Job ID = 2008309 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 14,880,759 reads read : 29,761,518 reads written : 29,761,518 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR629073.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: 00:11:35 14880759 reads; of these: 14880759 (100.00%) were paired; of these: 1073578 (7.21%) aligned concordantly 0 times 12993177 (87.32%) aligned concordantly exactly 1 time 814004 (5.47%) aligned concordantly >1 times ---- 1073578 pairs aligned concordantly 0 times; of these: 63197 (5.89%) aligned discordantly 1 time ---- 1010381 pairs aligned 0 times concordantly or discordantly; of these: 2020762 mates make up the pairs; of these: 1968323 (97.40%) aligned 0 times 38009 (1.88%) aligned exactly 1 time 14430 (0.71%) aligned >1 times 93.39% overall alignment rate Time searching: 00:11:35 Overall time: 00:11:35 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 12 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] 12844260 / 13864116 = 0.9264 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 18:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.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 18:47:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:47:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.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 18:48:00: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:48:00: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.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 18:48:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:48:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:48:08: 1000000 INFO @ Fri, 05 Jul 2019 18:48:08: 1000000 INFO @ Fri, 05 Jul 2019 18:48:09: 1000000 INFO @ Fri, 05 Jul 2019 18:48:16: 2000000 INFO @ Fri, 05 Jul 2019 18:48:16: 2000000 INFO @ Fri, 05 Jul 2019 18:48:17: 2000000 INFO @ Fri, 05 Jul 2019 18:48:17: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:48:17: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:48:17: #1 total tags in treatment: 980640 INFO @ Fri, 05 Jul 2019 18:48:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:48:17: #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 18:48:17: #1 tags after filtering in treatment: 764060 INFO @ Fri, 05 Jul 2019 18:48:17: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 05 Jul 2019 18:48:17: #1 finished! INFO @ Fri, 05 Jul 2019 18:48:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:48:17: #2 number of paired peaks: 88 WARNING @ Fri, 05 Jul 2019 18:48:17: Too few paired peaks (88) 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 18:48:17: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.10_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/ERX585819/ERX585819.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:48:17: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:48:17: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:48:17: #1 total tags in treatment: 980640 INFO @ Fri, 05 Jul 2019 18:48:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:48:17: #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 18:48:17: #1 tags after filtering in treatment: 764060 INFO @ Fri, 05 Jul 2019 18:48:17: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 05 Jul 2019 18:48:17: #1 finished! INFO @ Fri, 05 Jul 2019 18:48:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:48:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:48:17: #2 number of paired peaks: 88 WARNING @ Fri, 05 Jul 2019 18:48:17: Too few paired peaks (88) 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 18:48:17: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:48:18: #1 tag size is determined as 44 bps INFO @ Fri, 05 Jul 2019 18:48:18: #1 tag size = 44 INFO @ Fri, 05 Jul 2019 18:48:18: #1 total tags in treatment: 980640 INFO @ Fri, 05 Jul 2019 18:48:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:48:18: #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 18:48:18: #1 tags after filtering in treatment: 764060 INFO @ Fri, 05 Jul 2019 18:48:18: #1 Redundant rate of treatment: 0.22 INFO @ Fri, 05 Jul 2019 18:48:18: #1 finished! INFO @ Fri, 05 Jul 2019 18:48:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:48:18: #2 number of paired peaks: 88 WARNING @ Fri, 05 Jul 2019 18:48:18: Too few paired peaks (88) 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 18:48:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.20_peaks.narrowPeak: 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 needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585819/ERX585819.20_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。