Job ID = 11296943 sra ファイルのダウンロード中... Completed: 5378K bytes transferred in 2 seconds (16973K 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 282469 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856357/SRR6908174.sra Written 282469 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856357/SRR6908174.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: 00:00:04 282469 reads; of these: 282469 (100.00%) were unpaired; of these: 21755 (7.70%) aligned 0 times 207909 (73.60%) aligned exactly 1 time 52805 (18.69%) aligned >1 times 92.30% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 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] 14777 / 260714 = 0.0567 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 @ Mon, 05 Nov 2018 17:58:30: # Command line: callpeak -t SRX3856357.bam -f BAM -g 12100000 -n SRX3856357.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856357.20 # format = BAM # ChIP-seq file = ['SRX3856357.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 @ Mon, 05 Nov 2018 17:58:30: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:30: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:30: # Command line: callpeak -t SRX3856357.bam -f BAM -g 12100000 -n SRX3856357.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856357.05 # format = BAM # ChIP-seq file = ['SRX3856357.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 @ Mon, 05 Nov 2018 17:58:30: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:30: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:30: # Command line: callpeak -t SRX3856357.bam -f BAM -g 12100000 -n SRX3856357.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856357.10 # format = BAM # ChIP-seq file = ['SRX3856357.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 @ Mon, 05 Nov 2018 17:58:30: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:30: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:32: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:32: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:32: #1 total tags in treatment: 245937 INFO @ Mon, 05 Nov 2018 17:58:32: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:32: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:32: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:32: #1 total tags in treatment: 245937 INFO @ Mon, 05 Nov 2018 17:58:32: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:32: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:32: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:32: #1 total tags in treatment: 245937 INFO @ Mon, 05 Nov 2018 17:58:32: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:32: #1 tags after filtering in treatment: 245937 INFO @ Mon, 05 Nov 2018 17:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:32: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:32: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:32: #1 tags after filtering in treatment: 245937 INFO @ Mon, 05 Nov 2018 17:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:32: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:32: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:32: #1 tags after filtering in treatment: 245937 INFO @ Mon, 05 Nov 2018 17:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:32: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:32: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:32: #2 number of paired peaks: 54 WARNING @ Mon, 05 Nov 2018 17:58:32: Too few paired peaks (54) 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 @ Mon, 05 Nov 2018 17:58:32: Process for pairing-model is terminated! INFO @ Mon, 05 Nov 2018 17:58:32: #2 number of paired peaks: 54 WARNING @ Mon, 05 Nov 2018 17:58:32: Too few paired peaks (54) 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 @ Mon, 05 Nov 2018 17:58:32: Process for pairing-model is terminated! INFO @ Mon, 05 Nov 2018 17:58:32: #2 number of paired peaks: 54 WARNING @ Mon, 05 Nov 2018 17:58:32: Too few paired peaks (54) 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 @ Mon, 05 Nov 2018 17:58:32: Process for pairing-model is terminated! cat: SRX3856357.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3856357.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX3856357.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856357.10_model.r': そのようなファイルやディレクトリはありません pass1 - making usageList (0 chroms): 1 millis rm: cannot remove `SRX3856357.10_*.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 `SRX3856357.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis rm: cannot remove `SRX3856357.20_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 `SRX3856357.20_*.xls': そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856357.20_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 rm: cannot remove `SRX3856357.05_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 `SRX3856357.05_*.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 `SRX3856357.05_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。