Job ID = 9160042 sra ファイルのダウンロード中... Completed: 17673K bytes transferred in 3 seconds (45973K 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: PAIRED fastq に変換中... Written 582711 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2574979/SRR5270928.sra Written 582711 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: 00:00:13 582711 reads; of these: 582711 (100.00%) were paired; of these: 264901 (45.46%) aligned concordantly 0 times 223572 (38.37%) aligned concordantly exactly 1 time 94238 (16.17%) aligned concordantly >1 times ---- 264901 pairs aligned concordantly 0 times; of these: 1572 (0.59%) aligned discordantly 1 time ---- 263329 pairs aligned 0 times concordantly or discordantly; of these: 526658 mates make up the pairs; of these: 516395 (98.05%) aligned 0 times 4884 (0.93%) aligned exactly 1 time 5379 (1.02%) aligned >1 times 55.69% overall alignment rate Time searching: 00:00:13 Overall time: 00:00:13 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 3151 / 319163 = 0.0099 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 01:45:01: # Command line: callpeak -t SRX2574979.bam -f BAM -g 12100000 -n SRX2574979.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2574979.05 # format = BAM # ChIP-seq file = ['SRX2574979.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 01:45:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:01: # Command line: callpeak -t SRX2574979.bam -f BAM -g 12100000 -n SRX2574979.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2574979.10 # format = BAM # ChIP-seq file = ['SRX2574979.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 01:45:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:01: # Command line: callpeak -t SRX2574979.bam -f BAM -g 12100000 -n SRX2574979.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2574979.20 # format = BAM # ChIP-seq file = ['SRX2574979.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 01:45:01: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:45:01: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:45:05: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:05: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:05: #1 total tags in treatment: 314662 INFO @ Wed, 28 Jun 2017 01:45:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:05: #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 01:45:05: #1 tags after filtering in treatment: 269214 INFO @ Wed, 28 Jun 2017 01:45:05: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 01:45:05: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:05: #2 number of paired peaks: 27 WARNING @ Wed, 28 Jun 2017 01:45:05: 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 01:45:05: Process for pairing-model is terminated! cat: SRX2574979.10_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 `SRX2574979.10_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 `SRX2574979.10_*.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 `SRX2574979.10_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 01:45:05: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:05: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:05: #1 total tags in treatment: 314662 INFO @ Wed, 28 Jun 2017 01:45:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:05: #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 01:45:05: #1 tag size is determined as 26 bps INFO @ Wed, 28 Jun 2017 01:45:05: #1 tag size = 26 INFO @ Wed, 28 Jun 2017 01:45:05: #1 total tags in treatment: 314662 INFO @ Wed, 28 Jun 2017 01:45:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:45:05: #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 01:45:05: #1 tags after filtering in treatment: 269214 INFO @ Wed, 28 Jun 2017 01:45:05: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 01:45:05: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:05: #1 tags after filtering in treatment: 269214 INFO @ Wed, 28 Jun 2017 01:45:05: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 28 Jun 2017 01:45:05: #1 finished! INFO @ Wed, 28 Jun 2017 01:45:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:45:05: #2 number of paired peaks: 27 WARNING @ Wed, 28 Jun 2017 01:45:05: 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 01:45:05: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 01:45:05: #2 number of paired peaks: 27 WARNING @ Wed, 28 Jun 2017 01:45:05: 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 01:45:05: Process for pairing-model is terminated! cat: SRX2574979.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX2574979.20_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 `SRX2574979.05_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 `SRX2574979.05_*.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 `SRX2574979.05_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 pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2574979.20_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 `SRX2574979.20_*.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 `SRX2574979.20_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。