO @ Thu, 12 Dec 2019 02:22:39: 7000000 INFO @ Thu, 12 Dec 2019 02:22:41: 4000000 INFO @ Thu, 12 Dec 2019 02:22:46: 13000000 INFO @ Thu, 12 Dec 2019 02:22:48: 8000000 INFO @ Thu, 12 Dec 2019 02:22:50: 5000000 INFO @ Thu, 12 Dec 2019 02:22:53: 14000000 INFO @ Thu, 12 Dec 2019 02:22:57: 9000000 INFO @ Thu, 12 Dec 2019 02:22:59: 6000000 INFO @ Thu, 12 Dec 2019 02:23:01: 15000000 INFO @ Thu, 12 Dec 2019 02:23:06: 10000000 INFO @ Thu, 12 Dec 2019 02:23:07: 7000000 INFO @ Thu, 12 Dec 2019 02:23:09: 16000000 INFO @ Thu, 12 Dec 2019 02:23:15: 11000000 INFO @ Thu, 12 Dec 2019 02:23:16: 8000000 INFO @ Thu, 12 Dec 2019 02:23:16: 17000000 INFO @ Thu, 12 Dec 2019 02:23:24: 12000000 INFO @ Thu, 12 Dec 2019 02:23:24: 18000000 INFO @ Thu, 12 Dec 2019 02:23:25: 9000000 INFO @ Thu, 12 Dec 2019 02:23:32: 19000000 INFO @ Thu, 12 Dec 2019 02:23:33: 13000000 INFO @ Thu, 12 Dec 2019 02:23:34: 10000000 INFO @ Thu, 12 Dec 2019 02:23:39: 20000000 INFO @ Thu, 12 Dec 2019 02:23:42: 14000000 INFO @ Thu, 12 Dec 2019 02:23:43: 11000000 INFO @ Thu, 12 Dec 2019 02:23:47: 21000000 INFO @ Thu, 12 Dec 2019 02:23:51: 15000000 INFO @ Thu, 12 Dec 2019 02:23:52: 12000000 INFO @ Thu, 12 Dec 2019 02:23:54: 22000000 INFO @ Thu, 12 Dec 2019 02:24:00: 16000000 INFO @ Thu, 12 Dec 2019 02:24:00: 13000000 INFO @ Thu, 12 Dec 2019 02:24:02: 23000000 INFO @ Thu, 12 Dec 2019 02:24:09: 17000000 INFO @ Thu, 12 Dec 2019 02:24:09: 14000000 INFO @ Thu, 12 Dec 2019 02:24:09: 24000000 INFO @ Thu, 12 Dec 2019 02:24:17: 25000000 INFO @ Thu, 12 Dec 2019 02:24:18: 18000000 INFO @ Thu, 12 Dec 2019 02:24:18: 15000000 INFO @ Thu, 12 Dec 2019 02:24:24: 26000000 INFO @ Thu, 12 Dec 2019 02:24:27: 16000000 INFO @ Thu, 12 Dec 2019 02:24:27: 19000000 INFO @ Thu, 12 Dec 2019 02:24:32: 27000000 INFO @ Thu, 12 Dec 2019 02:24:36: 17000000 INFO @ Thu, 12 Dec 2019 02:24:36: 20000000 INFO @ Thu, 12 Dec 2019 02:24:39: 28000000 INFO @ Thu, 12 Dec 2019 02:24:45: 18000000 INFO @ Thu, 12 Dec 2019 02:24:45: 21000000 INFO @ Thu, 12 Dec 2019 02:24:47: 29000000 INFO @ Thu, 12 Dec 2019 02:24:53: 19000000 INFO @ Thu, 12 Dec 2019 02:24:54: 30000000 INFO @ Thu, 12 Dec 2019 02:24:54: 22000000 INFO @ Thu, 12 Dec 2019 02:25:01: 31000000 INFO @ Thu, 12 Dec 2019 02:25:02: 20000000 INFO @ Thu, 12 Dec 2019 02:25:03: 23000000 INFO @ Thu, 12 Dec 2019 02:25:08: 32000000 INFO @ Thu, 12 Dec 2019 02:25:11: 21000000 INFO @ Thu, 12 Dec 2019 02:25:12: 24000000 INFO @ Thu, 12 Dec 2019 02:25:16: 33000000 INFO @ Thu, 12 Dec 2019 02:25:20: 22000000 INFO @ Thu, 12 Dec 2019 02:25:20: 25000000 INFO @ Thu, 12 Dec 2019 02:25:23: 34000000 INFO @ Thu, 12 Dec 2019 02:25:28: 23000000 INFO @ Thu, 12 Dec 2019 02:25:29: 26000000 INFO @ Thu, 12 Dec 2019 02:25:30: 35000000 INFO @ Thu, 12 Dec 2019 02:25:37: 24000000 INFO @ Thu, 12 Dec 2019 02:25:38: 27000000 INFO @ Thu, 12 Dec 2019 02:25:38: 36000000 INFO @ Thu, 12 Dec 2019 02:25:45: 37000000 INFO @ Thu, 12 Dec 2019 02:25:45: 25000000 INFO @ Thu, 12 Dec 2019 02:25:46: 28000000 INFO @ Thu, 12 Dec 2019 02:25:52: 38000000 INFO @ Thu, 12 Dec 2019 02:25:54: 26000000 INFO @ Thu, 12 Dec 2019 02:25:55: 29000000 INFO @ Thu, 12 Dec 2019 02:26:00: 39000000 INFO @ Thu, 12 Dec 2019 02:26:02: 27000000 INFO @ Thu, 12 Dec 2019 02:26:03: 30000000 INFO @ Thu, 12 Dec 2019 02:26:07: 40000000 INFO @ Thu, 12 Dec 2019 02:26:11: 28000000 INFO @ Thu, 12 Dec 2019 02:26:12: 31000000 INFO @ Thu, 12 Dec 2019 02:26:13: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 02:26:13: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 02:26:13: #1 total tags in treatment: 20049082 INFO @ Thu, 12 Dec 2019 02:26:13: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:26:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:26:14: #1 tags after filtering in treatment: 18005201 INFO @ Thu, 12 Dec 2019 02:26:14: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 12 Dec 2019 02:26:14: #1 finished! INFO @ Thu, 12 Dec 2019 02:26:14: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:26:15: #2 number of paired peaks: 391 WARNING @ Thu, 12 Dec 2019 02:26:15: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Thu, 12 Dec 2019 02:26:15: start model_add_line... INFO @ Thu, 12 Dec 2019 02:26:16: start X-correlation... INFO @ Thu, 12 Dec 2019 02:26:16: end of X-cor INFO @ Thu, 12 Dec 2019 02:26:16: #2 finished! INFO @ Thu, 12 Dec 2019 02:26:16: #2 predicted fragment length is 87 bps INFO @ Thu, 12 Dec 2019 02:26:16: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 12 Dec 2019 02:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.05_model.r WARNING @ Thu, 12 Dec 2019 02:26:16: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 02:26:16: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Thu, 12 Dec 2019 02:26:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 02:26:16: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:26:19: 29000000 INFO @ Thu, 12 Dec 2019 02:26:20: 32000000 INFO @ Thu, 12 Dec 2019 02:26:28: 30000000 INFO @ Thu, 12 Dec 2019 02:26:29: 33000000 INFO @ Thu, 12 Dec 2019 02:26:36: 31000000 INFO @ Thu, 12 Dec 2019 02:26:37: 34000000 INFO @ Thu, 12 Dec 2019 02:26:44: 32000000 INFO @ Thu, 12 Dec 2019 02:26:46: 35000000 INFO @ Thu, 12 Dec 2019 02:26:52: 33000000 INFO @ Thu, 12 Dec 2019 02:26:54: 36000000 INFO @ Thu, 12 Dec 2019 02:27:01: 34000000 INFO @ Thu, 12 Dec 2019 02:27:02: 37000000 INFO @ Thu, 12 Dec 2019 02:27:03: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:27:09: 35000000 INFO @ Thu, 12 Dec 2019 02:27:11: 38000000 INFO @ Thu, 12 Dec 2019 02:27:17: 36000000 INFO @ Thu, 12 Dec 2019 02:27:19: 39000000 INFO @ Thu, 12 Dec 2019 02:27:25: 37000000 INFO @ Thu, 12 Dec 2019 02:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.05_peaks.xls INFO @ Thu, 12 Dec 2019 02:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.05_summits.bed INFO @ Thu, 12 Dec 2019 02:27:26: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5038 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 02:27:28: 40000000 INFO @ Thu, 12 Dec 2019 02:27:34: 38000000 INFO @ Thu, 12 Dec 2019 02:27:35: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 02:27:35: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 02:27:35: #1 total tags in treatment: 20049082 INFO @ Thu, 12 Dec 2019 02:27:35: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:27:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:27:35: #1 tags after filtering in treatment: 18005201 INFO @ Thu, 12 Dec 2019 02:27:35: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 12 Dec 2019 02:27:35: #1 finished! INFO @ Thu, 12 Dec 2019 02:27:35: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:27:37: #2 number of paired peaks: 391 WARNING @ Thu, 12 Dec 2019 02:27:37: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Thu, 12 Dec 2019 02:27:37: start model_add_line... INFO @ Thu, 12 Dec 2019 02:27:37: start X-correlation... INFO @ Thu, 12 Dec 2019 02:27:37: end of X-cor INFO @ Thu, 12 Dec 2019 02:27:37: #2 finished! INFO @ Thu, 12 Dec 2019 02:27:37: #2 predicted fragment length is 87 bps INFO @ Thu, 12 Dec 2019 02:27:37: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 12 Dec 2019 02:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.10_model.r WARNING @ Thu, 12 Dec 2019 02:27:37: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 02:27:37: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Thu, 12 Dec 2019 02:27:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 02:27:37: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:27:42: 39000000 INFO @ Thu, 12 Dec 2019 02:27:50: 40000000 INFO @ Thu, 12 Dec 2019 02:27:57: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 02:27:57: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 02:27:57: #1 total tags in treatment: 20049082 INFO @ Thu, 12 Dec 2019 02:27:57: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 02:27:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 02:27:57: #1 tags after filtering in treatment: 18005201 INFO @ Thu, 12 Dec 2019 02:27:57: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 12 Dec 2019 02:27:57: #1 finished! INFO @ Thu, 12 Dec 2019 02:27:57: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 02:27:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 02:27:59: #2 number of paired peaks: 391 WARNING @ Thu, 12 Dec 2019 02:27:59: Fewer paired peaks (391) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 391 pairs to build model! INFO @ Thu, 12 Dec 2019 02:27:59: start model_add_line... INFO @ Thu, 12 Dec 2019 02:27:59: start X-correlation... INFO @ Thu, 12 Dec 2019 02:27:59: end of X-cor INFO @ Thu, 12 Dec 2019 02:27:59: #2 finished! INFO @ Thu, 12 Dec 2019 02:27:59: #2 predicted fragment length is 87 bps INFO @ Thu, 12 Dec 2019 02:27:59: #2 alternative fragment length(s) may be 87 bps INFO @ Thu, 12 Dec 2019 02:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.20_model.r WARNING @ Thu, 12 Dec 2019 02:27:59: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 02:27:59: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Thu, 12 Dec 2019 02:27:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 02:27:59: #3 Call peaks... INFO @ Thu, 12 Dec 2019 02:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 02:28:24: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:28:47: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 02:28:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.10_peaks.xls INFO @ Thu, 12 Dec 2019 02:28:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:28:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.10_summits.bed INFO @ Thu, 12 Dec 2019 02:28:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2399 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 02:29:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.20_peaks.xls INFO @ Thu, 12 Dec 2019 02:29:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 02:29:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456151/SRX456151.20_summits.bed INFO @ Thu, 12 Dec 2019 02:29:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1160 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。