Job ID = 4178441 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 17,458,679 reads read : 34,917,358 reads written : 34,917,358 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: 01:09:55 17458679 reads; of these: 17458679 (100.00%) were paired; of these: 3952154 (22.64%) aligned concordantly 0 times 9899445 (56.70%) aligned concordantly exactly 1 time 3607080 (20.66%) aligned concordantly >1 times ---- 3952154 pairs aligned concordantly 0 times; of these: 1857250 (46.99%) aligned discordantly 1 time ---- 2094904 pairs aligned 0 times concordantly or discordantly; of these: 4189808 mates make up the pairs; of these: 2451383 (58.51%) aligned 0 times 656267 (15.66%) aligned exactly 1 time 1082158 (25.83%) aligned >1 times 92.98% overall alignment rate Time searching: 01:09:56 Overall time: 01:09:56 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] 828175 / 15313384 = 0.0541 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 14:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.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, 05 Dec 2019 14:14:32: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:14:32: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:14:40: 1000000 INFO @ Thu, 05 Dec 2019 14:14:48: 2000000 INFO @ Thu, 05 Dec 2019 14:14:56: 3000000 INFO @ Thu, 05 Dec 2019 14:15:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.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, 05 Dec 2019 14:15:02: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:15:02: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:15:05: 4000000 INFO @ Thu, 05 Dec 2019 14:15:11: 1000000 INFO @ Thu, 05 Dec 2019 14:15:14: 5000000 INFO @ Thu, 05 Dec 2019 14:15:20: 2000000 INFO @ Thu, 05 Dec 2019 14:15:23: 6000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 14:15:29: 3000000 INFO @ Thu, 05 Dec 2019 14:15:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.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, 05 Dec 2019 14:15:32: #1 read tag files... INFO @ Thu, 05 Dec 2019 14:15:32: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 14:15:33: 7000000 INFO @ Thu, 05 Dec 2019 14:15:39: 4000000 INFO @ Thu, 05 Dec 2019 14:15:39: 1000000 INFO @ Thu, 05 Dec 2019 14:15:42: 8000000 INFO @ Thu, 05 Dec 2019 14:15:47: 2000000 INFO @ Thu, 05 Dec 2019 14:15:49: 5000000 INFO @ Thu, 05 Dec 2019 14:15:52: 9000000 INFO @ Thu, 05 Dec 2019 14:15:55: 3000000 INFO @ Thu, 05 Dec 2019 14:15:59: 6000000 INFO @ Thu, 05 Dec 2019 14:16:02: 10000000 INFO @ Thu, 05 Dec 2019 14:16:03: 4000000 INFO @ Thu, 05 Dec 2019 14:16:09: 7000000 INFO @ Thu, 05 Dec 2019 14:16:10: 5000000 INFO @ Thu, 05 Dec 2019 14:16:12: 11000000 INFO @ Thu, 05 Dec 2019 14:16:18: 6000000 INFO @ Thu, 05 Dec 2019 14:16:18: 8000000 INFO @ Thu, 05 Dec 2019 14:16:22: 12000000 INFO @ Thu, 05 Dec 2019 14:16:25: 7000000 INFO @ Thu, 05 Dec 2019 14:16:28: 9000000 INFO @ Thu, 05 Dec 2019 14:16:31: 13000000 INFO @ Thu, 05 Dec 2019 14:16:33: 8000000 INFO @ Thu, 05 Dec 2019 14:16:38: 10000000 INFO @ Thu, 05 Dec 2019 14:16:40: 9000000 INFO @ Thu, 05 Dec 2019 14:16:41: 14000000 INFO @ Thu, 05 Dec 2019 14:16:47: 11000000 INFO @ Thu, 05 Dec 2019 14:16:48: 10000000 INFO @ Thu, 05 Dec 2019 14:16:51: 15000000 INFO @ Thu, 05 Dec 2019 14:16:55: 11000000 INFO @ Thu, 05 Dec 2019 14:16:57: 12000000 INFO @ Thu, 05 Dec 2019 14:17:00: 16000000 INFO @ Thu, 05 Dec 2019 14:17:02: 12000000 INFO @ Thu, 05 Dec 2019 14:17:06: 13000000 INFO @ Thu, 05 Dec 2019 14:17:10: 13000000 INFO @ Thu, 05 Dec 2019 14:17:10: 17000000 INFO @ Thu, 05 Dec 2019 14:17:15: 14000000 INFO @ Thu, 05 Dec 2019 14:17:17: 14000000 INFO @ Thu, 05 Dec 2019 14:17:20: 18000000 INFO @ Thu, 05 Dec 2019 14:17:25: 15000000 INFO @ Thu, 05 Dec 2019 14:17:25: 15000000 INFO @ Thu, 05 Dec 2019 14:17:30: 19000000 INFO @ Thu, 05 Dec 2019 14:17:32: 16000000 INFO @ Thu, 05 Dec 2019 14:17:35: 16000000 INFO @ Thu, 05 Dec 2019 14:17:39: 20000000 INFO @ Thu, 05 Dec 2019 14:17:40: 17000000 INFO @ Thu, 05 Dec 2019 14:17:45: 17000000 INFO @ Thu, 05 Dec 2019 14:17:47: 18000000 INFO @ Thu, 05 Dec 2019 14:17:48: 21000000 INFO @ Thu, 05 Dec 2019 14:17:55: 18000000 INFO @ Thu, 05 Dec 2019 14:17:55: 19000000 INFO @ Thu, 05 Dec 2019 14:17:58: 22000000 INFO @ Thu, 05 Dec 2019 14:18:03: 20000000 INFO @ Thu, 05 Dec 2019 14:18:05: 19000000 INFO @ Thu, 05 Dec 2019 14:18:08: 23000000 INFO @ Thu, 05 Dec 2019 14:18:10: 21000000 INFO @ Thu, 05 Dec 2019 14:18:14: 20000000 INFO @ Thu, 05 Dec 2019 14:18:18: 24000000 INFO @ Thu, 05 Dec 2019 14:18:18: 22000000 INFO @ Thu, 05 Dec 2019 14:18:24: 21000000 INFO @ Thu, 05 Dec 2019 14:18:26: 23000000 INFO @ Thu, 05 Dec 2019 14:18:28: 25000000 INFO @ Thu, 05 Dec 2019 14:18:33: 24000000 INFO @ Thu, 05 Dec 2019 14:18:34: 22000000 INFO @ Thu, 05 Dec 2019 14:18:38: 26000000 INFO @ Thu, 05 Dec 2019 14:18:41: 25000000 INFO @ Thu, 05 Dec 2019 14:18:44: 23000000 INFO @ Thu, 05 Dec 2019 14:18:48: 27000000 INFO @ Thu, 05 Dec 2019 14:18:49: 26000000 INFO @ Thu, 05 Dec 2019 14:18:53: 24000000 INFO @ Thu, 05 Dec 2019 14:18:56: 27000000 INFO @ Thu, 05 Dec 2019 14:18:57: 28000000 INFO @ Thu, 05 Dec 2019 14:19:03: 25000000 INFO @ Thu, 05 Dec 2019 14:19:04: 28000000 INFO @ Thu, 05 Dec 2019 14:19:07: 29000000 INFO @ Thu, 05 Dec 2019 14:19:11: 29000000 INFO @ Thu, 05 Dec 2019 14:19:13: 26000000 INFO @ Thu, 05 Dec 2019 14:19:16: 30000000 INFO @ Thu, 05 Dec 2019 14:19:18: 30000000 INFO @ Thu, 05 Dec 2019 14:19:22: 27000000 INFO @ Thu, 05 Dec 2019 14:19:24: #1 tag size is determined as 99 bps INFO @ Thu, 05 Dec 2019 14:19:24: #1 tag size = 99 INFO @ Thu, 05 Dec 2019 14:19:24: #1 total tags in treatment: 12808997 INFO @ Thu, 05 Dec 2019 14:19:24: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:19:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:19:24: #1 tag size is determined as 99 bps INFO @ Thu, 05 Dec 2019 14:19:24: #1 tag size = 99 INFO @ Thu, 05 Dec 2019 14:19:24: #1 total tags in treatment: 12808997 INFO @ Thu, 05 Dec 2019 14:19:24: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:19:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:19:24: #1 tags after filtering in treatment: 11884168 INFO @ Thu, 05 Dec 2019 14:19:24: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 14:19:24: #1 finished! INFO @ Thu, 05 Dec 2019 14:19:24: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:19:24: #1 tags after filtering in treatment: 11884168 INFO @ Thu, 05 Dec 2019 14:19:24: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 14:19:24: #1 finished! INFO @ Thu, 05 Dec 2019 14:19:24: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:19:25: #2 number of paired peaks: 622 WARNING @ Thu, 05 Dec 2019 14:19:25: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Thu, 05 Dec 2019 14:19:25: start model_add_line... INFO @ Thu, 05 Dec 2019 14:19:25: start X-correlation... INFO @ Thu, 05 Dec 2019 14:19:25: end of X-cor INFO @ Thu, 05 Dec 2019 14:19:25: #2 finished! INFO @ Thu, 05 Dec 2019 14:19:25: #2 predicted fragment length is 279 bps INFO @ Thu, 05 Dec 2019 14:19:25: #2 alternative fragment length(s) may be 279 bps INFO @ Thu, 05 Dec 2019 14:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.05_model.r INFO @ Thu, 05 Dec 2019 14:19:25: #2 number of paired peaks: 622 WARNING @ Thu, 05 Dec 2019 14:19:25: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Thu, 05 Dec 2019 14:19:25: start model_add_line... INFO @ Thu, 05 Dec 2019 14:19:25: start X-correlation... INFO @ Thu, 05 Dec 2019 14:19:25: end of X-cor INFO @ Thu, 05 Dec 2019 14:19:25: #2 finished! INFO @ Thu, 05 Dec 2019 14:19:25: #2 predicted fragment length is 279 bps INFO @ Thu, 05 Dec 2019 14:19:25: #2 alternative fragment length(s) may be 279 bps INFO @ Thu, 05 Dec 2019 14:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.20_model.r INFO @ Thu, 05 Dec 2019 14:19:27: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:19:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:19:27: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:19:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:19:31: 28000000 INFO @ Thu, 05 Dec 2019 14:19:39: 29000000 INFO @ Thu, 05 Dec 2019 14:19:47: 30000000 INFO @ Thu, 05 Dec 2019 14:19:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:19:51: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:19:54: #1 tag size is determined as 99 bps INFO @ Thu, 05 Dec 2019 14:19:54: #1 tag size = 99 INFO @ Thu, 05 Dec 2019 14:19:54: #1 total tags in treatment: 12808997 INFO @ Thu, 05 Dec 2019 14:19:54: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 14:19:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 14:19:54: #1 tags after filtering in treatment: 11884168 INFO @ Thu, 05 Dec 2019 14:19:54: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 05 Dec 2019 14:19:54: #1 finished! INFO @ Thu, 05 Dec 2019 14:19:54: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 14:19:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 14:19:55: #2 number of paired peaks: 622 WARNING @ Thu, 05 Dec 2019 14:19:55: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Thu, 05 Dec 2019 14:19:55: start model_add_line... INFO @ Thu, 05 Dec 2019 14:19:55: start X-correlation... INFO @ Thu, 05 Dec 2019 14:19:55: end of X-cor INFO @ Thu, 05 Dec 2019 14:19:55: #2 finished! INFO @ Thu, 05 Dec 2019 14:19:55: #2 predicted fragment length is 279 bps INFO @ Thu, 05 Dec 2019 14:19:55: #2 alternative fragment length(s) may be 279 bps INFO @ Thu, 05 Dec 2019 14:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.10_model.r INFO @ Thu, 05 Dec 2019 14:19:55: #3 Call peaks... INFO @ Thu, 05 Dec 2019 14:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 14:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.20_peaks.xls INFO @ Thu, 05 Dec 2019 14:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.20_summits.bed INFO @ Thu, 05 Dec 2019 14:20:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1329 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.05_peaks.xls INFO @ Thu, 05 Dec 2019 14:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.05_summits.bed INFO @ Thu, 05 Dec 2019 14:20:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3799 records, 4 fields): 244 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 14:20:20: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 14:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.10_peaks.xls INFO @ Thu, 05 Dec 2019 14:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 14:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4117266/SRX4117266.10_summits.bed INFO @ Thu, 05 Dec 2019 14:20:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2249 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。