Job ID = 11296914 sra ファイルのダウンロード中... Completed: 104676K bytes transferred in 4 seconds (210936K 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 6513116 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856329/SRR6908146.sra Written 6513116 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856329/SRR6908146.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: 00:01:05 6513116 reads; of these: 6513116 (100.00%) were unpaired; of these: 273423 (4.20%) aligned 0 times 5122881 (78.65%) aligned exactly 1 time 1116812 (17.15%) aligned >1 times 95.80% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 1465807 / 6239693 = 0.2349 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 17:55:33: # Command line: callpeak -t SRX3856329.bam -f BAM -g 12100000 -n SRX3856329.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856329.10 # format = BAM # ChIP-seq file = ['SRX3856329.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 17:55:33: # Command line: callpeak -t SRX3856329.bam -f BAM -g 12100000 -n SRX3856329.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856329.20 # format = BAM # ChIP-seq file = ['SRX3856329.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 17:55:33: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:55:33: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:55:33: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:55:33: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:55:33: # Command line: callpeak -t SRX3856329.bam -f BAM -g 12100000 -n SRX3856329.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856329.05 # format = BAM # ChIP-seq file = ['SRX3856329.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 17:55:33: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:55:33: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:55:39: 1000000 INFO @ Mon, 05 Nov 2018 17:55:40: 1000000 INFO @ Mon, 05 Nov 2018 17:55:40: 1000000 INFO @ Mon, 05 Nov 2018 17:55:46: 2000000 INFO @ Mon, 05 Nov 2018 17:55:46: 2000000 INFO @ Mon, 05 Nov 2018 17:55:47: 2000000 INFO @ Mon, 05 Nov 2018 17:55:53: 3000000 INFO @ Mon, 05 Nov 2018 17:55:53: 3000000 INFO @ Mon, 05 Nov 2018 17:55:54: 3000000 INFO @ Mon, 05 Nov 2018 17:56:00: 4000000 INFO @ Mon, 05 Nov 2018 17:56:00: 4000000 INFO @ Mon, 05 Nov 2018 17:56:02: 4000000 INFO @ Mon, 05 Nov 2018 17:56:05: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:56:05: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:56:05: #1 total tags in treatment: 4773886 INFO @ Mon, 05 Nov 2018 17:56:05: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:56:05: #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 17:56:05: #1 tags after filtering in treatment: 4773886 INFO @ Mon, 05 Nov 2018 17:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:56:05: #1 finished! INFO @ Mon, 05 Nov 2018 17:56:05: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:56:05: #2 number of paired peaks: 29 WARNING @ Mon, 05 Nov 2018 17:56:05: Too few paired peaks (29) 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 17:56:05: Process for pairing-model is terminated! cat: SRX3856329.10_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 `SRX3856329.10_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 `SRX3856329.10_*.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 `SRX3856329.10_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 @ Mon, 05 Nov 2018 17:56:05: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:56:05: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:56:05: #1 total tags in treatment: 4773886 INFO @ Mon, 05 Nov 2018 17:56:05: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:56:05: #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 17:56:05: #1 tags after filtering in treatment: 4773886 INFO @ Mon, 05 Nov 2018 17:56:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:56:05: #1 finished! INFO @ Mon, 05 Nov 2018 17:56:05: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:56:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:56:06: #2 number of paired peaks: 29 WARNING @ Mon, 05 Nov 2018 17:56:06: Too few paired peaks (29) 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 17:56:06: Process for pairing-model is terminated! cat: SRX3856329.05_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 `SRX3856329.05_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 `SRX3856329.05_*.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 `SRX3856329.05_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 17:56:07: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:56:07: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:56:07: #1 total tags in treatment: 4773886 INFO @ Mon, 05 Nov 2018 17:56:07: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:56:07: #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 17:56:07: #1 tags after filtering in treatment: 4773886 INFO @ Mon, 05 Nov 2018 17:56:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:56:07: #1 finished! INFO @ Mon, 05 Nov 2018 17:56:07: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:56:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:56:07: #2 number of paired peaks: 29 WARNING @ Mon, 05 Nov 2018 17:56:07: Too few paired peaks (29) 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 17:56:07: Process for pairing-model is terminated! cat: SRX3856329.20_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 `SRX3856329.20_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 `SRX3856329.20_*.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 `SRX3856329.20_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。