Job ID = 11296941 sra ファイルのダウンロード中... Completed: 5563K bytes transferred in 2 seconds (18064K 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... Read 292992 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856355/SRR6908172.sra Written 292992 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856355/SRR6908172.sra 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: 00:00:04 292992 reads; of these: 292992 (100.00%) were unpaired; of these: 19450 (6.64%) aligned 0 times 209513 (71.51%) aligned exactly 1 time 64029 (21.85%) aligned >1 times 93.36% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 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] 23500 / 273542 = 0.0859 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 @ Mon, 05 Nov 2018 17:58:15: # Command line: callpeak -t SRX3856355.bam -f BAM -g 12100000 -n SRX3856355.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856355.10 # format = BAM # ChIP-seq file = ['SRX3856355.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 @ Mon, 05 Nov 2018 17:58:15: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:15: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:15: # Command line: callpeak -t SRX3856355.bam -f BAM -g 12100000 -n SRX3856355.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856355.05 # format = BAM # ChIP-seq file = ['SRX3856355.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 @ Mon, 05 Nov 2018 17:58:15: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:15: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:15: # Command line: callpeak -t SRX3856355.bam -f BAM -g 12100000 -n SRX3856355.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856355.20 # format = BAM # ChIP-seq file = ['SRX3856355.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 @ Mon, 05 Nov 2018 17:58:15: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:15: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:17: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:17: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:17: #1 total tags in treatment: 250042 INFO @ Mon, 05 Nov 2018 17:58:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:17: #1 tags after filtering in treatment: 250042 INFO @ Mon, 05 Nov 2018 17:58:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:17: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:17: #2 number of paired peaks: 43 WARNING @ Mon, 05 Nov 2018 17:58:17: Too few paired peaks (43) 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 @ Mon, 05 Nov 2018 17:58:17: Process for pairing-model is terminated! INFO @ Mon, 05 Nov 2018 17:58:17: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:17: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:17: #1 total tags in treatment: 250042 INFO @ Mon, 05 Nov 2018 17:58:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) cat: SRX3856355.05_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 @ Mon, 05 Nov 2018 17:58:17: #1 tags after filtering in treatment: 250042 INFO @ Mon, 05 Nov 2018 17:58:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:17: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:17: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856355.05_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 `SRX3856355.05_*.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 `SRX3856355.05_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 @ Mon, 05 Nov 2018 17:58:17: #2 number of paired peaks: 43 WARNING @ Mon, 05 Nov 2018 17:58:17: Too few paired peaks (43) 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 @ Mon, 05 Nov 2018 17:58:17: Process for pairing-model is terminated! cat: SRX3856355.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856355.10_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 `SRX3856355.10_*.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 `SRX3856355.10_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 @ Mon, 05 Nov 2018 17:58:17: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:17: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:17: #1 total tags in treatment: 250042 INFO @ Mon, 05 Nov 2018 17:58:17: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:17: #1 tags after filtering in treatment: 250042 INFO @ Mon, 05 Nov 2018 17:58:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:17: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:17: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:17: #2 number of paired peaks: 43 WARNING @ Mon, 05 Nov 2018 17:58:17: Too few paired peaks (43) 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 @ Mon, 05 Nov 2018 17:58:17: Process for pairing-model is terminated! cat: SRX3856355.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856355.20_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 `SRX3856355.20_*.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 `SRX3856355.20_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。