Job ID = 2640773 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,117,407 reads read : 18,234,814 reads written : 18,234,814 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: 00:06:44 9117407 reads; of these: 9117407 (100.00%) were paired; of these: 329894 (3.62%) aligned concordantly 0 times 7974659 (87.47%) aligned concordantly exactly 1 time 812854 (8.92%) aligned concordantly >1 times ---- 329894 pairs aligned concordantly 0 times; of these: 56839 (17.23%) aligned discordantly 1 time ---- 273055 pairs aligned 0 times concordantly or discordantly; of these: 546110 mates make up the pairs; of these: 469162 (85.91%) aligned 0 times 54730 (10.02%) aligned exactly 1 time 22218 (4.07%) aligned >1 times 97.43% overall alignment rate Time searching: 00:06:44 Overall time: 00:06:44 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] 399894 / 8803871 = 0.0454 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:21:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.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 @ Sat, 24 Aug 2019 19:21:12: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:12: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:18: 1000000 INFO @ Sat, 24 Aug 2019 19:21:24: 2000000 INFO @ Sat, 24 Aug 2019 19:21:30: 3000000 INFO @ Sat, 24 Aug 2019 19:21:36: 4000000 INFO @ Sat, 24 Aug 2019 19:21:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.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 @ Sat, 24 Aug 2019 19:21:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:21:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:21:42: 5000000 INFO @ Sat, 24 Aug 2019 19:21:48: 6000000 INFO @ Sat, 24 Aug 2019 19:21:49: 1000000 INFO @ Sat, 24 Aug 2019 19:21:53: 7000000 INFO @ Sat, 24 Aug 2019 19:21:56: 2000000 INFO @ Sat, 24 Aug 2019 19:21:59: 8000000 INFO @ Sat, 24 Aug 2019 19:22:03: 3000000 INFO @ Sat, 24 Aug 2019 19:22:05: 9000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:22:10: 4000000 INFO @ Sat, 24 Aug 2019 19:22:11: 10000000 INFO @ Sat, 24 Aug 2019 19:22:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.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 @ Sat, 24 Aug 2019 19:22:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:22:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:22:16: 11000000 INFO @ Sat, 24 Aug 2019 19:22:18: 5000000 INFO @ Sat, 24 Aug 2019 19:22:19: 1000000 INFO @ Sat, 24 Aug 2019 19:22:22: 12000000 INFO @ Sat, 24 Aug 2019 19:22:26: 6000000 INFO @ Sat, 24 Aug 2019 19:22:27: 2000000 INFO @ Sat, 24 Aug 2019 19:22:27: 13000000 INFO @ Sat, 24 Aug 2019 19:22:33: 7000000 INFO @ Sat, 24 Aug 2019 19:22:33: 14000000 INFO @ Sat, 24 Aug 2019 19:22:35: 3000000 INFO @ Sat, 24 Aug 2019 19:22:39: 15000000 INFO @ Sat, 24 Aug 2019 19:22:41: 8000000 INFO @ Sat, 24 Aug 2019 19:22:42: 4000000 INFO @ Sat, 24 Aug 2019 19:22:44: 16000000 INFO @ Sat, 24 Aug 2019 19:22:48: 9000000 INFO @ Sat, 24 Aug 2019 19:22:50: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 19:22:50: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 19:22:50: #1 total tags in treatment: 8387945 INFO @ Sat, 24 Aug 2019 19:22:50: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:22:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:22:50: 5000000 INFO @ Sat, 24 Aug 2019 19:22:50: #1 tags after filtering in treatment: 5956498 INFO @ Sat, 24 Aug 2019 19:22:50: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 19:22:50: #1 finished! INFO @ Sat, 24 Aug 2019 19:22:50: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:22:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:22:50: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:22:50: Too few paired peaks (0) 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 @ Sat, 24 Aug 2019 19:22:50: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.05_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/ERX2732458/ERX2732458.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:22:56: 10000000 INFO @ Sat, 24 Aug 2019 19:22:57: 6000000 INFO @ Sat, 24 Aug 2019 19:23:03: 11000000 INFO @ Sat, 24 Aug 2019 19:23:05: 7000000 INFO @ Sat, 24 Aug 2019 19:23:11: 12000000 INFO @ Sat, 24 Aug 2019 19:23:12: 8000000 INFO @ Sat, 24 Aug 2019 19:23:18: 13000000 INFO @ Sat, 24 Aug 2019 19:23:20: 9000000 INFO @ Sat, 24 Aug 2019 19:23:25: 14000000 INFO @ Sat, 24 Aug 2019 19:23:27: 10000000 INFO @ Sat, 24 Aug 2019 19:23:33: 15000000 INFO @ Sat, 24 Aug 2019 19:23:35: 11000000 INFO @ Sat, 24 Aug 2019 19:23:40: 16000000 INFO @ Sat, 24 Aug 2019 19:23:42: 12000000 INFO @ Sat, 24 Aug 2019 19:23:47: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 19:23:47: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 19:23:47: #1 total tags in treatment: 8387945 INFO @ Sat, 24 Aug 2019 19:23:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:23:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:23:48: #1 tags after filtering in treatment: 5956498 INFO @ Sat, 24 Aug 2019 19:23:48: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 19:23:48: #1 finished! INFO @ Sat, 24 Aug 2019 19:23:48: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:23:48: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:23:48: Too few paired peaks (0) 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 @ Sat, 24 Aug 2019 19:23:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.10_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/ERX2732458/ERX2732458.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:23:50: 13000000 INFO @ Sat, 24 Aug 2019 19:23:57: 14000000 INFO @ Sat, 24 Aug 2019 19:24:03: 15000000 INFO @ Sat, 24 Aug 2019 19:24:10: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 19:24:17: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 19:24:17: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 19:24:17: #1 total tags in treatment: 8387945 INFO @ Sat, 24 Aug 2019 19:24:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:24:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:24:17: #1 tags after filtering in treatment: 5956498 INFO @ Sat, 24 Aug 2019 19:24:17: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 24 Aug 2019 19:24:17: #1 finished! INFO @ Sat, 24 Aug 2019 19:24:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:24:18: #2 number of paired peaks: 0 WARNING @ Sat, 24 Aug 2019 19:24:18: Too few paired peaks (0) 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 @ Sat, 24 Aug 2019 19:24:18: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.20_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/ERX2732458/ERX2732458.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX2732458/ERX2732458.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。