Job ID = 2008209 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,663,508 reads read : 15,327,016 reads written : 15,327,016 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628935.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: 00:09:13 7663508 reads; of these: 7663508 (100.00%) were paired; of these: 636422 (8.30%) aligned concordantly 0 times 6104973 (79.66%) aligned concordantly exactly 1 time 922113 (12.03%) aligned concordantly >1 times ---- 636422 pairs aligned concordantly 0 times; of these: 213190 (33.50%) aligned discordantly 1 time ---- 423232 pairs aligned 0 times concordantly or discordantly; of these: 846464 mates make up the pairs; of these: 744048 (87.90%) aligned 0 times 42747 (5.05%) aligned exactly 1 time 59669 (7.05%) aligned >1 times 95.15% overall alignment rate Time searching: 00:09:13 Overall time: 00:09:13 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] 945787 / 7200929 = 0.1313 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 17:58:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.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 17:58:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:58:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:58:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.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 17:58:28: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:58:28: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.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 17:58:29: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:58:29: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:58:38: 1000000 INFO @ Fri, 05 Jul 2019 17:58:39: 1000000 INFO @ Fri, 05 Jul 2019 17:58:40: 1000000 INFO @ Fri, 05 Jul 2019 17:58:47: 2000000 INFO @ Fri, 05 Jul 2019 17:58:49: 2000000 INFO @ Fri, 05 Jul 2019 17:58:50: 2000000 INFO @ Fri, 05 Jul 2019 17:58:56: 3000000 INFO @ Fri, 05 Jul 2019 17:58:58: 3000000 INFO @ Fri, 05 Jul 2019 17:59:00: 3000000 INFO @ Fri, 05 Jul 2019 17:59:06: 4000000 INFO @ Fri, 05 Jul 2019 17:59:08: 4000000 INFO @ Fri, 05 Jul 2019 17:59:11: 4000000 INFO @ Fri, 05 Jul 2019 17:59:17: 5000000 INFO @ Fri, 05 Jul 2019 17:59:19: 5000000 INFO @ Fri, 05 Jul 2019 17:59:22: 5000000 INFO @ Fri, 05 Jul 2019 17:59:28: 6000000 INFO @ Fri, 05 Jul 2019 17:59:30: 6000000 INFO @ Fri, 05 Jul 2019 17:59:33: 6000000 INFO @ Fri, 05 Jul 2019 17:59:39: 7000000 INFO @ Fri, 05 Jul 2019 17:59:41: 7000000 INFO @ Fri, 05 Jul 2019 17:59:44: 7000000 INFO @ Fri, 05 Jul 2019 17:59:50: 8000000 INFO @ Fri, 05 Jul 2019 17:59:53: 8000000 INFO @ Fri, 05 Jul 2019 17:59:55: 8000000 INFO @ Fri, 05 Jul 2019 18:00:01: 9000000 INFO @ Fri, 05 Jul 2019 18:00:04: 9000000 INFO @ Fri, 05 Jul 2019 18:00:07: 9000000 INFO @ Fri, 05 Jul 2019 18:00:13: 10000000 INFO @ Fri, 05 Jul 2019 18:00:15: 10000000 INFO @ Fri, 05 Jul 2019 18:00:18: 10000000 INFO @ Fri, 05 Jul 2019 18:00:24: 11000000 INFO @ Fri, 05 Jul 2019 18:00:26: 11000000 INFO @ Fri, 05 Jul 2019 18:00:29: 11000000 INFO @ Fri, 05 Jul 2019 18:00:35: 12000000 INFO @ Fri, 05 Jul 2019 18:00:37: 12000000 INFO @ Fri, 05 Jul 2019 18:00:40: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 18:00:43: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:00:43: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:00:43: #1 total tags in treatment: 6086644 INFO @ Fri, 05 Jul 2019 18:00:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:00:43: #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 18:00:43: #1 tags after filtering in treatment: 3729137 INFO @ Fri, 05 Jul 2019 18:00:43: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 18:00:43: #1 finished! INFO @ Fri, 05 Jul 2019 18:00:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:00:43: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:00:43: 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 18:00:43: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.10_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/ERX585740/ERX585740.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:00:45: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:00:45: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:00:45: #1 total tags in treatment: 6086644 INFO @ Fri, 05 Jul 2019 18:00:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:00:45: #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 18:00:45: #1 tags after filtering in treatment: 3729137 INFO @ Fri, 05 Jul 2019 18:00:45: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 18:00:45: #1 finished! INFO @ Fri, 05 Jul 2019 18:00:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:00:45: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:00:45: 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 18:00:45: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.20_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/ERX585740/ERX585740.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.20_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:00:47: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:00:47: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:00:47: #1 total tags in treatment: 6086644 INFO @ Fri, 05 Jul 2019 18:00:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:00:47: #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 18:00:47: #1 tags after filtering in treatment: 3729137 INFO @ Fri, 05 Jul 2019 18:00:47: #1 Redundant rate of treatment: 0.39 INFO @ Fri, 05 Jul 2019 18:00:47: #1 finished! INFO @ Fri, 05 Jul 2019 18:00:47: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:00:48: #2 number of paired peaks: 0 WARNING @ Fri, 05 Jul 2019 18:00:48: 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 @ Fri, 05 Jul 2019 18:00:48: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.05_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/ERX585740/ERX585740.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585740/ERX585740.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling BigWig に変換しました。