Job ID = 2641109 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,488,843 reads read : 22,977,686 reads written : 22,977,686 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: 00:16:11 11488843 reads; of these: 11488843 (100.00%) were paired; of these: 6901264 (60.07%) aligned concordantly 0 times 4210527 (36.65%) aligned concordantly exactly 1 time 377052 (3.28%) aligned concordantly >1 times ---- 6901264 pairs aligned concordantly 0 times; of these: 5056557 (73.27%) aligned discordantly 1 time ---- 1844707 pairs aligned 0 times concordantly or discordantly; of these: 3689414 mates make up the pairs; of these: 2035873 (55.18%) aligned 0 times 614280 (16.65%) aligned exactly 1 time 1039261 (28.17%) aligned >1 times 91.14% overall alignment rate Time searching: 00:16:11 Overall time: 00:16:11 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] 949002 / 9639265 = 0.0985 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:08:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.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 22:08:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:49: 1000000 INFO @ Sat, 24 Aug 2019 22:09:00: 2000000 INFO @ Sat, 24 Aug 2019 22:09:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.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 22:09:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:12: 3000000 INFO @ Sat, 24 Aug 2019 22:09:19: 1000000 INFO @ Sat, 24 Aug 2019 22:09:24: 4000000 INFO @ Sat, 24 Aug 2019 22:09:31: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:09:35: 5000000 INFO @ Sat, 24 Aug 2019 22:09:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.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 22:09:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:09:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:09:43: 3000000 INFO @ Sat, 24 Aug 2019 22:09:47: 6000000 INFO @ Sat, 24 Aug 2019 22:09:49: 1000000 INFO @ Sat, 24 Aug 2019 22:09:55: 4000000 INFO @ Sat, 24 Aug 2019 22:09:59: 7000000 INFO @ Sat, 24 Aug 2019 22:10:01: 2000000 INFO @ Sat, 24 Aug 2019 22:10:07: 5000000 INFO @ Sat, 24 Aug 2019 22:10:11: 8000000 INFO @ Sat, 24 Aug 2019 22:10:13: 3000000 INFO @ Sat, 24 Aug 2019 22:10:18: 6000000 INFO @ Sat, 24 Aug 2019 22:10:22: 9000000 INFO @ Sat, 24 Aug 2019 22:10:25: 4000000 INFO @ Sat, 24 Aug 2019 22:10:30: 7000000 INFO @ Sat, 24 Aug 2019 22:10:34: 10000000 INFO @ Sat, 24 Aug 2019 22:10:36: 5000000 INFO @ Sat, 24 Aug 2019 22:10:42: 8000000 INFO @ Sat, 24 Aug 2019 22:10:46: 11000000 INFO @ Sat, 24 Aug 2019 22:10:48: 6000000 INFO @ Sat, 24 Aug 2019 22:10:54: 9000000 INFO @ Sat, 24 Aug 2019 22:10:58: 12000000 INFO @ Sat, 24 Aug 2019 22:11:00: 7000000 INFO @ Sat, 24 Aug 2019 22:11:06: 10000000 INFO @ Sat, 24 Aug 2019 22:11:09: 13000000 INFO @ Sat, 24 Aug 2019 22:11:11: 8000000 INFO @ Sat, 24 Aug 2019 22:11:17: 11000000 INFO @ Sat, 24 Aug 2019 22:11:21: 14000000 INFO @ Sat, 24 Aug 2019 22:11:23: 9000000 INFO @ Sat, 24 Aug 2019 22:11:29: 12000000 INFO @ Sat, 24 Aug 2019 22:11:33: 15000000 INFO @ Sat, 24 Aug 2019 22:11:35: 10000000 INFO @ Sat, 24 Aug 2019 22:11:41: 13000000 INFO @ Sat, 24 Aug 2019 22:11:44: 16000000 INFO @ Sat, 24 Aug 2019 22:11:46: 11000000 INFO @ Sat, 24 Aug 2019 22:11:53: 14000000 INFO @ Sat, 24 Aug 2019 22:11:56: 17000000 INFO @ Sat, 24 Aug 2019 22:11:58: 12000000 INFO @ Sat, 24 Aug 2019 22:12:04: 15000000 INFO @ Sat, 24 Aug 2019 22:12:08: 18000000 INFO @ Sat, 24 Aug 2019 22:12:10: 13000000 INFO @ Sat, 24 Aug 2019 22:12:16: 16000000 INFO @ Sat, 24 Aug 2019 22:12:19: 19000000 INFO @ Sat, 24 Aug 2019 22:12:20: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:12:20: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:12:20: #1 total tags in treatment: 4110282 INFO @ Sat, 24 Aug 2019 22:12:20: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:12:20: #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 22:12:20: #1 tags after filtering in treatment: 3652412 INFO @ Sat, 24 Aug 2019 22:12:20: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:12:20: #1 finished! INFO @ Sat, 24 Aug 2019 22:12:20: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:12:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:12:20: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:12:20: Too few paired peaks (26) 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 22:12:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.05_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/SRX5546550/SRX5546550.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:12:21: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:12:27: 17000000 INFO @ Sat, 24 Aug 2019 22:12:33: 15000000 INFO @ Sat, 24 Aug 2019 22:12:39: 18000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:12:44: 16000000 INFO @ Sat, 24 Aug 2019 22:12:50: 19000000 INFO @ Sat, 24 Aug 2019 22:12:51: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:12:51: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:12:51: #1 total tags in treatment: 4110282 INFO @ Sat, 24 Aug 2019 22:12:51: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:12:51: #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 22:12:51: #1 tags after filtering in treatment: 3652412 INFO @ Sat, 24 Aug 2019 22:12:51: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:12:51: #1 finished! INFO @ Sat, 24 Aug 2019 22:12:51: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:12:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:12:51: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:12:51: Too few paired peaks (26) 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 22:12:51: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.10_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/SRX5546550/SRX5546550.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:12:55: 17000000 INFO @ Sat, 24 Aug 2019 22:13:07: 18000000 INFO @ Sat, 24 Aug 2019 22:13:18: 19000000 INFO @ Sat, 24 Aug 2019 22:13:18: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:13:18: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:13:18: #1 total tags in treatment: 4110282 INFO @ Sat, 24 Aug 2019 22:13:18: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:13:18: #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 22:13:18: #1 tags after filtering in treatment: 3652412 INFO @ Sat, 24 Aug 2019 22:13:18: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:13:18: #1 finished! INFO @ Sat, 24 Aug 2019 22:13:18: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:13:19: #2 number of paired peaks: 26 WARNING @ Sat, 24 Aug 2019 22:13:19: Too few paired peaks (26) 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 22:13:19: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.20_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/SRX5546550/SRX5546550.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546550/SRX5546550.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling