Job ID = 2590953 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 18,548,763 reads read : 37,097,526 reads written : 37,097,526 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: 00:38:44 18548763 reads; of these: 18548763 (100.00%) were paired; of these: 3840338 (20.70%) aligned concordantly 0 times 11096476 (59.82%) aligned concordantly exactly 1 time 3611949 (19.47%) aligned concordantly >1 times ---- 3840338 pairs aligned concordantly 0 times; of these: 575400 (14.98%) aligned discordantly 1 time ---- 3264938 pairs aligned 0 times concordantly or discordantly; of these: 6529876 mates make up the pairs; of these: 5439128 (83.30%) aligned 0 times 487844 (7.47%) aligned exactly 1 time 602904 (9.23%) aligned >1 times 85.34% overall alignment rate Time searching: 00:38:44 Overall time: 00:38:44 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] 1253959 / 15196201 = 0.0825 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 01:15:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.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 01:15:36: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:15:36: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.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 01:15:37: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:15:37: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.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 01:15:38: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:15:38: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:15:45: 1000000 INFO @ Tue, 13 Aug 2019 01:15:47: 1000000 INFO @ Tue, 13 Aug 2019 01:15:47: 1000000 INFO @ Tue, 13 Aug 2019 01:15:54: 2000000 INFO @ Tue, 13 Aug 2019 01:15:56: 2000000 INFO @ Tue, 13 Aug 2019 01:15:57: 2000000 INFO @ Tue, 13 Aug 2019 01:16:03: 3000000 INFO @ Tue, 13 Aug 2019 01:16:05: 3000000 INFO @ Tue, 13 Aug 2019 01:16:08: 3000000 INFO @ Tue, 13 Aug 2019 01:16:12: 4000000 INFO @ Tue, 13 Aug 2019 01:16:14: 4000000 INFO @ Tue, 13 Aug 2019 01:16:19: 4000000 INFO @ Tue, 13 Aug 2019 01:16:21: 5000000 INFO @ Tue, 13 Aug 2019 01:16:23: 5000000 INFO @ Tue, 13 Aug 2019 01:16:30: 5000000 INFO @ Tue, 13 Aug 2019 01:16:30: 6000000 INFO @ Tue, 13 Aug 2019 01:16:31: 6000000 INFO @ Tue, 13 Aug 2019 01:16:39: 7000000 INFO @ Tue, 13 Aug 2019 01:16:40: 6000000 INFO @ Tue, 13 Aug 2019 01:16:40: 7000000 INFO @ Tue, 13 Aug 2019 01:16:48: 8000000 INFO @ Tue, 13 Aug 2019 01:16:49: 8000000 INFO @ Tue, 13 Aug 2019 01:16:51: 7000000 INFO @ Tue, 13 Aug 2019 01:16:57: 9000000 INFO @ Tue, 13 Aug 2019 01:16:58: 9000000 INFO @ Tue, 13 Aug 2019 01:17:02: 8000000 INFO @ Tue, 13 Aug 2019 01:17:06: 10000000 INFO @ Tue, 13 Aug 2019 01:17:07: 10000000 INFO @ Tue, 13 Aug 2019 01:17:13: 9000000 INFO @ Tue, 13 Aug 2019 01:17:15: 11000000 INFO @ Tue, 13 Aug 2019 01:17:16: 11000000 INFO @ Tue, 13 Aug 2019 01:17:23: 10000000 INFO @ Tue, 13 Aug 2019 01:17:24: 12000000 INFO @ Tue, 13 Aug 2019 01:17:25: 12000000 INFO @ Tue, 13 Aug 2019 01:17:33: 13000000 INFO @ Tue, 13 Aug 2019 01:17:34: 13000000 INFO @ Tue, 13 Aug 2019 01:17:34: 11000000 INFO @ Tue, 13 Aug 2019 01:17:42: 14000000 INFO @ Tue, 13 Aug 2019 01:17:43: 14000000 INFO @ Tue, 13 Aug 2019 01:17:45: 12000000 INFO @ Tue, 13 Aug 2019 01:17:51: 15000000 INFO @ Tue, 13 Aug 2019 01:17:52: 15000000 INFO @ Tue, 13 Aug 2019 01:17:56: 13000000 INFO @ Tue, 13 Aug 2019 01:18:00: 16000000 INFO @ Tue, 13 Aug 2019 01:18:00: 16000000 INFO @ Tue, 13 Aug 2019 01:18:07: 14000000 INFO @ Tue, 13 Aug 2019 01:18:09: 17000000 INFO @ Tue, 13 Aug 2019 01:18:10: 17000000 INFO @ Tue, 13 Aug 2019 01:18:17: 15000000 INFO @ Tue, 13 Aug 2019 01:18:18: 18000000 INFO @ Tue, 13 Aug 2019 01:18:19: 18000000 INFO @ Tue, 13 Aug 2019 01:18:28: 19000000 INFO @ Tue, 13 Aug 2019 01:18:28: 19000000 INFO @ Tue, 13 Aug 2019 01:18:28: 16000000 INFO @ Tue, 13 Aug 2019 01:18:37: 20000000 INFO @ Tue, 13 Aug 2019 01:18:37: 20000000 INFO @ Tue, 13 Aug 2019 01:18:39: 17000000 INFO @ Tue, 13 Aug 2019 01:18:46: 21000000 INFO @ Tue, 13 Aug 2019 01:18:46: 21000000 INFO @ Tue, 13 Aug 2019 01:18:50: 18000000 INFO @ Tue, 13 Aug 2019 01:18:55: 22000000 INFO @ Tue, 13 Aug 2019 01:18:56: 22000000 INFO @ Tue, 13 Aug 2019 01:19:00: 19000000 INFO @ Tue, 13 Aug 2019 01:19:04: 23000000 INFO @ Tue, 13 Aug 2019 01:19:05: 23000000 INFO @ Tue, 13 Aug 2019 01:19:11: 20000000 INFO @ Tue, 13 Aug 2019 01:19:13: 24000000 INFO @ Tue, 13 Aug 2019 01:19:14: 24000000 INFO @ Tue, 13 Aug 2019 01:19:22: 21000000 INFO @ Tue, 13 Aug 2019 01:19:22: 25000000 INFO @ Tue, 13 Aug 2019 01:19:23: 25000000 INFO @ Tue, 13 Aug 2019 01:19:31: 26000000 INFO @ Tue, 13 Aug 2019 01:19:32: 26000000 INFO @ Tue, 13 Aug 2019 01:19:33: 22000000 INFO @ Tue, 13 Aug 2019 01:19:40: 27000000 INFO @ Tue, 13 Aug 2019 01:19:41: 27000000 INFO @ Tue, 13 Aug 2019 01:19:43: 23000000 INFO @ Tue, 13 Aug 2019 01:19:48: 28000000 INFO @ Tue, 13 Aug 2019 01:19:49: 28000000 INFO @ Tue, 13 Aug 2019 01:19:54: 24000000 INFO @ Tue, 13 Aug 2019 01:19:57: 29000000 INFO @ Tue, 13 Aug 2019 01:19:58: 29000000 INFO @ Tue, 13 Aug 2019 01:19:59: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:19:59: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:19:59: #1 total tags in treatment: 13482444 INFO @ Tue, 13 Aug 2019 01:19:59: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:19:59: #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 01:19:59: #1 tags after filtering in treatment: 11418267 INFO @ Tue, 13 Aug 2019 01:19:59: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 13 Aug 2019 01:19:59: #1 finished! INFO @ Tue, 13 Aug 2019 01:19:59: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:20:00: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:20:00: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:20:00: #1 total tags in treatment: 13482444 INFO @ Tue, 13 Aug 2019 01:20:00: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:20:00: #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 01:20:00: #2 number of paired peaks: 291 WARNING @ Tue, 13 Aug 2019 01:20:00: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 13 Aug 2019 01:20:00: start model_add_line... INFO @ Tue, 13 Aug 2019 01:20:00: start X-correlation... INFO @ Tue, 13 Aug 2019 01:20:00: end of X-cor INFO @ Tue, 13 Aug 2019 01:20:00: #2 finished! INFO @ Tue, 13 Aug 2019 01:20:00: #2 predicted fragment length is 103 bps INFO @ Tue, 13 Aug 2019 01:20:00: #2 alternative fragment length(s) may be 2,103,518,591 bps INFO @ Tue, 13 Aug 2019 01:20:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.20_model.r INFO @ Tue, 13 Aug 2019 01:20:00: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:20:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:20:00: #1 tags after filtering in treatment: 11418267 INFO @ Tue, 13 Aug 2019 01:20:00: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 13 Aug 2019 01:20:00: #1 finished! INFO @ Tue, 13 Aug 2019 01:20:00: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:20:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:20:01: #2 number of paired peaks: 291 WARNING @ Tue, 13 Aug 2019 01:20:01: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 13 Aug 2019 01:20:01: start model_add_line... INFO @ Tue, 13 Aug 2019 01:20:01: start X-correlation... INFO @ Tue, 13 Aug 2019 01:20:01: end of X-cor INFO @ Tue, 13 Aug 2019 01:20:01: #2 finished! INFO @ Tue, 13 Aug 2019 01:20:01: #2 predicted fragment length is 103 bps INFO @ Tue, 13 Aug 2019 01:20:01: #2 alternative fragment length(s) may be 2,103,518,591 bps INFO @ Tue, 13 Aug 2019 01:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.05_model.r INFO @ Tue, 13 Aug 2019 01:20:01: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:20:04: 25000000 INFO @ Tue, 13 Aug 2019 01:20:15: 26000000 INFO @ Tue, 13 Aug 2019 01:20:25: 27000000 INFO @ Tue, 13 Aug 2019 01:20:31: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:20:33: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:20:34: 28000000 INFO @ Tue, 13 Aug 2019 01:20:44: 29000000 INFO @ Tue, 13 Aug 2019 01:20:46: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:20:46: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:20:46: #1 total tags in treatment: 13482444 INFO @ Tue, 13 Aug 2019 01:20:46: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:20:46: #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 01:20:46: #1 tags after filtering in treatment: 11418267 INFO @ Tue, 13 Aug 2019 01:20:46: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 13 Aug 2019 01:20:46: #1 finished! INFO @ Tue, 13 Aug 2019 01:20:46: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:20:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:20:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:20:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:20:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.20_summits.bed INFO @ Tue, 13 Aug 2019 01:20:47: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:20:47: #2 number of paired peaks: 291 WARNING @ Tue, 13 Aug 2019 01:20:47: Fewer paired peaks (291) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 291 pairs to build model! INFO @ Tue, 13 Aug 2019 01:20:47: start model_add_line... INFO @ Tue, 13 Aug 2019 01:20:47: start X-correlation... INFO @ Tue, 13 Aug 2019 01:20:47: end of X-cor INFO @ Tue, 13 Aug 2019 01:20:47: #2 finished! INFO @ Tue, 13 Aug 2019 01:20:47: #2 predicted fragment length is 103 bps INFO @ Tue, 13 Aug 2019 01:20:47: #2 alternative fragment length(s) may be 2,103,518,591 bps INFO @ Tue, 13 Aug 2019 01:20:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.10_model.r INFO @ Tue, 13 Aug 2019 01:20:48: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:20:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:20:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:20:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:20:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.05_summits.bed INFO @ Tue, 13 Aug 2019 01:20:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:21:19: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:21:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:21:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:21:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865769/SRX5865769.10_summits.bed INFO @ Tue, 13 Aug 2019 01:21:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (255 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。