Job ID = 9384078 sra ファイルのダウンロード中... Completed: 107042K bytes transferred in 5 seconds (173647K 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: SINGLE fastq に変換中... Written 3768054 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2767789/SRR5484580.sra Written 3768054 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: 00:00:56 3768054 reads; of these: 3768054 (100.00%) were unpaired; of these: 1038820 (27.57%) aligned 0 times 2282315 (60.57%) aligned exactly 1 time 446919 (11.86%) aligned >1 times 72.43% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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_rmdupse_core] 1180943 / 2729234 = 0.4327 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 @ Sun, 06 Aug 2017 00:30:11: # Command line: callpeak -t SRX2767789.bam -f BAM -g 12100000 -n SRX2767789.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2767789.05 # format = BAM # ChIP-seq file = ['SRX2767789.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 @ Sun, 06 Aug 2017 00:30:11: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:30:11: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:30:11: # Command line: callpeak -t SRX2767789.bam -f BAM -g 12100000 -n SRX2767789.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2767789.20 # format = BAM # ChIP-seq file = ['SRX2767789.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 @ Sun, 06 Aug 2017 00:30:11: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:30:11: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:30:11: # Command line: callpeak -t SRX2767789.bam -f BAM -g 12100000 -n SRX2767789.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2767789.10 # format = BAM # ChIP-seq file = ['SRX2767789.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 @ Sun, 06 Aug 2017 00:30:11: #1 read tag files... INFO @ Sun, 06 Aug 2017 00:30:11: #1 read treatment tags... INFO @ Sun, 06 Aug 2017 00:30:18: 1000000 INFO @ Sun, 06 Aug 2017 00:30:18: 1000000 INFO @ Sun, 06 Aug 2017 00:30:18: 1000000 INFO @ Sun, 06 Aug 2017 00:30:21: #1 tag size is determined as 50 bps INFO @ Sun, 06 Aug 2017 00:30:21: #1 tag size = 50 INFO @ Sun, 06 Aug 2017 00:30:21: #1 total tags in treatment: 1548291 INFO @ Sun, 06 Aug 2017 00:30:21: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:30:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:30:21: #1 tags after filtering in treatment: 1548291 INFO @ Sun, 06 Aug 2017 00:30:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 06 Aug 2017 00:30:21: #1 finished! INFO @ Sun, 06 Aug 2017 00:30:21: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:30:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:30:21: #2 number of paired peaks: 27 WARNING @ Sun, 06 Aug 2017 00:30:21: Too few paired peaks (27) 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 @ Sun, 06 Aug 2017 00:30:21: Process for pairing-model is terminated! cat: SRX2767789.10_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 `SRX2767789.10_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 `SRX2767789.10_*.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 `SRX2767789.10_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 @ Sun, 06 Aug 2017 00:30:22: #1 tag size is determined as 50 bps INFO @ Sun, 06 Aug 2017 00:30:22: #1 tag size = 50 INFO @ Sun, 06 Aug 2017 00:30:22: #1 total tags in treatment: 1548291 INFO @ Sun, 06 Aug 2017 00:30:22: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:30:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:30:22: #1 tags after filtering in treatment: 1548291 INFO @ Sun, 06 Aug 2017 00:30:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 06 Aug 2017 00:30:22: #1 finished! INFO @ Sun, 06 Aug 2017 00:30:22: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:30:22: #2 number of paired peaks: 27 WARNING @ Sun, 06 Aug 2017 00:30:22: Too few paired peaks (27) 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 @ Sun, 06 Aug 2017 00:30:22: Process for pairing-model is terminated! cat: SRX2767789.20_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 `SRX2767789.20_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 `SRX2767789.20_*.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 `SRX2767789.20_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 @ Sun, 06 Aug 2017 00:30:22: #1 tag size is determined as 50 bps INFO @ Sun, 06 Aug 2017 00:30:22: #1 tag size = 50 INFO @ Sun, 06 Aug 2017 00:30:22: #1 total tags in treatment: 1548291 INFO @ Sun, 06 Aug 2017 00:30:22: #1 user defined the maximum tags... INFO @ Sun, 06 Aug 2017 00:30:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 06 Aug 2017 00:30:22: #1 tags after filtering in treatment: 1548291 INFO @ Sun, 06 Aug 2017 00:30:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 06 Aug 2017 00:30:22: #1 finished! INFO @ Sun, 06 Aug 2017 00:30:22: #2 Build Peak Model... INFO @ Sun, 06 Aug 2017 00:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 06 Aug 2017 00:30:22: #2 number of paired peaks: 27 WARNING @ Sun, 06 Aug 2017 00:30:22: Too few paired peaks (27) 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 @ Sun, 06 Aug 2017 00:30:22: Process for pairing-model is terminated! cat: SRX2767789.05_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): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2767789.05_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 `SRX2767789.05_*.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 `SRX2767789.05_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。