Job ID = 2640897 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,983,787 reads read : 19,967,574 reads written : 19,967,574 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: 00:07:22 9983787 reads; of these: 9983787 (100.00%) were paired; of these: 1126445 (11.28%) aligned concordantly 0 times 6566116 (65.77%) aligned concordantly exactly 1 time 2291226 (22.95%) aligned concordantly >1 times ---- 1126445 pairs aligned concordantly 0 times; of these: 9492 (0.84%) aligned discordantly 1 time ---- 1116953 pairs aligned 0 times concordantly or discordantly; of these: 2233906 mates make up the pairs; of these: 2000267 (89.54%) aligned 0 times 119390 (5.34%) aligned exactly 1 time 114249 (5.11%) aligned >1 times 89.98% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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 8 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] 501467 / 8862658 = 0.0566 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 20:09:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.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 20:09:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:09:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:09:21: 1000000 INFO @ Sat, 24 Aug 2019 20:09:32: 2000000 INFO @ Sat, 24 Aug 2019 20:09:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.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 20:09:38: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:09:38: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:09:44: 3000000 INFO @ Sat, 24 Aug 2019 20:09:46: 1000000 INFO @ Sat, 24 Aug 2019 20:09:53: 2000000 INFO @ Sat, 24 Aug 2019 20:09:56: 4000000 INFO @ Sat, 24 Aug 2019 20:10:01: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 20:10:07: 5000000 INFO @ Sat, 24 Aug 2019 20:10:08: 4000000 INFO @ Sat, 24 Aug 2019 20:10:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.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 20:10:08: #1 read tag files... INFO @ Sat, 24 Aug 2019 20:10:08: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 20:10:17: 5000000 INFO @ Sat, 24 Aug 2019 20:10:18: 1000000 INFO @ Sat, 24 Aug 2019 20:10:20: 6000000 INFO @ Sat, 24 Aug 2019 20:10:26: 6000000 INFO @ Sat, 24 Aug 2019 20:10:27: 2000000 INFO @ Sat, 24 Aug 2019 20:10:33: 7000000 INFO @ Sat, 24 Aug 2019 20:10:36: 7000000 INFO @ Sat, 24 Aug 2019 20:10:36: 3000000 INFO @ Sat, 24 Aug 2019 20:10:45: 8000000 INFO @ Sat, 24 Aug 2019 20:10:45: 8000000 INFO @ Sat, 24 Aug 2019 20:10:45: 4000000 INFO @ Sat, 24 Aug 2019 20:10:54: 9000000 INFO @ Sat, 24 Aug 2019 20:10:54: 5000000 INFO @ Sat, 24 Aug 2019 20:10:57: 9000000 INFO @ Sat, 24 Aug 2019 20:11:03: 10000000 INFO @ Sat, 24 Aug 2019 20:11:03: 6000000 INFO @ Sat, 24 Aug 2019 20:11:10: 10000000 INFO @ Sat, 24 Aug 2019 20:11:12: 11000000 INFO @ Sat, 24 Aug 2019 20:11:12: 7000000 INFO @ Sat, 24 Aug 2019 20:11:20: 12000000 INFO @ Sat, 24 Aug 2019 20:11:21: 8000000 INFO @ Sat, 24 Aug 2019 20:11:23: 11000000 INFO @ Sat, 24 Aug 2019 20:11:29: 13000000 INFO @ Sat, 24 Aug 2019 20:11:30: 9000000 INFO @ Sat, 24 Aug 2019 20:11:35: 12000000 INFO @ Sat, 24 Aug 2019 20:11:39: 14000000 INFO @ Sat, 24 Aug 2019 20:11:39: 10000000 INFO @ Sat, 24 Aug 2019 20:11:47: 13000000 INFO @ Sat, 24 Aug 2019 20:11:47: 15000000 INFO @ Sat, 24 Aug 2019 20:11:48: 11000000 INFO @ Sat, 24 Aug 2019 20:11:56: 16000000 INFO @ Sat, 24 Aug 2019 20:11:57: 12000000 INFO @ Sat, 24 Aug 2019 20:11:59: 14000000 INFO @ Sat, 24 Aug 2019 20:12:05: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:12:05: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:12:05: #1 total tags in treatment: 8355998 INFO @ Sat, 24 Aug 2019 20:12:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:12:05: #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 20:12:05: #1 tags after filtering in treatment: 5506284 INFO @ Sat, 24 Aug 2019 20:12:05: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 24 Aug 2019 20:12:05: #1 finished! INFO @ Sat, 24 Aug 2019 20:12:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:12:05: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:12:05: 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 20:12:05: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.10_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/SRX404610/SRX404610.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:12:06: 13000000 INFO @ Sat, 24 Aug 2019 20:12:11: 15000000 INFO @ Sat, 24 Aug 2019 20:12:13: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 20:12:20: 15000000 INFO @ Sat, 24 Aug 2019 20:12:23: 16000000 INFO @ Sat, 24 Aug 2019 20:12:28: 16000000 INFO @ Sat, 24 Aug 2019 20:12:34: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:12:34: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:12:34: #1 total tags in treatment: 8355998 INFO @ Sat, 24 Aug 2019 20:12:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:12:34: #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 20:12:35: #1 tags after filtering in treatment: 5506284 INFO @ Sat, 24 Aug 2019 20:12:35: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 24 Aug 2019 20:12:35: #1 finished! INFO @ Sat, 24 Aug 2019 20:12:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 20:12:35: #1 tag size is determined as 45 bps INFO @ Sat, 24 Aug 2019 20:12:35: #1 tag size = 45 INFO @ Sat, 24 Aug 2019 20:12:35: #1 total tags in treatment: 8355998 INFO @ Sat, 24 Aug 2019 20:12:35: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 20:12:35: #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 20:12:35: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:12:35: 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 20:12:35: Process for pairing-model is terminated! INFO @ Sat, 24 Aug 2019 20:12:35: #1 tags after filtering in treatment: 5506284 INFO @ Sat, 24 Aug 2019 20:12:35: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 24 Aug 2019 20:12:35: #1 finished! INFO @ Sat, 24 Aug 2019 20:12:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 20:12:35: #2 looking for paired plus/minus strand peaks... cut: /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.05_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/SRX404610/SRX404610.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 20:12:35: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 20:12:35: 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 20:12:35: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.20_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/SRX404610/SRX404610.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX404610/SRX404610.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。