Job ID = 2010820 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,515,194 reads read : 11,030,388 reads written : 5,515,194 reads 0-length : 5,515,194 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: 00:01:53 5515194 reads; of these: 5515194 (100.00%) were unpaired; of these: 358276 (6.50%) aligned 0 times 4133304 (74.94%) aligned exactly 1 time 1023614 (18.56%) aligned >1 times 93.50% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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_rmdupse_core] 1418020 / 5156918 = 0.2750 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Sat, 06 Jul 2019 00:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.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, 06 Jul 2019 00:57:44: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:57:44: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:57:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.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, 06 Jul 2019 00:57:45: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:57:45: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:57:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.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, 06 Jul 2019 00:57:47: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:57:47: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:57:54: 1000000 INFO @ Sat, 06 Jul 2019 00:57:57: 1000000 INFO @ Sat, 06 Jul 2019 00:57:59: 1000000 INFO @ Sat, 06 Jul 2019 00:58:03: 2000000 INFO @ Sat, 06 Jul 2019 00:58:09: 2000000 INFO @ Sat, 06 Jul 2019 00:58:10: 2000000 INFO @ Sat, 06 Jul 2019 00:58:11: 3000000 INFO @ Sat, 06 Jul 2019 00:58:18: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:58:18: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:58:18: #1 total tags in treatment: 3738898 INFO @ Sat, 06 Jul 2019 00:58:18: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:58:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:58:18: #1 tags after filtering in treatment: 3738898 INFO @ Sat, 06 Jul 2019 00:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:58:18: #1 finished! INFO @ Sat, 06 Jul 2019 00:58:18: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:58:18: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 00:58:18: Too few paired peaks (28) 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, 06 Jul 2019 00:58:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.05_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/SRX4140929/SRX4140929.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:58:20: 3000000 INFO @ Sat, 06 Jul 2019 00:58:21: 3000000 INFO @ Sat, 06 Jul 2019 00:58:28: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:58:28: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:58:28: #1 total tags in treatment: 3738898 INFO @ Sat, 06 Jul 2019 00:58:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:58:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:58:28: #1 tags after filtering in treatment: 3738898 INFO @ Sat, 06 Jul 2019 00:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:58:28: #1 finished! INFO @ Sat, 06 Jul 2019 00:58:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:58:28: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 00:58:28: Too few paired peaks (28) 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, 06 Jul 2019 00:58:28: Process for pairing-model is terminated! INFO @ Sat, 06 Jul 2019 00:58:29: #1 tag size is determined as 100 bps INFO @ Sat, 06 Jul 2019 00:58:29: #1 tag size = 100 INFO @ Sat, 06 Jul 2019 00:58:29: #1 total tags in treatment: 3738898 INFO @ Sat, 06 Jul 2019 00:58:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:58:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 00:58:29: #1 tags after filtering in treatment: 3738898 INFO @ Sat, 06 Jul 2019 00:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:58:29: #1 finished! INFO @ Sat, 06 Jul 2019 00:58:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:58:29: #2 number of paired peaks: 28 WARNING @ Sat, 06 Jul 2019 00:58:29: Too few paired peaks (28) 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, 06 Jul 2019 00:58:29: Process for pairing-model is terminated! BedGraph に変換しました。 cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.10_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.20_peaks.narrowPeak: No such file or directory BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.20_model.r’: No such file or directory rm: CompletedMACS2peakCalling cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX4140929/SRX4140929.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。