Job ID = 11296928 sra ファイルのダウンロード中... Completed: 192738K bytes transferred in 5 seconds (300066K 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 9812701 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856343/SRR6908160.sra Written 9812701 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856343/SRR6908160.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: 00:01:39 9812701 reads; of these: 9812701 (100.00%) were unpaired; of these: 369192 (3.76%) aligned 0 times 7961481 (81.13%) aligned exactly 1 time 1482028 (15.10%) aligned >1 times 96.24% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 2570663 / 9443509 = 0.2722 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 17:59:17: # Command line: callpeak -t SRX3856343.bam -f BAM -g 12100000 -n SRX3856343.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856343.05 # format = BAM # ChIP-seq file = ['SRX3856343.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 17:59:17: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:59:17: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:59:17: # Command line: callpeak -t SRX3856343.bam -f BAM -g 12100000 -n SRX3856343.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856343.10 # format = BAM # ChIP-seq file = ['SRX3856343.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 17:59:17: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:59:17: # Command line: callpeak -t SRX3856343.bam -f BAM -g 12100000 -n SRX3856343.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856343.20 # format = BAM # ChIP-seq file = ['SRX3856343.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 17:59:17: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:59:17: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:59:17: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:59:24: 1000000 INFO @ Mon, 05 Nov 2018 17:59:25: 1000000 INFO @ Mon, 05 Nov 2018 17:59:25: 1000000 INFO @ Mon, 05 Nov 2018 17:59:31: 2000000 INFO @ Mon, 05 Nov 2018 17:59:32: 2000000 INFO @ Mon, 05 Nov 2018 17:59:32: 2000000 INFO @ Mon, 05 Nov 2018 17:59:38: 3000000 INFO @ Mon, 05 Nov 2018 17:59:39: 3000000 INFO @ Mon, 05 Nov 2018 17:59:39: 3000000 INFO @ Mon, 05 Nov 2018 17:59:45: 4000000 INFO @ Mon, 05 Nov 2018 17:59:46: 4000000 INFO @ Mon, 05 Nov 2018 17:59:46: 4000000 INFO @ Mon, 05 Nov 2018 17:59:52: 5000000 INFO @ Mon, 05 Nov 2018 17:59:53: 5000000 INFO @ Mon, 05 Nov 2018 17:59:53: 5000000 INFO @ Mon, 05 Nov 2018 17:59:59: 6000000 INFO @ Mon, 05 Nov 2018 18:00:01: 6000000 INFO @ Mon, 05 Nov 2018 18:00:01: 6000000 INFO @ Mon, 05 Nov 2018 18:00:05: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:00:05: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:00:05: #1 total tags in treatment: 6872846 INFO @ Mon, 05 Nov 2018 18:00:05: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:00:05: #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 18:00:05: #1 tags after filtering in treatment: 6872846 INFO @ Mon, 05 Nov 2018 18:00:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:00:05: #1 finished! INFO @ Mon, 05 Nov 2018 18:00:05: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:00:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:00:05: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:00:05: Too few paired peaks (0) 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 18:00:05: Process for pairing-model is terminated! cat: SRX3856343.05_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 `SRX3856343.05_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 `SRX3856343.05_*.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 `SRX3856343.05_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 @ Mon, 05 Nov 2018 18:00:07: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:00:07: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:00:07: #1 total tags in treatment: 6872846 INFO @ Mon, 05 Nov 2018 18:00:07: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:00:07: #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 18:00:07: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 18:00:07: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 18:00:07: #1 total tags in treatment: 6872846 INFO @ Mon, 05 Nov 2018 18:00:07: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 18:00:07: #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 18:00:07: #1 tags after filtering in treatment: 6872846 INFO @ Mon, 05 Nov 2018 18:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:00:07: #1 finished! INFO @ Mon, 05 Nov 2018 18:00:07: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:00:07: #1 tags after filtering in treatment: 6872846 INFO @ Mon, 05 Nov 2018 18:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 18:00:07: #1 finished! INFO @ Mon, 05 Nov 2018 18:00:07: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 18:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 18:00:07: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:00:07: Too few paired peaks (0) 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 18:00:07: Process for pairing-model is terminated! cat: SRX3856343.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Mon, 05 Nov 2018 18:00:07: #2 number of paired peaks: 0 WARNING @ Mon, 05 Nov 2018 18:00:07: Too few paired peaks (0) 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 18:00:07: Process for pairing-model is terminated! rm: cannot remove `SRX3856343.20_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 `SRX3856343.20_*.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 `SRX3856343.20_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 cat: SRX3856343.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856343.10_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 `SRX3856343.10_*.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 `SRX3856343.10_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。