Job ID = 10254385 sra ファイルのダウンロード中... Completed: 185599K bytes transferred in 5 seconds (269466K 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 6199518 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2588005/SRR5284433.sra Written 6199518 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: 00:01:25 6199518 reads; of these: 6199518 (100.00%) were unpaired; of these: 2532618 (40.85%) aligned 0 times 3370981 (54.37%) aligned exactly 1 time 295919 (4.77%) aligned >1 times 59.15% overall alignment rate Time searching: 00:01:25 Overall time: 00:01:25 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] 1636427 / 3666900 = 0.4463 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 17:44:13: # Command line: callpeak -t SRX2588005.bam -f BAM -g 12100000 -n SRX2588005.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2588005.10 # format = BAM # ChIP-seq file = ['SRX2588005.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 17:44:13: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:44:13: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:44:13: # Command line: callpeak -t SRX2588005.bam -f BAM -g 12100000 -n SRX2588005.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2588005.05 # format = BAM # ChIP-seq file = ['SRX2588005.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 17:44:13: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:44:13: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:44:13: # Command line: callpeak -t SRX2588005.bam -f BAM -g 12100000 -n SRX2588005.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2588005.20 # format = BAM # ChIP-seq file = ['SRX2588005.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 17:44:13: #1 read tag files... INFO @ Wed, 06 Dec 2017 17:44:13: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 17:44:20: 1000000 INFO @ Wed, 06 Dec 2017 17:44:21: 1000000 INFO @ Wed, 06 Dec 2017 17:44:21: 1000000 INFO @ Wed, 06 Dec 2017 17:44:27: 2000000 INFO @ Wed, 06 Dec 2017 17:44:27: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:44:27: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:44:27: #1 total tags in treatment: 2030473 INFO @ Wed, 06 Dec 2017 17:44:27: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:44:27: #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 17:44:27: #1 tags after filtering in treatment: 2030473 INFO @ Wed, 06 Dec 2017 17:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:44:27: #1 finished! INFO @ Wed, 06 Dec 2017 17:44:27: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:44:27: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 17:44:27: 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 17:44:27: Process for pairing-model is terminated! cat: SRX2588005.10_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 `SRX2588005.10_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 `SRX2588005.10_*.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 `SRX2588005.10_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 17:44:28: 2000000 INFO @ Wed, 06 Dec 2017 17:44:28: 2000000 INFO @ Wed, 06 Dec 2017 17:44:29: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:44:29: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:44:29: #1 total tags in treatment: 2030473 INFO @ Wed, 06 Dec 2017 17:44:29: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:44:29: #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 17:44:29: #1 tag size is determined as 50 bps INFO @ Wed, 06 Dec 2017 17:44:29: #1 tag size = 50 INFO @ Wed, 06 Dec 2017 17:44:29: #1 total tags in treatment: 2030473 INFO @ Wed, 06 Dec 2017 17:44:29: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 17:44:29: #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 17:44:29: #1 tags after filtering in treatment: 2030473 INFO @ Wed, 06 Dec 2017 17:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:44:29: #1 finished! INFO @ Wed, 06 Dec 2017 17:44:29: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:44:29: #1 tags after filtering in treatment: 2030473 INFO @ Wed, 06 Dec 2017 17:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 17:44:29: #1 finished! INFO @ Wed, 06 Dec 2017 17:44:29: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 17:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 17:44:29: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 17:44:29: 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 17:44:29: Process for pairing-model is terminated! INFO @ Wed, 06 Dec 2017 17:44:29: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 17:44:29: 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 17:44:29: Process for pairing-model is terminated! cat: SRX2588005.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX2588005.05_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 `SRX2588005.20_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 `SRX2588005.20_*.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 `SRX2588005.20_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 CompletedMACS2peakCalling needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2588005.05_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 `SRX2588005.05_*.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 `SRX2588005.05_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。