Job ID = 2007965 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,851,766 reads read : 3,703,532 reads written : 3,703,532 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: 00:02:21 1851766 reads; of these: 1851766 (100.00%) were paired; of these: 234546 (12.67%) aligned concordantly 0 times 1494190 (80.69%) aligned concordantly exactly 1 time 123030 (6.64%) aligned concordantly >1 times ---- 234546 pairs aligned concordantly 0 times; of these: 133704 (57.01%) aligned discordantly 1 time ---- 100842 pairs aligned 0 times concordantly or discordantly; of these: 201684 mates make up the pairs; of these: 148110 (73.44%) aligned 0 times 27358 (13.56%) aligned exactly 1 time 26216 (13.00%) aligned >1 times 96.00% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 13237 / 1744810 = 0.0076 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 17:05:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.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 17:05:05: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:05: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.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 17:05:06: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:06: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.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 17:05:08: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:08: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:14: 1000000 INFO @ Fri, 05 Jul 2019 17:05:16: 1000000 INFO @ Fri, 05 Jul 2019 17:05:19: 1000000 INFO @ Fri, 05 Jul 2019 17:05:22: 2000000 INFO @ Fri, 05 Jul 2019 17:05:25: 2000000 INFO @ Fri, 05 Jul 2019 17:05:30: 2000000 INFO @ Fri, 05 Jul 2019 17:05:31: 3000000 INFO @ Fri, 05 Jul 2019 17:05:34: 3000000 INFO @ Fri, 05 Jul 2019 17:05:35: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:35: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:35: #1 total tags in treatment: 1604510 INFO @ Fri, 05 Jul 2019 17:05:35: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:35: #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 17:05:35: #1 tags after filtering in treatment: 1544679 INFO @ Fri, 05 Jul 2019 17:05:35: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:05:35: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:35: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:35: #2 number of paired peaks: 2 WARNING @ Fri, 05 Jul 2019 17:05:35: Too few paired peaks (2) 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 17:05:35: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 17:05:39: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:39: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:39: #1 total tags in treatment: 1604510 INFO @ Fri, 05 Jul 2019 17:05:39: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:39: #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 17:05:39: #1 tags after filtering in treatment: 1544679 INFO @ Fri, 05 Jul 2019 17:05:39: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:05:39: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:39: #2 number of paired peaks: 2 WARNING @ Fri, 05 Jul 2019 17:05:39: Too few paired peaks (2) 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 17:05:39: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 17:05:41: 3000000 INFO @ Fri, 05 Jul 2019 17:05:46: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:05:46: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:05:46: #1 total tags in treatment: 1604510 INFO @ Fri, 05 Jul 2019 17:05:46: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:05:46: #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 17:05:46: #1 tags after filtering in treatment: 1544679 INFO @ Fri, 05 Jul 2019 17:05:46: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:05:46: #1 finished! INFO @ Fri, 05 Jul 2019 17:05:46: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:05:47: #2 number of paired peaks: 2 WARNING @ Fri, 05 Jul 2019 17:05:47: Too few paired peaks (2) 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! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.05_peaks.narrowPeak: No such file or directory cut: /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.20_peaks.narrowPeakcut: /home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.10_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 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/ERX471756/ERX471756.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.05_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.10_model.r’: No such file or directory CompletedMACS2peakCalling rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.10_peaks.narrowPeak’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471756/ERX471756.20_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。