Job ID = 2641112 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,346,986 reads read : 20,693,972 reads written : 20,693,972 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: 00:15:54 10346986 reads; of these: 10346986 (100.00%) were paired; of these: 7141909 (69.02%) aligned concordantly 0 times 2860320 (27.64%) aligned concordantly exactly 1 time 344757 (3.33%) aligned concordantly >1 times ---- 7141909 pairs aligned concordantly 0 times; of these: 5011643 (70.17%) aligned discordantly 1 time ---- 2130266 pairs aligned 0 times concordantly or discordantly; of these: 4260532 mates make up the pairs; of these: 2478974 (58.18%) aligned 0 times 511724 (12.01%) aligned exactly 1 time 1269834 (29.80%) aligned >1 times 88.02% overall alignment rate Time searching: 00:15:54 Overall time: 00:15:54 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] 146898 / 8206371 = 0.0179 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.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 22:07:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:10: 1000000 INFO @ Sat, 24 Aug 2019 22:07:19: 2000000 INFO @ Sat, 24 Aug 2019 22:07:29: 3000000 INFO @ Sat, 24 Aug 2019 22:07:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.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 22:07:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:38: 4000000 INFO @ Sat, 24 Aug 2019 22:07:45: 1000000 INFO @ Sat, 24 Aug 2019 22:07:48: 5000000 INFO @ Sat, 24 Aug 2019 22:07:57: 6000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:07:59: 2000000 INFO @ Sat, 24 Aug 2019 22:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.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 22:08:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:07: 7000000 INFO @ Sat, 24 Aug 2019 22:08:12: 1000000 INFO @ Sat, 24 Aug 2019 22:08:13: 3000000 INFO @ Sat, 24 Aug 2019 22:08:18: 8000000 INFO @ Sat, 24 Aug 2019 22:08:21: 2000000 INFO @ Sat, 24 Aug 2019 22:08:24: 4000000 INFO @ Sat, 24 Aug 2019 22:08:30: 9000000 INFO @ Sat, 24 Aug 2019 22:08:32: 3000000 INFO @ Sat, 24 Aug 2019 22:08:36: 5000000 INFO @ Sat, 24 Aug 2019 22:08:42: 10000000 INFO @ Sat, 24 Aug 2019 22:08:44: 4000000 INFO @ Sat, 24 Aug 2019 22:08:49: 6000000 INFO @ Sat, 24 Aug 2019 22:08:54: 5000000 INFO @ Sat, 24 Aug 2019 22:08:55: 11000000 INFO @ Sat, 24 Aug 2019 22:09:03: 7000000 INFO @ Sat, 24 Aug 2019 22:09:04: 6000000 INFO @ Sat, 24 Aug 2019 22:09:08: 12000000 INFO @ Sat, 24 Aug 2019 22:09:15: 7000000 INFO @ Sat, 24 Aug 2019 22:09:16: 8000000 INFO @ Sat, 24 Aug 2019 22:09:20: 13000000 INFO @ Sat, 24 Aug 2019 22:09:25: 8000000 INFO @ Sat, 24 Aug 2019 22:09:28: 9000000 INFO @ Sat, 24 Aug 2019 22:09:32: 14000000 INFO @ Sat, 24 Aug 2019 22:09:35: 9000000 INFO @ Sat, 24 Aug 2019 22:09:41: 10000000 INFO @ Sat, 24 Aug 2019 22:09:44: 15000000 INFO @ Sat, 24 Aug 2019 22:09:45: 10000000 INFO @ Sat, 24 Aug 2019 22:09:53: 11000000 INFO @ Sat, 24 Aug 2019 22:09:55: 11000000 INFO @ Sat, 24 Aug 2019 22:09:56: 16000000 INFO @ Sat, 24 Aug 2019 22:10:05: 12000000 INFO @ Sat, 24 Aug 2019 22:10:06: 12000000 INFO @ Sat, 24 Aug 2019 22:10:07: 17000000 INFO @ Sat, 24 Aug 2019 22:10:16: 13000000 INFO @ Sat, 24 Aug 2019 22:10:17: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:17: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:17: #1 total tags in treatment: 3154126 INFO @ Sat, 24 Aug 2019 22:10:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:17: #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 22:10:17: #1 tags after filtering in treatment: 2864685 INFO @ Sat, 24 Aug 2019 22:10:17: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 24 Aug 2019 22:10:17: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:18: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:10:18: Too few paired peaks (31) 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 22:10:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.05_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/SRX5546553/SRX5546553.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:10:19: 13000000 INFO @ Sat, 24 Aug 2019 22:10:26: 14000000 INFO @ Sat, 24 Aug 2019 22:10:31: 14000000 INFO @ Sat, 24 Aug 2019 22:10:35: 15000000 INFO @ Sat, 24 Aug 2019 22:10:44: 15000000 INFO @ Sat, 24 Aug 2019 22:10:45: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:10:56: 17000000 INFO @ Sat, 24 Aug 2019 22:10:57: 16000000 BigWig に変換しました。 INFO @ Sat, 24 Aug 2019 22:11:05: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:05: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:05: #1 total tags in treatment: 3154126 INFO @ Sat, 24 Aug 2019 22:11:05: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:05: #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 22:11:05: #1 tags after filtering in treatment: 2864685 INFO @ Sat, 24 Aug 2019 22:11:05: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 24 Aug 2019 22:11:05: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:05: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:06: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:11:06: Too few paired peaks (31) 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 22:11:06: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.20_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/SRX5546553/SRX5546553.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:11:11: 17000000 INFO @ Sat, 24 Aug 2019 22:11:21: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:21: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:21: #1 total tags in treatment: 3154126 INFO @ Sat, 24 Aug 2019 22:11:21: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:21: #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 22:11:21: #1 tags after filtering in treatment: 2864685 INFO @ Sat, 24 Aug 2019 22:11:21: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 24 Aug 2019 22:11:21: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:21: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:22: #2 number of paired peaks: 31 WARNING @ Sat, 24 Aug 2019 22:11:22: Too few paired peaks (31) 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 22:11:22: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.10_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/SRX5546553/SRX5546553.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX5546553/SRX5546553.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling