Job ID = 11296920 sra ファイルのダウンロード中... Completed: 88363K bytes transferred in 4 seconds (175451K 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 5474860 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856335/SRR6908152.sra Written 5474860 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856335/SRR6908152.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: 00:01:06 5474860 reads; of these: 5474860 (100.00%) were unpaired; of these: 170792 (3.12%) aligned 0 times 4300738 (78.55%) aligned exactly 1 time 1003330 (18.33%) aligned >1 times 96.88% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 1171990 / 5304068 = 0.2210 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 17:56:26: # Command line: callpeak -t SRX3856335.bam -f BAM -g 12100000 -n SRX3856335.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856335.10 # format = BAM # ChIP-seq file = ['SRX3856335.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 17:56:26: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:56:26: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:56:26: # Command line: callpeak -t SRX3856335.bam -f BAM -g 12100000 -n SRX3856335.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856335.05 # format = BAM # ChIP-seq file = ['SRX3856335.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 17:56:26: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:56:26: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:56:26: # Command line: callpeak -t SRX3856335.bam -f BAM -g 12100000 -n SRX3856335.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856335.20 # format = BAM # ChIP-seq file = ['SRX3856335.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 17:56:26: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:56:26: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:56:33: 1000000 INFO @ Mon, 05 Nov 2018 17:56:33: 1000000 INFO @ Mon, 05 Nov 2018 17:56:33: 1000000 INFO @ Mon, 05 Nov 2018 17:56:39: 2000000 INFO @ Mon, 05 Nov 2018 17:56:40: 2000000 INFO @ Mon, 05 Nov 2018 17:56:40: 2000000 INFO @ Mon, 05 Nov 2018 17:56:46: 3000000 INFO @ Mon, 05 Nov 2018 17:56:47: 3000000 INFO @ Mon, 05 Nov 2018 17:56:47: 3000000 INFO @ Mon, 05 Nov 2018 17:56:53: 4000000 INFO @ Mon, 05 Nov 2018 17:56:53: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:56:53: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:56:53: #1 total tags in treatment: 4132078 INFO @ Mon, 05 Nov 2018 17:56:53: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:56:53: #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 17:56:53: #1 tags after filtering in treatment: 4132078 INFO @ Mon, 05 Nov 2018 17:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:56:53: #1 finished! INFO @ Mon, 05 Nov 2018 17:56:53: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:56:54: #2 number of paired peaks: 32 WARNING @ Mon, 05 Nov 2018 17:56:54: Too few paired peaks (32) 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 17:56:54: Process for pairing-model is terminated! cat: SRX3856335.05_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 `SRX3856335.05_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 `SRX3856335.05_*.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 `SRX3856335.05_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 17:56:54: 4000000 INFO @ Mon, 05 Nov 2018 17:56:55: 4000000 INFO @ Mon, 05 Nov 2018 17:56:55: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:56:55: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:56:55: #1 total tags in treatment: 4132078 INFO @ Mon, 05 Nov 2018 17:56:55: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:56:55: #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 17:56:55: #1 tags after filtering in treatment: 4132078 INFO @ Mon, 05 Nov 2018 17:56:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:56:55: #1 finished! INFO @ Mon, 05 Nov 2018 17:56:55: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:56:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:56:55: #2 number of paired peaks: 32 WARNING @ Mon, 05 Nov 2018 17:56:55: Too few paired peaks (32) 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 17:56:55: Process for pairing-model is terminated! cat: SRX3856335.20_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 `SRX3856335.20_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 `SRX3856335.20_*.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 `SRX3856335.20_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 @ Mon, 05 Nov 2018 17:56:56: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:56:56: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:56:56: #1 total tags in treatment: 4132078 INFO @ Mon, 05 Nov 2018 17:56:56: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:56:56: #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 17:56:56: #1 tags after filtering in treatment: 4132078 INFO @ Mon, 05 Nov 2018 17:56:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:56:56: #1 finished! INFO @ Mon, 05 Nov 2018 17:56:56: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:56:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:56:56: #2 number of paired peaks: 32 WARNING @ Mon, 05 Nov 2018 17:56:56: Too few paired peaks (32) 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 17:56:56: Process for pairing-model is terminated! cat: SRX3856335.10_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 `SRX3856335.10_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 `SRX3856335.10_*.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 `SRX3856335.10_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。