Job ID = 2007970 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,817,431 reads read : 3,634,862 reads written : 3,634,862 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: 00:01:45 1817431 reads; of these: 1817431 (100.00%) were paired; of these: 456723 (25.13%) aligned concordantly 0 times 1263060 (69.50%) aligned concordantly exactly 1 time 97648 (5.37%) aligned concordantly >1 times ---- 456723 pairs aligned concordantly 0 times; of these: 75533 (16.54%) aligned discordantly 1 time ---- 381190 pairs aligned 0 times concordantly or discordantly; of these: 762380 mates make up the pairs; of these: 731952 (96.01%) aligned 0 times 17565 (2.30%) aligned exactly 1 time 12863 (1.69%) aligned >1 times 79.86% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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_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] 128899 / 1434225 = 0.0899 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 @ Fri, 05 Jul 2019 17:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.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 @ Fri, 05 Jul 2019 17:05:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.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 @ Fri, 05 Jul 2019 17:05:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.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 @ Fri, 05 Jul 2019 17:05:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:22: 1000000 INFO @ Fri, 05 Jul 2019 17:05:27: 1000000 INFO @ Fri, 05 Jul 2019 17:05:27: 1000000 INFO @ Fri, 05 Jul 2019 17:05:31: 2000000 INFO @ Fri, 05 Jul 2019 17:05:36: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:36: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:36: #1 total tags in treatment: 1234927 INFO @ Fri, 05 Jul 2019 17:05:36: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:05:36: #1 tags after filtering in treatment: 1170272 INFO @ Fri, 05 Jul 2019 17:05:36: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:05:36: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:36: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:36: #2 number of paired peaks: 47 WARNING @ Fri, 05 Jul 2019 17:05:36: Too few paired peaks (47) 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 @ Fri, 05 Jul 2019 17:05:36: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 17:05:40: 2000000 INFO @ Fri, 05 Jul 2019 17:05:40: 2000000 INFO @ Fri, 05 Jul 2019 17:05:47: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:47: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:47: #1 total tags in treatment: 1234927 INFO @ Fri, 05 Jul 2019 17:05:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:05:47: #1 tags after filtering in treatment: 1170272 INFO @ Fri, 05 Jul 2019 17:05:47: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:05:47: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:47: #2 number of paired peaks: 47 WARNING @ Fri, 05 Jul 2019 17:05:47: Too few paired peaks (47) 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 @ Fri, 05 Jul 2019 17:05:47: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 17:05:48: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:48: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:48: #1 total tags in treatment: 1234927 INFO @ Fri, 05 Jul 2019 17:05:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 17:05:48: #1 tags after filtering in treatment: 1170272 INFO @ Fri, 05 Jul 2019 17:05:48: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:05:48: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:48: #2 number of paired peaks: 47 WARNING @ Fri, 05 Jul 2019 17:05:48: Too few paired peaks (47) 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 @ Fri, 05 Jul 2019 17:05:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.10_peaks.narrowPeakcut: /home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.20_peaks.narrowPeak: No such file or directory : No such file or directory pass1 - making usageList (0 chroms): 2 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.05_peaks.narrowPeak’: No such file or directory rm: rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.10_model.r’cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.20_*.xls’: No such file or directory: No such file or directory rm: CompletedMACS2peakCalling cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.20_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471761/ERX471761.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。