Job ID = 2008343 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,120,338 reads read : 6,240,676 reads written : 6,240,676 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR628987.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: 00:05:09 3120338 reads; of these: 3120338 (100.00%) were paired; of these: 577400 (18.50%) aligned concordantly 0 times 2393807 (76.72%) aligned concordantly exactly 1 time 149131 (4.78%) aligned concordantly >1 times ---- 577400 pairs aligned concordantly 0 times; of these: 98610 (17.08%) aligned discordantly 1 time ---- 478790 pairs aligned 0 times concordantly or discordantly; of these: 957580 mates make up the pairs; of these: 884684 (92.39%) aligned 0 times 58134 (6.07%) aligned exactly 1 time 14762 (1.54%) aligned >1 times 85.82% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 1378945 / 2622639 = 0.5258 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 18:47:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.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 18:47:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:47:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:47:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.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 18:47:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:47:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:47:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.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 18:47:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 18:47:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 18:48:02: 1000000 INFO @ Fri, 05 Jul 2019 18:48:02: 1000000 INFO @ Fri, 05 Jul 2019 18:48:06: 1000000 INFO @ Fri, 05 Jul 2019 18:48:09: 2000000 INFO @ Fri, 05 Jul 2019 18:48:11: 2000000 INFO @ Fri, 05 Jul 2019 18:48:15: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:48:15: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:48:15: #1 total tags in treatment: 1189072 INFO @ Fri, 05 Jul 2019 18:48:15: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:48:15: #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 18:48:15: #1 tags after filtering in treatment: 947253 INFO @ Fri, 05 Jul 2019 18:48:15: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 18:48:15: #1 finished! INFO @ Fri, 05 Jul 2019 18:48:15: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:48:15: #2 number of paired peaks: 2 WARNING @ Fri, 05 Jul 2019 18:48:15: 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 18:48:15: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.05_peaks.narrowPeak: No such file or directory INFO @ Fri, 05 Jul 2019 18:48:16: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:48:16: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:48:16: #1 total tags in treatment: 1189072 INFO @ Fri, 05 Jul 2019 18:48:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:48:16: #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 18:48:16: #1 tags after filtering in treatment: 947253 INFO @ Fri, 05 Jul 2019 18:48:16: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 18:48:16: #1 finished! INFO @ Fri, 05 Jul 2019 18:48:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:48:16: #2 number of paired peaks: 2 WARNING @ Fri, 05 Jul 2019 18:48:16: 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 18:48:16: Process for pairing-model is terminated! INFO @ Fri, 05 Jul 2019 18:48:16: 2000000 cut: /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.10_peaks.narrowPeak: No such file or directory pass1 - making usageList (0 chroms): 879 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.05_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.05_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.05_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.10_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.10_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.10_peaks.narrowPeak’: No such file or directory CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 18:48:21: #1 tag size is determined as 94 bps INFO @ Fri, 05 Jul 2019 18:48:21: #1 tag size = 94 INFO @ Fri, 05 Jul 2019 18:48:21: #1 total tags in treatment: 1189072 INFO @ Fri, 05 Jul 2019 18:48:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 18:48:21: #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 18:48:21: #1 tags after filtering in treatment: 947253 INFO @ Fri, 05 Jul 2019 18:48:21: #1 Redundant rate of treatment: 0.20 INFO @ Fri, 05 Jul 2019 18:48:21: #1 finished! INFO @ Fri, 05 Jul 2019 18:48:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 18:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 18:48:21: #2 number of paired peaks: 2 WARNING @ Fri, 05 Jul 2019 18:48:21: 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 18:48:21: Process for pairing-model is terminated! cut: /home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.20_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/ERX585849/ERX585849.20_model.r’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.20_*.xls’: No such file or directory rm: cannot remove ‘/home/okishinya/chipatlas/results/sacCer3/ERX585849/ERX585849.20_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。