Job ID = 9384010 sra ファイルのダウンロード中... Completed: 243569K bytes transferred in 9 seconds (221468K 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 7597725 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2174500/SRR4254728.sra Written 7597725 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: 00:01:21 7597725 reads; of these: 7597725 (100.00%) were unpaired; of these: 516100 (6.79%) aligned 0 times 6057534 (79.73%) aligned exactly 1 time 1024091 (13.48%) aligned >1 times 93.21% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 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] 2934820 / 7081625 = 0.4144 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 @ Sat, 05 Aug 2017 23:58:09: # Command line: callpeak -t SRX2174500.bam -f BAM -g 12100000 -n SRX2174500.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2174500.20 # format = BAM # ChIP-seq file = ['SRX2174500.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 @ Sat, 05 Aug 2017 23:58:09: #1 read tag files... INFO @ Sat, 05 Aug 2017 23:58:09: #1 read treatment tags... INFO @ Sat, 05 Aug 2017 23:58:09: # Command line: callpeak -t SRX2174500.bam -f BAM -g 12100000 -n SRX2174500.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2174500.05 # format = BAM # ChIP-seq file = ['SRX2174500.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 @ Sat, 05 Aug 2017 23:58:09: #1 read tag files... INFO @ Sat, 05 Aug 2017 23:58:09: #1 read treatment tags... INFO @ Sat, 05 Aug 2017 23:58:09: # Command line: callpeak -t SRX2174500.bam -f BAM -g 12100000 -n SRX2174500.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2174500.10 # format = BAM # ChIP-seq file = ['SRX2174500.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 @ Sat, 05 Aug 2017 23:58:09: #1 read tag files... INFO @ Sat, 05 Aug 2017 23:58:09: #1 read treatment tags... INFO @ Sat, 05 Aug 2017 23:58:16: 1000000 INFO @ Sat, 05 Aug 2017 23:58:16: 1000000 INFO @ Sat, 05 Aug 2017 23:58:16: 1000000 INFO @ Sat, 05 Aug 2017 23:58:22: 2000000 INFO @ Sat, 05 Aug 2017 23:58:22: 2000000 INFO @ Sat, 05 Aug 2017 23:58:22: 2000000 INFO @ Sat, 05 Aug 2017 23:58:28: 3000000 INFO @ Sat, 05 Aug 2017 23:58:28: 3000000 INFO @ Sat, 05 Aug 2017 23:58:29: 3000000 INFO @ Sat, 05 Aug 2017 23:58:35: 4000000 INFO @ Sat, 05 Aug 2017 23:58:35: 4000000 INFO @ Sat, 05 Aug 2017 23:58:35: 4000000 INFO @ Sat, 05 Aug 2017 23:58:36: #1 tag size is determined as 51 bps INFO @ Sat, 05 Aug 2017 23:58:36: #1 tag size = 51 INFO @ Sat, 05 Aug 2017 23:58:36: #1 total tags in treatment: 4146805 INFO @ Sat, 05 Aug 2017 23:58:36: #1 user defined the maximum tags... INFO @ Sat, 05 Aug 2017 23:58:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 05 Aug 2017 23:58:36: #1 tag size is determined as 51 bps INFO @ Sat, 05 Aug 2017 23:58:36: #1 tag size = 51 INFO @ Sat, 05 Aug 2017 23:58:36: #1 total tags in treatment: 4146805 INFO @ Sat, 05 Aug 2017 23:58:36: #1 user defined the maximum tags... INFO @ Sat, 05 Aug 2017 23:58:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 05 Aug 2017 23:58:36: #1 tags after filtering in treatment: 4146805 INFO @ Sat, 05 Aug 2017 23:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 05 Aug 2017 23:58:36: #1 finished! INFO @ Sat, 05 Aug 2017 23:58:36: #2 Build Peak Model... INFO @ Sat, 05 Aug 2017 23:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 05 Aug 2017 23:58:36: #1 tags after filtering in treatment: 4146805 INFO @ Sat, 05 Aug 2017 23:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 05 Aug 2017 23:58:36: #1 finished! INFO @ Sat, 05 Aug 2017 23:58:36: #2 Build Peak Model... INFO @ Sat, 05 Aug 2017 23:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 05 Aug 2017 23:58:36: #2 number of paired peaks: 27 WARNING @ Sat, 05 Aug 2017 23:58:36: 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 @ Sat, 05 Aug 2017 23:58:36: Process for pairing-model is terminated! cat: SRX2174500.10_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 `SRX2174500.10_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 `SRX2174500.10_*.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 `SRX2174500.10_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 @ Sat, 05 Aug 2017 23:58:36: #2 number of paired peaks: 27 WARNING @ Sat, 05 Aug 2017 23:58:36: 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 @ Sat, 05 Aug 2017 23:58:36: Process for pairing-model is terminated! cat: SRX2174500.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Sat, 05 Aug 2017 23:58:36: #1 tag size is determined as 51 bps INFO @ Sat, 05 Aug 2017 23:58:36: #1 tag size = 51 INFO @ Sat, 05 Aug 2017 23:58:36: #1 total tags in treatment: 4146805 INFO @ Sat, 05 Aug 2017 23:58:36: #1 user defined the maximum tags... INFO @ Sat, 05 Aug 2017 23:58:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2174500.05_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 `SRX2174500.05_*.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 `SRX2174500.05_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 INFO @ Sat, 05 Aug 2017 23:58:36: #1 tags after filtering in treatment: 4146805 INFO @ Sat, 05 Aug 2017 23:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 05 Aug 2017 23:58:36: #1 finished! INFO @ Sat, 05 Aug 2017 23:58:36: #2 Build Peak Model... INFO @ Sat, 05 Aug 2017 23:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 05 Aug 2017 23:58:36: #2 number of paired peaks: 27 WARNING @ Sat, 05 Aug 2017 23:58:36: 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 @ Sat, 05 Aug 2017 23:58:36: Process for pairing-model is terminated! cat: SRX2174500.20_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 `SRX2174500.20_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 `SRX2174500.20_*.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 `SRX2174500.20_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。