Job ID = 11296915 sra ファイルのダウンロード中... Completed: 28476K bytes transferred in 3 seconds (74647K 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 1739876 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856330/SRR6908147.sra Written 1739876 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856330/SRR6908147.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: 00:00:22 1739876 reads; of these: 1739876 (100.00%) were unpaired; of these: 132700 (7.63%) aligned 0 times 1098474 (63.14%) aligned exactly 1 time 508702 (29.24%) aligned >1 times 92.37% overall alignment rate Time searching: 00:00:22 Overall time: 00:00:22 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] 438755 / 1607176 = 0.2730 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 17:53:55: # Command line: callpeak -t SRX3856330.bam -f BAM -g 12100000 -n SRX3856330.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856330.10 # format = BAM # ChIP-seq file = ['SRX3856330.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 17:53:55: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:53:55: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:53:55: # Command line: callpeak -t SRX3856330.bam -f BAM -g 12100000 -n SRX3856330.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856330.05 # format = BAM # ChIP-seq file = ['SRX3856330.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 17:53:55: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:53:55: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:53:55: # Command line: callpeak -t SRX3856330.bam -f BAM -g 12100000 -n SRX3856330.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856330.20 # format = BAM # ChIP-seq file = ['SRX3856330.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 17:53:55: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:53:55: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:54:01: 1000000 INFO @ Mon, 05 Nov 2018 17:54:02: 1000000 INFO @ Mon, 05 Nov 2018 17:54:02: 1000000 INFO @ Mon, 05 Nov 2018 17:54:02: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:54:02: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:54:02: #1 total tags in treatment: 1168421 INFO @ Mon, 05 Nov 2018 17:54:02: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:54:02: #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 17:54:02: #1 tags after filtering in treatment: 1168421 INFO @ Mon, 05 Nov 2018 17:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:54:02: #1 finished! INFO @ Mon, 05 Nov 2018 17:54:02: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:54:03: #2 number of paired peaks: 81 WARNING @ Mon, 05 Nov 2018 17:54:03: Too few paired peaks (81) 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 17:54:03: Process for pairing-model is terminated! cat: SRX3856330.10_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3856330.10_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 `SRX3856330.10_*.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 `SRX3856330.10_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 17:54:03: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:54:03: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:54:03: #1 total tags in treatment: 1168421 INFO @ Mon, 05 Nov 2018 17:54:03: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:54:03: #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 17:54:03: #1 tag size is determined as 50 bps INFO @ Mon, 05 Nov 2018 17:54:03: #1 tag size = 50 INFO @ Mon, 05 Nov 2018 17:54:03: #1 total tags in treatment: 1168421 INFO @ Mon, 05 Nov 2018 17:54:03: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:54:03: #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 17:54:03: #1 tags after filtering in treatment: 1168421 INFO @ Mon, 05 Nov 2018 17:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:54:03: #1 finished! INFO @ Mon, 05 Nov 2018 17:54:03: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:54:03: #1 tags after filtering in treatment: 1168421 INFO @ Mon, 05 Nov 2018 17:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:54:03: #1 finished! INFO @ Mon, 05 Nov 2018 17:54:03: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:54:03: #2 number of paired peaks: 81 WARNING @ Mon, 05 Nov 2018 17:54:03: Too few paired peaks (81) 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 17:54:03: Process for pairing-model is terminated! cat: SRX3856330.05_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) INFO @ Mon, 05 Nov 2018 17:54:03: #2 number of paired peaks: 81 WARNING @ Mon, 05 Nov 2018 17:54:03: Too few paired peaks (81) 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 17:54:03: Process for pairing-model is terminated! rm: cannot remove `SRX3856330.05_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 `SRX3856330.05_*.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 `SRX3856330.05_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 cat: SRX3856330.20_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 `SRX3856330.20_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 `SRX3856330.20_*.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 `SRX3856330.20_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。