Job ID = 11245243 sra ファイルのダウンロード中... Completed: 237057K bytes transferred in 4 seconds (395378K bits/sec), in 1 file. 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... Read 5542334 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733453/SRR7896008.sra Written 5542334 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4733453/SRR7896008.sra rm: cannot remove `[DSE]RX*': 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 `[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: 00:01:20 5542334 reads; of these: 5542334 (100.00%) were unpaired; of these: 1290558 (23.29%) aligned 0 times 2470839 (44.58%) aligned exactly 1 time 1780937 (32.13%) aligned >1 times 76.71% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 3801269 / 4251776 = 0.8940 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, 10 Oct 2018 00:03:22: # Command line: callpeak -t SRX4733453.bam -f BAM -g 12100000 -n SRX4733453.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4733453.20 # format = BAM # ChIP-seq file = ['SRX4733453.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, 10 Oct 2018 00:03:22: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:03:22: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:03:22: # Command line: callpeak -t SRX4733453.bam -f BAM -g 12100000 -n SRX4733453.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4733453.05 # format = BAM # ChIP-seq file = ['SRX4733453.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, 10 Oct 2018 00:03:22: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:03:22: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:03:22: # Command line: callpeak -t SRX4733453.bam -f BAM -g 12100000 -n SRX4733453.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4733453.10 # format = BAM # ChIP-seq file = ['SRX4733453.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, 10 Oct 2018 00:03:22: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:03:22: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:03:25: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:03:25: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:03:25: #1 total tags in treatment: 450507 INFO @ Wed, 10 Oct 2018 00:03:25: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:03:25: #1 tags after filtering in treatment: 450507 INFO @ Wed, 10 Oct 2018 00:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:25: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:25: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:25: #2 number of paired peaks: 97 WARNING @ Wed, 10 Oct 2018 00:03:25: Too few paired peaks (97) 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, 10 Oct 2018 00:03:25: Process for pairing-model is terminated! cat: SRX4733453.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Wed, 10 Oct 2018 00:03:25: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:03:25: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:03:25: #1 total tags in treatment: 450507 INFO @ Wed, 10 Oct 2018 00:03:25: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4733453.10_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 `SRX4733453.10_*.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 `SRX4733453.10_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, 10 Oct 2018 00:03:25: #1 tags after filtering in treatment: 450507 INFO @ Wed, 10 Oct 2018 00:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:25: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:25: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:25: #1 tag size is determined as 101 bps INFO @ Wed, 10 Oct 2018 00:03:25: #1 tag size = 101 INFO @ Wed, 10 Oct 2018 00:03:25: #1 total tags in treatment: 450507 INFO @ Wed, 10 Oct 2018 00:03:25: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:03:25: #1 tags after filtering in treatment: 450507 INFO @ Wed, 10 Oct 2018 00:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:03:25: #1 finished! INFO @ Wed, 10 Oct 2018 00:03:25: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:03:25: #2 number of paired peaks: 97 WARNING @ Wed, 10 Oct 2018 00:03:25: Too few paired peaks (97) 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, 10 Oct 2018 00:03:25: Process for pairing-model is terminated! cat: SRX4733453.20_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 `SRX4733453.20_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 `SRX4733453.20_*.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 `SRX4733453.20_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, 10 Oct 2018 00:03:26: #2 number of paired peaks: 97 WARNING @ Wed, 10 Oct 2018 00:03:26: Too few paired peaks (97) 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, 10 Oct 2018 00:03:26: Process for pairing-model is terminated! cat: SRX4733453.05_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 `SRX4733453.05_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 `SRX4733453.05_*.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 `SRX4733453.05_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。