Job ID = 11244851 sra ファイルのダウンロード中... Completed: 195635K bytes transferred in 4 seconds (323169K 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 7720485 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732408/SRR6759919.sra Written 7720485 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732408/SRR6759919.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: 00:01:23 7720485 reads; of these: 7720485 (100.00%) were unpaired; of these: 274078 (3.55%) aligned 0 times 5681265 (73.59%) aligned exactly 1 time 1765142 (22.86%) aligned >1 times 96.45% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 2920043 / 7446407 = 0.3921 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 @ Tue, 09 Oct 2018 22:09:12: # Command line: callpeak -t SRX3732408.bam -f BAM -g 12100000 -n SRX3732408.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3732408.05 # format = BAM # ChIP-seq file = ['SRX3732408.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 @ Tue, 09 Oct 2018 22:09:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:09:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:09:12: # Command line: callpeak -t SRX3732408.bam -f BAM -g 12100000 -n SRX3732408.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3732408.20 # format = BAM # ChIP-seq file = ['SRX3732408.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 @ Tue, 09 Oct 2018 22:09:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:09:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:09:12: # Command line: callpeak -t SRX3732408.bam -f BAM -g 12100000 -n SRX3732408.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3732408.10 # format = BAM # ChIP-seq file = ['SRX3732408.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 @ Tue, 09 Oct 2018 22:09:12: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:09:12: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:09:19: 1000000 INFO @ Tue, 09 Oct 2018 22:09:19: 1000000 INFO @ Tue, 09 Oct 2018 22:09:19: 1000000 INFO @ Tue, 09 Oct 2018 22:09:26: 2000000 INFO @ Tue, 09 Oct 2018 22:09:26: 2000000 INFO @ Tue, 09 Oct 2018 22:09:26: 2000000 INFO @ Tue, 09 Oct 2018 22:09:33: 3000000 INFO @ Tue, 09 Oct 2018 22:09:34: 3000000 INFO @ Tue, 09 Oct 2018 22:09:34: 3000000 INFO @ Tue, 09 Oct 2018 22:09:41: 4000000 INFO @ Tue, 09 Oct 2018 22:09:41: 4000000 INFO @ Tue, 09 Oct 2018 22:09:41: 4000000 INFO @ Tue, 09 Oct 2018 22:09:44: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:09:44: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:09:44: #1 total tags in treatment: 4526364 INFO @ Tue, 09 Oct 2018 22:09:44: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:09:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:09:44: #1 tags after filtering in treatment: 4526364 INFO @ Tue, 09 Oct 2018 22:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:09:44: #1 finished! INFO @ Tue, 09 Oct 2018 22:09:44: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:09:45: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:09:45: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:09:45: #1 total tags in treatment: 4526364 INFO @ Tue, 09 Oct 2018 22:09:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:09:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:09:45: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:09:45: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:09:45: #1 total tags in treatment: 4526364 INFO @ Tue, 09 Oct 2018 22:09:45: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:09:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:09:45: #1 tags after filtering in treatment: 4526364 INFO @ Tue, 09 Oct 2018 22:09:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:09:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:09:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:09:45: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 22:09:45: Too few paired peaks (28) 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 @ Tue, 09 Oct 2018 22:09:45: Process for pairing-model is terminated! cat: SRX3732408.20_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): 2 millis INFO @ Tue, 09 Oct 2018 22:09:45: #1 tags after filtering in treatment: 4526364 INFO @ Tue, 09 Oct 2018 22:09:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:09:45: #1 finished! INFO @ Tue, 09 Oct 2018 22:09:45: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:09:45: #2 looking for paired plus/minus strand peaks... needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3732408.20_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 `SRX3732408.20_*.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 `SRX3732408.20_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 @ Tue, 09 Oct 2018 22:09:45: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 22:09:45: Too few paired peaks (28) 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 @ Tue, 09 Oct 2018 22:09:45: Process for pairing-model is terminated! cat: SRX3732408.05_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 `SRX3732408.05_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 `SRX3732408.05_*.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 `SRX3732408.05_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 INFO @ Tue, 09 Oct 2018 22:09:45: #2 number of paired peaks: 28 WARNING @ Tue, 09 Oct 2018 22:09:45: Too few paired peaks (28) 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 @ Tue, 09 Oct 2018 22:09:45: Process for pairing-model is terminated! cat: SRX3732408.10_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 `SRX3732408.10_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 `SRX3732408.10_*.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 `SRX3732408.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。