Job ID = 2007984 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,780,122 reads read : 3,560,244 reads written : 3,560,244 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: 00:02:05 1780122 reads; of these: 1780122 (100.00%) were paired; of these: 251842 (14.15%) aligned concordantly 0 times 1401398 (78.72%) aligned concordantly exactly 1 time 126882 (7.13%) aligned concordantly >1 times ---- 251842 pairs aligned concordantly 0 times; of these: 153403 (60.91%) aligned discordantly 1 time ---- 98439 pairs aligned 0 times concordantly or discordantly; of these: 196878 mates make up the pairs; of these: 133579 (67.85%) aligned 0 times 30467 (15.48%) aligned exactly 1 time 32832 (16.68%) aligned >1 times 96.25% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 11435 / 1674484 = 0.0068 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 17:05:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.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 17:05:47: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:47: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.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 17:05:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.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 17:05:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:05:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:05:59: 1000000 INFO @ Fri, 05 Jul 2019 17:06:00: 1000000 INFO @ Fri, 05 Jul 2019 17:06:00: 1000000 INFO @ Fri, 05 Jul 2019 17:06:10: 2000000 INFO @ Fri, 05 Jul 2019 17:06:11: 2000000 INFO @ Fri, 05 Jul 2019 17:06:11: 2000000 INFO @ Fri, 05 Jul 2019 17:06:20: 3000000 INFO @ Fri, 05 Jul 2019 17:06:23: 3000000 INFO @ Fri, 05 Jul 2019 17:06:23: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:06:23: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:06:23: #1 total tags in treatment: 1517403 INFO @ Fri, 05 Jul 2019 17:06:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:06:23: #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 17:06:23: #1 tags after filtering in treatment: 1460440 INFO @ Fri, 05 Jul 2019 17:06:23: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:06:23: #1 finished! INFO @ Fri, 05 Jul 2019 17:06:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:06:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:06:23: 3000000 INFO @ Fri, 05 Jul 2019 17:06:24: #2 number of paired peaks: 18 WARNING @ Fri, 05 Jul 2019 17:06:24: Too few paired peaks (18) 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 17:06:24: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.20_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/ERX471774/ERX471774.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:06:28: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:06:28: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:06:28: #1 total tags in treatment: 1517403 INFO @ Fri, 05 Jul 2019 17:06:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:06:28: #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 17:06:28: #1 tags after filtering in treatment: 1460440 INFO @ Fri, 05 Jul 2019 17:06:28: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:06:28: #1 finished! INFO @ Fri, 05 Jul 2019 17:06:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:06:28: #2 number of paired peaks: 18 WARNING @ Fri, 05 Jul 2019 17:06:28: Too few paired peaks (18) 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 17:06:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.10_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/ERX471774/ERX471774.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:06:28: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:06:28: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:06:28: #1 total tags in treatment: 1517403 INFO @ Fri, 05 Jul 2019 17:06:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:06:28: #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 17:06:28: #1 tags after filtering in treatment: 1460440 INFO @ Fri, 05 Jul 2019 17:06:28: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 05 Jul 2019 17:06:28: #1 finished! INFO @ Fri, 05 Jul 2019 17:06:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:06:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:06:28: #2 number of paired peaks: 18 WARNING @ Fri, 05 Jul 2019 17:06:28: Too few paired peaks (18) 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 17:06:28: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.05_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/ERX471774/ERX471774.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX471774/ERX471774.05_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。