Job ID = 2640761 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,537,744 reads read : 3,075,488 reads written : 3,075,488 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: 00:00:54 1537744 reads; of these: 1537744 (100.00%) were paired; of these: 438788 (28.53%) aligned concordantly 0 times 816491 (53.10%) aligned concordantly exactly 1 time 282465 (18.37%) aligned concordantly >1 times ---- 438788 pairs aligned concordantly 0 times; of these: 2167 (0.49%) aligned discordantly 1 time ---- 436621 pairs aligned 0 times concordantly or discordantly; of these: 873242 mates make up the pairs; of these: 861000 (98.60%) aligned 0 times 5226 (0.60%) aligned exactly 1 time 7016 (0.80%) aligned >1 times 72.00% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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_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] 63619 / 1100246 = 0.0578 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.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 19:04:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:04:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:04:30: 1000000 INFO @ Sat, 24 Aug 2019 19:04:38: 2000000 INFO @ Sat, 24 Aug 2019 19:04:38: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:04:38: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:04:38: #1 total tags in treatment: 1035422 INFO @ Sat, 24 Aug 2019 19:04:38: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:04:38: #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 19:04:38: #1 tags after filtering in treatment: 828468 INFO @ Sat, 24 Aug 2019 19:04:38: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 24 Aug 2019 19:04:38: #1 finished! INFO @ Sat, 24 Aug 2019 19:04:38: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:04:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:04:38: #2 number of paired peaks: 41 WARNING @ Sat, 24 Aug 2019 19:04:38: Too few paired peaks (41) 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 19:04:38: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.05_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/ERX2732452/ERX2732452.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:04:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.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 19:04:52: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:04:52: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:05:00: 1000000 INFO @ Sat, 24 Aug 2019 19:05:08: 2000000 INFO @ Sat, 24 Aug 2019 19:05:08: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:05:08: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:05:08: #1 total tags in treatment: 1035422 INFO @ Sat, 24 Aug 2019 19:05:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:05:08: #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 19:05:08: #1 tags after filtering in treatment: 828468 INFO @ Sat, 24 Aug 2019 19:05:08: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 24 Aug 2019 19:05:08: #1 finished! INFO @ Sat, 24 Aug 2019 19:05:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:05:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:05:09: #2 number of paired peaks: 41 WARNING @ Sat, 24 Aug 2019 19:05:09: Too few paired peaks (41) 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 19:05:09: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.10_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/ERX2732452/ERX2732452.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.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 19:05:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:05:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:05:30: 1000000 INFO @ Sat, 24 Aug 2019 19:05:38: 2000000 INFO @ Sat, 24 Aug 2019 19:05:39: #1 tag size is determined as 34 bps INFO @ Sat, 24 Aug 2019 19:05:39: #1 tag size = 34 INFO @ Sat, 24 Aug 2019 19:05:39: #1 total tags in treatment: 1035422 INFO @ Sat, 24 Aug 2019 19:05:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:05:39: #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 19:05:39: #1 tags after filtering in treatment: 828468 INFO @ Sat, 24 Aug 2019 19:05:39: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 24 Aug 2019 19:05:39: #1 finished! INFO @ Sat, 24 Aug 2019 19:05:39: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:05:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:05:39: #2 number of paired peaks: 41 WARNING @ Sat, 24 Aug 2019 19:05:39: Too few paired peaks (41) 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 19:05:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.20_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/ERX2732452/ERX2732452.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732452/ERX2732452.20_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。