Job ID = 9162516 sra ファイルのダウンロード中... Completed: 208244K bytes transferred in 5 seconds (330673K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 3501710 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360913/SRR1003635.sra Written 3501710 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:02:10 3501710 reads; of these: 3501710 (100.00%) were paired; of these: 1423533 (40.65%) aligned concordantly 0 times 1697028 (48.46%) aligned concordantly exactly 1 time 381149 (10.88%) aligned concordantly >1 times ---- 1423533 pairs aligned concordantly 0 times; of these: 31079 (2.18%) aligned discordantly 1 time ---- 1392454 pairs aligned 0 times concordantly or discordantly; of these: 2784908 mates make up the pairs; of these: 2666591 (95.75%) aligned 0 times 86044 (3.09%) aligned exactly 1 time 32273 (1.16%) aligned >1 times 61.92% overall alignment rate Time searching: 00:02:10 Overall time: 00:02:10 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] 594510 / 2095251 = 0.2837 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 @ Wed, 28 Jun 2017 08:04:24: # Command line: callpeak -t SRX360913.bam -f BAM -g 12100000 -n SRX360913.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360913.10 # format = BAM # ChIP-seq file = ['SRX360913.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 @ Wed, 28 Jun 2017 08:04:24: # Command line: callpeak -t SRX360913.bam -f BAM -g 12100000 -n SRX360913.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360913.05 # format = BAM # ChIP-seq file = ['SRX360913.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 @ Wed, 28 Jun 2017 08:04:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:04:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:04:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:04:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:04:24: # Command line: callpeak -t SRX360913.bam -f BAM -g 12100000 -n SRX360913.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360913.20 # format = BAM # ChIP-seq file = ['SRX360913.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 @ Wed, 28 Jun 2017 08:04:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:04:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:04:31: 1000000 INFO @ Wed, 28 Jun 2017 08:04:31: 1000000 INFO @ Wed, 28 Jun 2017 08:04:31: 1000000 INFO @ Wed, 28 Jun 2017 08:04:38: 2000000 INFO @ Wed, 28 Jun 2017 08:04:38: 2000000 INFO @ Wed, 28 Jun 2017 08:04:38: 2000000 INFO @ Wed, 28 Jun 2017 08:04:44: 3000000 INFO @ Wed, 28 Jun 2017 08:04:45: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:04:45: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:04:45: #1 total tags in treatment: 1490423 INFO @ Wed, 28 Jun 2017 08:04:45: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:04:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:04:45: #1 tags after filtering in treatment: 1298715 INFO @ Wed, 28 Jun 2017 08:04:45: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 28 Jun 2017 08:04:45: #1 finished! INFO @ Wed, 28 Jun 2017 08:04:45: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:04:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:04:45: #2 number of paired peaks: 55 WARNING @ Wed, 28 Jun 2017 08:04:45: Too few paired peaks (55) 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 @ Wed, 28 Jun 2017 08:04:45: Process for pairing-model is terminated! cat: SRX360913.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX360913.20_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX360913.20_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX360913.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 08:04:45: 3000000 INFO @ Wed, 28 Jun 2017 08:04:45: 3000000 INFO @ Wed, 28 Jun 2017 08:04:46: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:04:46: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:04:46: #1 total tags in treatment: 1490423 INFO @ Wed, 28 Jun 2017 08:04:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:04:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:04:46: #1 tags after filtering in treatment: 1298715 INFO @ Wed, 28 Jun 2017 08:04:46: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 28 Jun 2017 08:04:46: #1 finished! INFO @ Wed, 28 Jun 2017 08:04:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:04:46: #2 number of paired peaks: 55 WARNING @ Wed, 28 Jun 2017 08:04:46: Too few paired peaks (55) 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 @ Wed, 28 Jun 2017 08:04:46: Process for pairing-model is terminated! cat: SRX360913.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX360913.10_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX360913.10_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX360913.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 08:04:46: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:04:46: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:04:46: #1 total tags in treatment: 1490423 INFO @ Wed, 28 Jun 2017 08:04:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:04:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:04:46: #1 tags after filtering in treatment: 1298715 INFO @ Wed, 28 Jun 2017 08:04:46: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 28 Jun 2017 08:04:46: #1 finished! INFO @ Wed, 28 Jun 2017 08:04:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:04:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:04:46: #2 number of paired peaks: 55 WARNING @ Wed, 28 Jun 2017 08:04:46: Too few paired peaks (55) 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 @ Wed, 28 Jun 2017 08:04:46: Process for pairing-model is terminated! cat: SRX360913.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX360913.05_model.r': そのようなファイルやディレクトリはありません rm: cannot remove `SRX360913.05_*.xls': そのようなファイルやディレクトリはありません rm: cannot remove `SRX360913.05_peaks.narrowPeak': そのようなファイルやディレクトリはありません CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。