Job ID = 9161873 sra ファイルのダウンロード中... Completed: 483641K bytes transferred in 7 seconds (544798K bits/sec), in 1 file, 2 directories. 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 11288310 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1181999/SRR2239567.sra Written 11288310 spots total 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: 00:02:57 11288310 reads; of these: 11288310 (100.00%) were unpaired; of these: 318067 (2.82%) aligned 0 times 8732297 (77.36%) aligned exactly 1 time 2237946 (19.83%) aligned >1 times 97.18% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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_sort_core] merging from 8 files... [bam_rmdupse_core] 6477978 / 10970243 = 0.5905 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, 28 Jun 2017 04:56:08: # Command line: callpeak -t SRX1181999.bam -f BAM -g 12100000 -n SRX1181999.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1181999.05 # format = BAM # ChIP-seq file = ['SRX1181999.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, 28 Jun 2017 04:56:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:56:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:56:08: # Command line: callpeak -t SRX1181999.bam -f BAM -g 12100000 -n SRX1181999.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1181999.10 # format = BAM # ChIP-seq file = ['SRX1181999.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, 28 Jun 2017 04:56:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:56:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:56:08: # Command line: callpeak -t SRX1181999.bam -f BAM -g 12100000 -n SRX1181999.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1181999.20 # format = BAM # ChIP-seq file = ['SRX1181999.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, 28 Jun 2017 04:56:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:56:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:56:14: 1000000 INFO @ Wed, 28 Jun 2017 04:56:14: 1000000 INFO @ Wed, 28 Jun 2017 04:56:15: 1000000 INFO @ Wed, 28 Jun 2017 04:56:21: 2000000 INFO @ Wed, 28 Jun 2017 04:56:22: 2000000 INFO @ Wed, 28 Jun 2017 04:56:24: 2000000 INFO @ Wed, 28 Jun 2017 04:56:29: 3000000 INFO @ Wed, 28 Jun 2017 04:56:30: 3000000 INFO @ Wed, 28 Jun 2017 04:56:33: 3000000 INFO @ Wed, 28 Jun 2017 04:56:37: 4000000 INFO @ Wed, 28 Jun 2017 04:56:38: 4000000 INFO @ Wed, 28 Jun 2017 04:56:41: #1 tag size is determined as 49 bps INFO @ Wed, 28 Jun 2017 04:56:41: #1 tag size = 49 INFO @ Wed, 28 Jun 2017 04:56:41: #1 total tags in treatment: 4492265 INFO @ Wed, 28 Jun 2017 04:56:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:56:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:56:41: #1 tags after filtering in treatment: 4492265 INFO @ Wed, 28 Jun 2017 04:56:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:56:41: #1 finished! INFO @ Wed, 28 Jun 2017 04:56:41: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:56:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:56:42: #2 number of paired peaks: 27 WARNING @ Wed, 28 Jun 2017 04:56:42: Too few paired peaks (27) 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, 28 Jun 2017 04:56:42: Process for pairing-model is terminated! cat: SRX1181999.20_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) rm: cannot remove `SRX1181999.20_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 `SRX1181999.20_*.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 `SRX1181999.20_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, 28 Jun 2017 04:56:42: #1 tag size is determined as 49 bps INFO @ Wed, 28 Jun 2017 04:56:42: #1 tag size = 49 INFO @ Wed, 28 Jun 2017 04:56:42: #1 total tags in treatment: 4492265 INFO @ Wed, 28 Jun 2017 04:56:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:56:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:56:42: #1 tags after filtering in treatment: 4492265 INFO @ Wed, 28 Jun 2017 04:56:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:56:42: #1 finished! INFO @ Wed, 28 Jun 2017 04:56:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:56:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:56:43: #2 number of paired peaks: 27 WARNING @ Wed, 28 Jun 2017 04:56:43: Too few paired peaks (27) 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, 28 Jun 2017 04:56:43: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 04:56:43: 4000000 cat: SRX1181999.10_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 `SRX1181999.10_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 `SRX1181999.10_*.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 `SRX1181999.10_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, 28 Jun 2017 04:56:47: #1 tag size is determined as 49 bps INFO @ Wed, 28 Jun 2017 04:56:47: #1 tag size = 49 INFO @ Wed, 28 Jun 2017 04:56:47: #1 total tags in treatment: 4492265 INFO @ Wed, 28 Jun 2017 04:56:47: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:56:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 04:56:47: #1 tags after filtering in treatment: 4492265 INFO @ Wed, 28 Jun 2017 04:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:56:47: #1 finished! INFO @ Wed, 28 Jun 2017 04:56:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:56:47: #2 number of paired peaks: 27 WARNING @ Wed, 28 Jun 2017 04:56:47: Too few paired peaks (27) 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, 28 Jun 2017 04:56:47: Process for pairing-model is terminated! cat: SRX1181999.05_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 `SRX1181999.05_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 `SRX1181999.05_*.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 `SRX1181999.05_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。