Job ID = 10254456 sra ファイルのダウンロード中... Completed: 133047K bytes transferred in 5 seconds (199563K bits/sec), in 1 file. Completed: 117709K bytes transferred in 7 seconds (123828K 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 4625075 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353394/SRR6246263.sra Written 4625075 spots total Written 5229898 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353394/SRR6246262.sra Written 5229898 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 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: 00:01:29 9854973 reads; of these: 9854973 (100.00%) were unpaired; of these: 2961308 (30.05%) aligned 0 times 5754863 (58.40%) aligned exactly 1 time 1138802 (11.56%) aligned >1 times 69.95% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 2415432 / 6893665 = 0.3504 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 18:20:16: # Command line: callpeak -t SRX3353394.bam -f BAM -g 12100000 -n SRX3353394.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3353394.05 # format = BAM # ChIP-seq file = ['SRX3353394.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 18:20:16: # Command line: callpeak -t SRX3353394.bam -f BAM -g 12100000 -n SRX3353394.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3353394.20 # format = BAM # ChIP-seq file = ['SRX3353394.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 18:20:16: # Command line: callpeak -t SRX3353394.bam -f BAM -g 12100000 -n SRX3353394.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3353394.10 # format = BAM # ChIP-seq file = ['SRX3353394.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 18:20:16: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:20:16: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:20:16: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:20:16: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:20:16: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:20:16: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:20:22: 1000000 INFO @ Wed, 06 Dec 2017 18:20:22: 1000000 INFO @ Wed, 06 Dec 2017 18:20:22: 1000000 INFO @ Wed, 06 Dec 2017 18:20:28: 2000000 INFO @ Wed, 06 Dec 2017 18:20:29: 2000000 INFO @ Wed, 06 Dec 2017 18:20:29: 2000000 INFO @ Wed, 06 Dec 2017 18:20:34: 3000000 INFO @ Wed, 06 Dec 2017 18:20:35: 3000000 INFO @ Wed, 06 Dec 2017 18:20:35: 3000000 INFO @ Wed, 06 Dec 2017 18:20:40: 4000000 INFO @ Wed, 06 Dec 2017 18:20:41: 4000000 INFO @ Wed, 06 Dec 2017 18:20:41: 4000000 INFO @ Wed, 06 Dec 2017 18:20:42: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:20:42: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:20:42: #1 total tags in treatment: 4478233 INFO @ Wed, 06 Dec 2017 18:20:42: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:20:42: #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 18:20:42: #1 tags after filtering in treatment: 4478233 INFO @ Wed, 06 Dec 2017 18:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 18:20:42: #1 finished! INFO @ Wed, 06 Dec 2017 18:20:42: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:20:43: #2 number of paired peaks: 28 WARNING @ Wed, 06 Dec 2017 18:20:43: 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 @ Wed, 06 Dec 2017 18:20:43: Process for pairing-model is terminated! cat: SRX3353394.10_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 `SRX3353394.10_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 `SRX3353394.10_*.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 `SRX3353394.10_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 18:20:43: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:20:43: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:20:43: #1 total tags in treatment: 4478233 INFO @ Wed, 06 Dec 2017 18:20:43: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:20:43: #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 18:20:44: #1 tags after filtering in treatment: 4478233 INFO @ Wed, 06 Dec 2017 18:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 18:20:44: #1 finished! INFO @ Wed, 06 Dec 2017 18:20:44: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:20:44: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:20:44: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:20:44: #1 total tags in treatment: 4478233 INFO @ Wed, 06 Dec 2017 18:20:44: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:20:44: #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 18:20:44: #1 tags after filtering in treatment: 4478233 INFO @ Wed, 06 Dec 2017 18:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 18:20:44: #1 finished! INFO @ Wed, 06 Dec 2017 18:20:44: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:20:44: #2 number of paired peaks: 28 WARNING @ Wed, 06 Dec 2017 18:20:44: 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 @ Wed, 06 Dec 2017 18:20:44: Process for pairing-model is terminated! cat: SRX3353394.20_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 `SRX3353394.20_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 `SRX3353394.20_*.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 `SRX3353394.20_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 18:20:44: #2 number of paired peaks: 28 WARNING @ Wed, 06 Dec 2017 18:20:44: 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 @ Wed, 06 Dec 2017 18:20:44: Process for pairing-model is terminated! cat: SRX3353394.05_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 `SRX3353394.05_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 `SRX3353394.05_*.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 `SRX3353394.05_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。