Job ID = 9162311 sra ファイルのダウンロード中... Completed: 631170K bytes transferred in 11 seconds (440039K 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 5088790 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1872758/SRR3713231.sra Written 5088790 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: 00:03:54 5088790 reads; of these: 5088790 (100.00%) were paired; of these: 3005954 (59.07%) aligned concordantly 0 times 1685931 (33.13%) aligned concordantly exactly 1 time 396905 (7.80%) aligned concordantly >1 times ---- 3005954 pairs aligned concordantly 0 times; of these: 100374 (3.34%) aligned discordantly 1 time ---- 2905580 pairs aligned 0 times concordantly or discordantly; of these: 5811160 mates make up the pairs; of these: 5714680 (98.34%) aligned 0 times 25590 (0.44%) aligned exactly 1 time 70890 (1.22%) aligned >1 times 43.85% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 1126767 / 2164652 = 0.5205 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 07:21:07: # Command line: callpeak -t SRX1872758.bam -f BAM -g 12100000 -n SRX1872758.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1872758.20 # format = BAM # ChIP-seq file = ['SRX1872758.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 07:21:07: # Command line: callpeak -t SRX1872758.bam -f BAM -g 12100000 -n SRX1872758.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1872758.10 # format = BAM # ChIP-seq file = ['SRX1872758.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 07:21:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:21:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:21:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:21:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:21:07: # Command line: callpeak -t SRX1872758.bam -f BAM -g 12100000 -n SRX1872758.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1872758.05 # format = BAM # ChIP-seq file = ['SRX1872758.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 07:21:07: #1 read tag files... INFO @ Wed, 28 Jun 2017 07:21:07: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 07:21:18: 1000000 INFO @ Wed, 28 Jun 2017 07:21:18: 1000000 INFO @ Wed, 28 Jun 2017 07:21:18: 1000000 INFO @ Wed, 28 Jun 2017 07:21:29: 2000000 INFO @ Wed, 28 Jun 2017 07:21:29: 2000000 INFO @ Wed, 28 Jun 2017 07:21:29: 2000000 INFO @ Wed, 28 Jun 2017 07:21:31: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:21:31: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:21:31: #1 total tags in treatment: 976562 INFO @ Wed, 28 Jun 2017 07:21:31: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:21:31: #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 07:21:31: #1 tags after filtering in treatment: 751444 INFO @ Wed, 28 Jun 2017 07:21:31: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 07:21:31: #1 finished! INFO @ Wed, 28 Jun 2017 07:21:31: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:21:31: #2 number of paired peaks: 42 WARNING @ Wed, 28 Jun 2017 07:21:31: Too few paired peaks (42) 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 07:21:31: Process for pairing-model is terminated! cat: SRX1872758.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX1872758.10_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 `SRX1872758.10_*.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 `SRX1872758.10_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 07:21:31: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:21:31: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:21:31: #1 total tags in treatment: 976562 INFO @ Wed, 28 Jun 2017 07:21:31: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:21:31: #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 07:21:31: #1 tags after filtering in treatment: 751444 INFO @ Wed, 28 Jun 2017 07:21:31: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 07:21:31: #1 finished! INFO @ Wed, 28 Jun 2017 07:21:31: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:21:31: #1 tag size is determined as 101 bps INFO @ Wed, 28 Jun 2017 07:21:31: #1 tag size = 101 INFO @ Wed, 28 Jun 2017 07:21:31: #1 total tags in treatment: 976562 INFO @ Wed, 28 Jun 2017 07:21:31: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 07:21:31: #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 07:21:31: #1 tags after filtering in treatment: 751444 INFO @ Wed, 28 Jun 2017 07:21:31: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 28 Jun 2017 07:21:31: #1 finished! INFO @ Wed, 28 Jun 2017 07:21:31: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 07:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 07:21:31: #2 number of paired peaks: 42 WARNING @ Wed, 28 Jun 2017 07:21:31: Too few paired peaks (42) 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 07:21:31: Process for pairing-model is terminated! cat: SRX1872758.20_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 `SRX1872758.20_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 `SRX1872758.20_*.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 `SRX1872758.20_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 07:21:31: #2 number of paired peaks: 42 WARNING @ Wed, 28 Jun 2017 07:21:31: Too few paired peaks (42) 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 07:21:31: Process for pairing-model is terminated! cat: SRX1872758.05_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 `SRX1872758.05_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 `SRX1872758.05_*.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 `SRX1872758.05_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。