Job ID = 2641244 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,336,353 reads read : 8,672,706 reads written : 8,672,706 spots read : 4,268,087 reads read : 8,536,174 reads written : 8,536,174 spots read : 4,317,072 reads read : 8,634,144 reads written : 8,634,144 spots read : 4,285,694 reads read : 8,571,388 reads written : 8,571,388 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: 00:07:28 17207206 reads; of these: 17207206 (100.00%) were paired; of these: 6235712 (36.24%) aligned concordantly 0 times 10177495 (59.15%) aligned concordantly exactly 1 time 793999 (4.61%) aligned concordantly >1 times ---- 6235712 pairs aligned concordantly 0 times; of these: 31347 (0.50%) aligned discordantly 1 time ---- 6204365 pairs aligned 0 times concordantly or discordantly; of these: 12408730 mates make up the pairs; of these: 10254001 (82.64%) aligned 0 times 1981675 (15.97%) aligned exactly 1 time 173054 (1.39%) aligned >1 times 70.20% overall alignment rate Time searching: 00:07:28 Overall time: 00:07:28 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] 300774 / 11000096 = 0.0273 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.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 22:37:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:37:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:37:26: 1000000 INFO @ Sat, 24 Aug 2019 22:37:34: 2000000 INFO @ Sat, 24 Aug 2019 22:37:41: 3000000 INFO @ Sat, 24 Aug 2019 22:37:48: 4000000 INFO @ Sat, 24 Aug 2019 22:37:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.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 22:37:48: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:37:48: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:37:55: 5000000 INFO @ Sat, 24 Aug 2019 22:37:56: 1000000 INFO @ Sat, 24 Aug 2019 22:38:02: 6000000 INFO @ Sat, 24 Aug 2019 22:38:03: 2000000 INFO @ Sat, 24 Aug 2019 22:38:09: 7000000 INFO @ Sat, 24 Aug 2019 22:38:10: 3000000 INFO @ Sat, 24 Aug 2019 22:38:16: 8000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:38:17: 4000000 INFO @ Sat, 24 Aug 2019 22:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.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 22:38:19: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:38:19: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:38:23: 9000000 INFO @ Sat, 24 Aug 2019 22:38:24: 1000000 INFO @ Sat, 24 Aug 2019 22:38:24: 5000000 INFO @ Sat, 24 Aug 2019 22:38:30: 2000000 INFO @ Sat, 24 Aug 2019 22:38:30: 10000000 INFO @ Sat, 24 Aug 2019 22:38:32: 6000000 INFO @ Sat, 24 Aug 2019 22:38:35: 3000000 INFO @ Sat, 24 Aug 2019 22:38:37: 11000000 INFO @ Sat, 24 Aug 2019 22:38:39: 7000000 INFO @ Sat, 24 Aug 2019 22:38:41: 4000000 INFO @ Sat, 24 Aug 2019 22:38:44: 12000000 INFO @ Sat, 24 Aug 2019 22:38:46: 8000000 INFO @ Sat, 24 Aug 2019 22:38:46: 5000000 INFO @ Sat, 24 Aug 2019 22:38:51: 13000000 INFO @ Sat, 24 Aug 2019 22:38:52: 6000000 INFO @ Sat, 24 Aug 2019 22:38:53: 9000000 INFO @ Sat, 24 Aug 2019 22:38:58: 7000000 INFO @ Sat, 24 Aug 2019 22:38:58: 14000000 INFO @ Sat, 24 Aug 2019 22:39:00: 10000000 INFO @ Sat, 24 Aug 2019 22:39:03: 8000000 INFO @ Sat, 24 Aug 2019 22:39:05: 15000000 INFO @ Sat, 24 Aug 2019 22:39:08: 11000000 INFO @ Sat, 24 Aug 2019 22:39:09: 9000000 INFO @ Sat, 24 Aug 2019 22:39:12: 16000000 INFO @ Sat, 24 Aug 2019 22:39:14: 10000000 INFO @ Sat, 24 Aug 2019 22:39:15: 12000000 INFO @ Sat, 24 Aug 2019 22:39:19: 17000000 INFO @ Sat, 24 Aug 2019 22:39:20: 11000000 INFO @ Sat, 24 Aug 2019 22:39:22: 13000000 INFO @ Sat, 24 Aug 2019 22:39:26: 12000000 INFO @ Sat, 24 Aug 2019 22:39:26: 18000000 INFO @ Sat, 24 Aug 2019 22:39:29: 14000000 INFO @ Sat, 24 Aug 2019 22:39:31: 13000000 INFO @ Sat, 24 Aug 2019 22:39:33: 19000000 INFO @ Sat, 24 Aug 2019 22:39:36: 15000000 INFO @ Sat, 24 Aug 2019 22:39:37: 14000000 INFO @ Sat, 24 Aug 2019 22:39:40: 20000000 INFO @ Sat, 24 Aug 2019 22:39:42: 15000000 INFO @ Sat, 24 Aug 2019 22:39:43: 16000000 INFO @ Sat, 24 Aug 2019 22:39:47: 21000000 INFO @ Sat, 24 Aug 2019 22:39:48: 16000000 INFO @ Sat, 24 Aug 2019 22:39:50: 17000000 INFO @ Sat, 24 Aug 2019 22:39:53: 17000000 INFO @ Sat, 24 Aug 2019 22:39:54: 22000000 INFO @ Sat, 24 Aug 2019 22:39:58: 18000000 INFO @ Sat, 24 Aug 2019 22:39:59: 18000000 INFO @ Sat, 24 Aug 2019 22:40:01: 23000000 INFO @ Sat, 24 Aug 2019 22:40:04: 19000000 INFO @ Sat, 24 Aug 2019 22:40:05: 19000000 INFO @ Sat, 24 Aug 2019 22:40:05: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:40:05: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:40:05: #1 total tags in treatment: 10671032 INFO @ Sat, 24 Aug 2019 22:40:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:40:05: #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 22:40:05: #1 tags after filtering in treatment: 7368861 INFO @ Sat, 24 Aug 2019 22:40:05: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 24 Aug 2019 22:40:05: #1 finished! INFO @ Sat, 24 Aug 2019 22:40:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:40:06: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:40:06: 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 22:40:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.05_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/SRX6403221/SRX6403221.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:40:10: 20000000 INFO @ Sat, 24 Aug 2019 22:40:12: 20000000 INFO @ Sat, 24 Aug 2019 22:40:15: 21000000 INFO @ Sat, 24 Aug 2019 22:40:19: 21000000 INFO @ Sat, 24 Aug 2019 22:40:21: 22000000 INFO @ Sat, 24 Aug 2019 22:40:26: 22000000 INFO @ Sat, 24 Aug 2019 22:40:26: 23000000 INFO @ Sat, 24 Aug 2019 22:40:29: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:40:29: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:40:29: #1 total tags in treatment: 10671032 INFO @ Sat, 24 Aug 2019 22:40:29: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:40:29: #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 22:40:30: #1 tags after filtering in treatment: 7368861 INFO @ Sat, 24 Aug 2019 22:40:30: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 24 Aug 2019 22:40:30: #1 finished! INFO @ Sat, 24 Aug 2019 22:40:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:40:30: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:40:30: 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 22:40:30: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.20_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/SRX6403221/SRX6403221.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:40:33: 23000000 INFO @ Sat, 24 Aug 2019 22:40:37: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:40:37: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:40:37: #1 total tags in treatment: 10671032 INFO @ Sat, 24 Aug 2019 22:40:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:40:37: #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 22:40:37: #1 tags after filtering in treatment: 7368861 INFO @ Sat, 24 Aug 2019 22:40:37: #1 Redundant rate of treatment: 0.31 INFO @ Sat, 24 Aug 2019 22:40:37: #1 finished! INFO @ Sat, 24 Aug 2019 22:40:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:40:38: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 22:40:38: 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 22:40:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.10_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/SRX6403221/SRX6403221.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX6403221/SRX6403221.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。