Job ID = 2641009 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,414,977 reads read : 28,829,954 reads written : 28,829,954 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: 00:17:25 14414977 reads; of these: 14414977 (100.00%) were paired; of these: 2812278 (19.51%) aligned concordantly 0 times 9176730 (63.66%) aligned concordantly exactly 1 time 2425969 (16.83%) aligned concordantly >1 times ---- 2812278 pairs aligned concordantly 0 times; of these: 795983 (28.30%) aligned discordantly 1 time ---- 2016295 pairs aligned 0 times concordantly or discordantly; of these: 4032590 mates make up the pairs; of these: 3487397 (86.48%) aligned 0 times 162570 (4.03%) aligned exactly 1 time 382623 (9.49%) aligned >1 times 87.90% overall alignment rate Time searching: 00:17:25 Overall time: 00:17:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 2355787 / 12395303 = 0.1901 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 21:12:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 21:12:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:12:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:12:44: 1000000 INFO @ Sat, 24 Aug 2019 21:12:52: 2000000 INFO @ Sat, 24 Aug 2019 21:13:01: 3000000 INFO @ Sat, 24 Aug 2019 21:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 21:13:04: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:13:04: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:13:10: 4000000 INFO @ Sat, 24 Aug 2019 21:13:15: 1000000 INFO @ Sat, 24 Aug 2019 21:13:19: 5000000 INFO @ Sat, 24 Aug 2019 21:13:26: 2000000 INFO @ Sat, 24 Aug 2019 21:13:27: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 21:13:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sat, 24 Aug 2019 21:13:34: #1 read tag files... INFO @ Sat, 24 Aug 2019 21:13:34: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 21:13:36: 7000000 INFO @ Sat, 24 Aug 2019 21:13:37: 3000000 INFO @ Sat, 24 Aug 2019 21:13:44: 1000000 INFO @ Sat, 24 Aug 2019 21:13:45: 8000000 INFO @ Sat, 24 Aug 2019 21:13:47: 4000000 INFO @ Sat, 24 Aug 2019 21:13:54: 9000000 INFO @ Sat, 24 Aug 2019 21:13:55: 2000000 INFO @ Sat, 24 Aug 2019 21:13:58: 5000000 INFO @ Sat, 24 Aug 2019 21:14:03: 10000000 INFO @ Sat, 24 Aug 2019 21:14:05: 3000000 INFO @ Sat, 24 Aug 2019 21:14:08: 6000000 INFO @ Sat, 24 Aug 2019 21:14:11: 11000000 INFO @ Sat, 24 Aug 2019 21:14:16: 4000000 INFO @ Sat, 24 Aug 2019 21:14:19: 7000000 INFO @ Sat, 24 Aug 2019 21:14:20: 12000000 INFO @ Sat, 24 Aug 2019 21:14:27: 5000000 INFO @ Sat, 24 Aug 2019 21:14:29: 8000000 INFO @ Sat, 24 Aug 2019 21:14:29: 13000000 INFO @ Sat, 24 Aug 2019 21:14:37: 6000000 INFO @ Sat, 24 Aug 2019 21:14:38: 14000000 INFO @ Sat, 24 Aug 2019 21:14:39: 9000000 INFO @ Sat, 24 Aug 2019 21:14:47: 15000000 INFO @ Sat, 24 Aug 2019 21:14:48: 7000000 INFO @ Sat, 24 Aug 2019 21:14:50: 10000000 INFO @ Sat, 24 Aug 2019 21:14:56: 16000000 INFO @ Sat, 24 Aug 2019 21:14:58: 8000000 INFO @ Sat, 24 Aug 2019 21:15:00: 11000000 INFO @ Sat, 24 Aug 2019 21:15:05: 17000000 INFO @ Sat, 24 Aug 2019 21:15:09: 9000000 INFO @ Sat, 24 Aug 2019 21:15:11: 12000000 INFO @ Sat, 24 Aug 2019 21:15:14: 18000000 INFO @ Sat, 24 Aug 2019 21:15:20: 10000000 INFO @ Sat, 24 Aug 2019 21:15:22: 13000000 INFO @ Sat, 24 Aug 2019 21:15:23: 19000000 INFO @ Sat, 24 Aug 2019 21:15:31: 11000000 INFO @ Sat, 24 Aug 2019 21:15:32: 20000000 INFO @ Sat, 24 Aug 2019 21:15:32: 14000000 INFO @ Sat, 24 Aug 2019 21:15:37: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:15:37: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:15:37: #1 total tags in treatment: 9321281 INFO @ Sat, 24 Aug 2019 21:15:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:15:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:15:38: #1 tags after filtering in treatment: 6664434 INFO @ Sat, 24 Aug 2019 21:15:38: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:15:38: #1 finished! INFO @ Sat, 24 Aug 2019 21:15:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:15:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:15:38: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 21:15:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.05_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:15:41: 12000000 INFO @ Sat, 24 Aug 2019 21:15:43: 15000000 INFO @ Sat, 24 Aug 2019 21:15:52: 13000000 INFO @ Sat, 24 Aug 2019 21:15:53: 16000000 INFO @ Sat, 24 Aug 2019 21:16:02: 14000000 INFO @ Sat, 24 Aug 2019 21:16:04: 17000000 INFO @ Sat, 24 Aug 2019 21:16:13: 15000000 INFO @ Sat, 24 Aug 2019 21:16:14: 18000000 INFO @ Sat, 24 Aug 2019 21:16:23: 16000000 INFO @ Sat, 24 Aug 2019 21:16:25: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 21:16:33: 17000000 INFO @ Sat, 24 Aug 2019 21:16:35: 20000000 INFO @ Sat, 24 Aug 2019 21:16:41: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:16:41: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:16:41: #1 total tags in treatment: 9321281 INFO @ Sat, 24 Aug 2019 21:16:41: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:16:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:16:42: #1 tags after filtering in treatment: 6664434 INFO @ Sat, 24 Aug 2019 21:16:42: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:16:42: #1 finished! INFO @ Sat, 24 Aug 2019 21:16:42: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:16:42: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:16:42: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 21:16:42: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 21:16:44: 18000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 21:16:54: 19000000 INFO @ Sat, 24 Aug 2019 21:17:05: 20000000 INFO @ Sat, 24 Aug 2019 21:17:12: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 21:17:12: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 21:17:12: #1 total tags in treatment: 9321281 INFO @ Sat, 24 Aug 2019 21:17:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 21:17:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 21:17:12: #1 tags after filtering in treatment: 6664434 INFO @ Sat, 24 Aug 2019 21:17:12: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 21:17:12: #1 finished! INFO @ Sat, 24 Aug 2019 21:17:12: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 21:17:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 21:17:12: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 21:17:12: Too few paired peaks (0) so I can not build the model! Broader your MFOLD range parameter may erase this error. If it still can't build the model, we suggest to use --nomodel and --extsize 147 or other fixed number instead. WARNING @ Sat, 24 Aug 2019 21:17:12: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4936115/SRX4936115.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling