Job ID = 2010586 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,649,688 reads read : 7,299,376 reads written : 7,299,376 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: 00:02:24 3649688 reads; of these: 3649688 (100.00%) were paired; of these: 1314964 (36.03%) aligned concordantly 0 times 1870906 (51.26%) aligned concordantly exactly 1 time 463818 (12.71%) aligned concordantly >1 times ---- 1314964 pairs aligned concordantly 0 times; of these: 66675 (5.07%) aligned discordantly 1 time ---- 1248289 pairs aligned 0 times concordantly or discordantly; of these: 2496578 mates make up the pairs; of these: 2380333 (95.34%) aligned 0 times 62316 (2.50%) aligned exactly 1 time 53929 (2.16%) aligned >1 times 67.39% overall alignment rate Time searching: 00:02:24 Overall time: 00:02:24 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] 212937 / 2399441 = 0.0887 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 23:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.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 23:28:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.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 23:28:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:28:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.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 23:28:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:28:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:29:07: 1000000 INFO @ Fri, 05 Jul 2019 23:29:07: 1000000 INFO @ Fri, 05 Jul 2019 23:29:09: 1000000 INFO @ Fri, 05 Jul 2019 23:29:18: 2000000 INFO @ Fri, 05 Jul 2019 23:29:21: 2000000 INFO @ Fri, 05 Jul 2019 23:29:22: 2000000 INFO @ Fri, 05 Jul 2019 23:29:28: 3000000 INFO @ Fri, 05 Jul 2019 23:29:34: 3000000 INFO @ Fri, 05 Jul 2019 23:29:34: 3000000 INFO @ Fri, 05 Jul 2019 23:29:39: 4000000 INFO @ Fri, 05 Jul 2019 23:29:44: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:29:44: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:29:44: #1 total tags in treatment: 2127166 INFO @ Fri, 05 Jul 2019 23:29:44: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:44: #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 23:29:44: #1 tags after filtering in treatment: 1734664 INFO @ Fri, 05 Jul 2019 23:29:44: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 23:29:44: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:44: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:44: #2 number of paired peaks: 61 WARNING @ Fri, 05 Jul 2019 23:29:44: Too few paired peaks (61) 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 23:29:44: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.10_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/SRX381287/SRX381287.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:29:46: 4000000 INFO @ Fri, 05 Jul 2019 23:29:47: 4000000 INFO @ Fri, 05 Jul 2019 23:29:52: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:29:52: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:29:52: #1 total tags in treatment: 2127166 INFO @ Fri, 05 Jul 2019 23:29:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:52: #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 23:29:52: #1 tags after filtering in treatment: 1734664 INFO @ Fri, 05 Jul 2019 23:29:52: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 23:29:52: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:52: #2 number of paired peaks: 61 WARNING @ Fri, 05 Jul 2019 23:29:52: Too few paired peaks (61) 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 23:29:52: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.05_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/SRX381287/SRX381287.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:29:53: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:29:53: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:29:53: #1 total tags in treatment: 2127166 INFO @ Fri, 05 Jul 2019 23:29:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:29:53: #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 23:29:53: #1 tags after filtering in treatment: 1734664 INFO @ Fri, 05 Jul 2019 23:29:53: #1 Redundant rate of treatment: 0.18 INFO @ Fri, 05 Jul 2019 23:29:53: #1 finished! INFO @ Fri, 05 Jul 2019 23:29:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:29:53: #2 number of paired peaks: 61 WARNING @ Fri, 05 Jul 2019 23:29:53: Too few paired peaks (61) 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 23:29:53: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.20_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/SRX381287/SRX381287.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/SRX381287/SRX381287.20_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。