Job ID = 2008331 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 13,512,519 reads read : 27,025,038 reads written : 27,025,038 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629028.sra.cache’: 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: 00:09:25 13512519 reads; of these: 13512519 (100.00%) were paired; of these: 523686 (3.88%) aligned concordantly 0 times 12460089 (92.21%) aligned concordantly exactly 1 time 528744 (3.91%) aligned concordantly >1 times ---- 523686 pairs aligned concordantly 0 times; of these: 119060 (22.73%) aligned discordantly 1 time ---- 404626 pairs aligned 0 times concordantly or discordantly; of these: 809252 mates make up the pairs; of these: 714720 (88.32%) aligned 0 times 77092 (9.53%) aligned exactly 1 time 17440 (2.16%) aligned >1 times 97.36% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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] 11360790 / 13095629 = 0.8675 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 18:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.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 18:56:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.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 18:56:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.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 18:56:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:56:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:56:36: 1000000 INFO @ Fri, 05 Jul 2019 18:56:36: 1000000 INFO @ Fri, 05 Jul 2019 18:56:40: 1000000 INFO @ Fri, 05 Jul 2019 18:56:42: 2000000 INFO @ Fri, 05 Jul 2019 18:56:43: 2000000 INFO @ Fri, 05 Jul 2019 18:56:47: 2000000 INFO @ Fri, 05 Jul 2019 18:56:47: 3000000 INFO @ Fri, 05 Jul 2019 18:56:49: 3000000 INFO @ Fri, 05 Jul 2019 18:56:51: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:56:51: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:56:51: #1 total tags in treatment: 1654152 INFO @ Fri, 05 Jul 2019 18:56:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:51: #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 18:56:51: #1 tags after filtering in treatment: 1132653 INFO @ Fri, 05 Jul 2019 18:56:51: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 18:56:51: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:51: #2 number of paired peaks: 30 WARNING @ Fri, 05 Jul 2019 18:56:51: Too few paired peaks (30) 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 18:56:51: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:56:52: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:56:52: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:56:52: #1 total tags in treatment: 1654152 INFO @ Fri, 05 Jul 2019 18:56:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:52: #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 18:56:52: #1 tags after filtering in treatment: 1132653 INFO @ Fri, 05 Jul 2019 18:56:52: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 18:56:52: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:53: #2 number of paired peaks: 30 WARNING @ Fri, 05 Jul 2019 18:56:53: Too few paired peaks (30) 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 18:56:53: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:56:54: 3000000 INFO @ Fri, 05 Jul 2019 18:56:58: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:56:58: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:56:58: #1 total tags in treatment: 1654152 INFO @ Fri, 05 Jul 2019 18:56:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:56:58: #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 18:56:58: #1 tags after filtering in treatment: 1132653 INFO @ Fri, 05 Jul 2019 18:56:58: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 05 Jul 2019 18:56:58: #1 finished! INFO @ Fri, 05 Jul 2019 18:56:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:56:58: #2 number of paired peaks: 30 WARNING @ Fri, 05 Jul 2019 18:56:58: Too few paired peaks (30) 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 18:56:58: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.10_peaks.narrowPeakcut: /home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.20_peaks.narrowPeak: No such file or directory : No such file or directory pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass1 - making usageList (0 chroms): 1 millis 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/ERX585839/ERX585839.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.10_model.r’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585839/ERX585839.20_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。