Job ID = 10254335 sra ファイルのダウンロード中... Completed: 135650K bytes transferred in 4 seconds (232060K 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... Written 4549352 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2587960/SRR5284388.sra Written 4549352 spots total 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: 00:00:58 4549352 reads; of these: 4549352 (100.00%) were unpaired; of these: 2092740 (46.00%) aligned 0 times 2304304 (50.65%) aligned exactly 1 time 152308 (3.35%) aligned >1 times 54.00% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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] 1388507 / 2456612 = 0.5652 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, 06 Dec 2017 17:31:24: # Command line: callpeak -t SRX2587960.bam -f BAM -g 12100000 -n SRX2587960.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2587960.05 # format = BAM # ChIP-seq file = ['SRX2587960.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, 06 Dec 2017 17:31:24: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:31:24: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:31:24: # Command line: callpeak -t SRX2587960.bam -f BAM -g 12100000 -n SRX2587960.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2587960.20 # format = BAM # ChIP-seq file = ['SRX2587960.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, 06 Dec 2017 17:31:24: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:31:24: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:31:24: # Command line: callpeak -t SRX2587960.bam -f BAM -g 12100000 -n SRX2587960.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2587960.10 # format = BAM # ChIP-seq file = ['SRX2587960.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, 06 Dec 2017 17:31:24: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:31:24: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:31:31: 1000000 INFO @ Wed, 06 Dec 2017 17:31:31: 1000000 INFO @ Wed, 06 Dec 2017 17:31:31: 1000000 INFO @ Wed, 06 Dec 2017 17:31:31: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:31:31: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:31:31: #1 total tags in treatment: 1068105 INFO @ Wed, 06 Dec 2017 17:31:31: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 17:31:31: #1 tags after filtering in treatment: 1068105 INFO @ Wed, 06 Dec 2017 17:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:31:31: #1 finished! INFO @ Wed, 06 Dec 2017 17:31:31: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:31:31: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 17:31:31: 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 @ Wed, 06 Dec 2017 17:31:31: Process for pairing-model is terminated! cat: SRX2587960.10_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) INFO @ Wed, 06 Dec 2017 17:31:31: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:31:31: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:31:31: #1 total tags in treatment: 1068105 INFO @ Wed, 06 Dec 2017 17:31:31: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) rm: cannot remove `SRX2587960.10_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 `SRX2587960.10_*.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 `SRX2587960.10_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, 06 Dec 2017 17:31:31: #1 tags after filtering in treatment: 1068105 INFO @ Wed, 06 Dec 2017 17:31:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:31:31: #1 finished! INFO @ Wed, 06 Dec 2017 17:31:31: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:31:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:31:31: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:31:31: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:31:31: #1 total tags in treatment: 1068105 INFO @ Wed, 06 Dec 2017 17:31:31: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:31:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 17:31:32: #1 tags after filtering in treatment: 1068105 INFO @ Wed, 06 Dec 2017 17:31:32: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:31:32: #1 finished! INFO @ Wed, 06 Dec 2017 17:31:32: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:31:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:31:32: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 17:31:32: 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 @ Wed, 06 Dec 2017 17:31:32: Process for pairing-model is terminated! cat: SRX2587960.20_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 `SRX2587960.20_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 `SRX2587960.20_*.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 `SRX2587960.20_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, 06 Dec 2017 17:31:32: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 17:31:32: 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 @ Wed, 06 Dec 2017 17:31:32: Process for pairing-model is terminated! cat: SRX2587960.05_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 `SRX2587960.05_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 `SRX2587960.05_*.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 `SRX2587960.05_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。