Job ID = 2008235 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,415,804 reads read : 42,831,608 reads written : 42,831,608 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628977.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: 00:21:01 21415804 reads; of these: 21415804 (100.00%) were paired; of these: 7961540 (37.18%) aligned concordantly 0 times 10822252 (50.53%) aligned concordantly exactly 1 time 2632012 (12.29%) aligned concordantly >1 times ---- 7961540 pairs aligned concordantly 0 times; of these: 432573 (5.43%) aligned discordantly 1 time ---- 7528967 pairs aligned 0 times concordantly or discordantly; of these: 15057934 mates make up the pairs; of these: 14450294 (95.96%) aligned 0 times 197033 (1.31%) aligned exactly 1 time 410607 (2.73%) aligned >1 times 66.26% overall alignment rate Time searching: 00:21:01 Overall time: 00:21:01 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] 3411461 / 13839302 = 0.2465 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 18:36:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.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 18:36:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:36:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:36:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.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 18:36:30: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:36:30: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:36:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.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 18:36:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:36:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:36:39: 1000000 INFO @ Fri, 05 Jul 2019 18:36:40: 1000000 INFO @ Fri, 05 Jul 2019 18:36:42: 1000000 INFO @ Fri, 05 Jul 2019 18:36:48: 2000000 INFO @ Fri, 05 Jul 2019 18:36:49: 2000000 INFO @ Fri, 05 Jul 2019 18:36:53: 2000000 INFO @ Fri, 05 Jul 2019 18:36:58: 3000000 INFO @ Fri, 05 Jul 2019 18:36:59: 3000000 INFO @ Fri, 05 Jul 2019 18:37:04: 3000000 INFO @ Fri, 05 Jul 2019 18:37:07: 4000000 INFO @ Fri, 05 Jul 2019 18:37:08: 4000000 INFO @ Fri, 05 Jul 2019 18:37:14: 4000000 INFO @ Fri, 05 Jul 2019 18:37:16: 5000000 INFO @ Fri, 05 Jul 2019 18:37:17: 5000000 INFO @ Fri, 05 Jul 2019 18:37:25: 5000000 INFO @ Fri, 05 Jul 2019 18:37:25: 6000000 INFO @ Fri, 05 Jul 2019 18:37:27: 6000000 INFO @ Fri, 05 Jul 2019 18:37:35: 7000000 INFO @ Fri, 05 Jul 2019 18:37:36: 6000000 INFO @ Fri, 05 Jul 2019 18:37:36: 7000000 INFO @ Fri, 05 Jul 2019 18:37:44: 8000000 INFO @ Fri, 05 Jul 2019 18:37:45: 8000000 INFO @ Fri, 05 Jul 2019 18:37:46: 7000000 INFO @ Fri, 05 Jul 2019 18:37:53: 9000000 INFO @ Fri, 05 Jul 2019 18:37:55: 9000000 INFO @ Fri, 05 Jul 2019 18:37:57: 8000000 INFO @ Fri, 05 Jul 2019 18:38:03: 10000000 INFO @ Fri, 05 Jul 2019 18:38:04: 10000000 INFO @ Fri, 05 Jul 2019 18:38:07: 9000000 INFO @ Fri, 05 Jul 2019 18:38:12: 11000000 INFO @ Fri, 05 Jul 2019 18:38:13: 11000000 INFO @ Fri, 05 Jul 2019 18:38:18: 10000000 INFO @ Fri, 05 Jul 2019 18:38:21: 12000000 INFO @ Fri, 05 Jul 2019 18:38:22: 12000000 INFO @ Fri, 05 Jul 2019 18:38:28: 11000000 INFO @ Fri, 05 Jul 2019 18:38:31: 13000000 INFO @ Fri, 05 Jul 2019 18:38:32: 13000000 INFO @ Fri, 05 Jul 2019 18:38:39: 14000000 INFO @ Fri, 05 Jul 2019 18:38:40: 12000000 INFO @ Fri, 05 Jul 2019 18:38:40: 14000000 INFO @ Fri, 05 Jul 2019 18:38:48: 15000000 INFO @ Fri, 05 Jul 2019 18:38:51: 15000000 INFO @ Fri, 05 Jul 2019 18:38:52: 13000000 INFO @ Fri, 05 Jul 2019 18:38:55: 16000000 INFO @ Fri, 05 Jul 2019 18:38:59: 16000000 INFO @ Fri, 05 Jul 2019 18:39:02: 14000000 INFO @ Fri, 05 Jul 2019 18:39:03: 17000000 INFO @ Fri, 05 Jul 2019 18:39:07: 17000000 INFO @ Fri, 05 Jul 2019 18:39:11: 18000000 INFO @ Fri, 05 Jul 2019 18:39:12: 15000000 INFO @ Fri, 05 Jul 2019 18:39:15: 18000000 INFO @ Fri, 05 Jul 2019 18:39:19: 19000000 INFO @ Fri, 05 Jul 2019 18:39:22: 19000000 INFO @ Fri, 05 Jul 2019 18:39:22: 16000000 INFO @ Fri, 05 Jul 2019 18:39:26: 20000000 INFO @ Fri, 05 Jul 2019 18:39:30: 20000000 INFO @ Fri, 05 Jul 2019 18:39:33: 17000000 INFO @ Fri, 05 Jul 2019 18:39:34: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:39:38: 21000000 INFO @ Fri, 05 Jul 2019 18:39:38: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:39:38: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:39:38: #1 total tags in treatment: 10078908 INFO @ Fri, 05 Jul 2019 18:39:38: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:39:38: #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 18:39:39: #1 tags after filtering in treatment: 5062059 INFO @ Fri, 05 Jul 2019 18:39:39: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 05 Jul 2019 18:39:39: #1 finished! INFO @ Fri, 05 Jul 2019 18:39:39: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:39:39: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:39:39: 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 @ Fri, 05 Jul 2019 18:39:39: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.10_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/ERX585759/ERX585759.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:39:42: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:39:42: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:39:42: #1 total tags in treatment: 10078908 INFO @ Fri, 05 Jul 2019 18:39:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:39:42: #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 18:39:43: #1 tags after filtering in treatment: 5062059 INFO @ Fri, 05 Jul 2019 18:39:43: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 05 Jul 2019 18:39:43: #1 finished! INFO @ Fri, 05 Jul 2019 18:39:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:39:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:39:43: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:39:43: 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 @ Fri, 05 Jul 2019 18:39:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.05_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/ERX585759/ERX585759.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:39:44: 18000000 INFO @ Fri, 05 Jul 2019 18:39:54: 19000000 BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 18:40:03: 20000000 INFO @ Fri, 05 Jul 2019 18:40:13: 21000000 INFO @ Fri, 05 Jul 2019 18:40:19: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:40:19: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:40:19: #1 total tags in treatment: 10078908 INFO @ Fri, 05 Jul 2019 18:40:19: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:40:19: #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 18:40:19: #1 tags after filtering in treatment: 5062059 INFO @ Fri, 05 Jul 2019 18:40:19: #1 Redundant rate of treatment: 0.50 INFO @ Fri, 05 Jul 2019 18:40:19: #1 finished! INFO @ Fri, 05 Jul 2019 18:40:19: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:40:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:40:20: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:40:20: 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 @ Fri, 05 Jul 2019 18:40:20: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.20_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585759/ERX585759.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling