Job ID = 11192911 sra ファイルのダウンロード中... Completed: 333626K bytes transferred in 10 seconds (270578K 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: PAIRED fastq に変換中... Read 8767888 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242026/SRR6129636.sra Written 8767888 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3242026/SRR6129636.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: 00:01:23 8767888 reads; of these: 8767888 (100.00%) were paired; of these: 8638899 (98.53%) aligned concordantly 0 times 106404 (1.21%) aligned concordantly exactly 1 time 22585 (0.26%) aligned concordantly >1 times ---- 8638899 pairs aligned concordantly 0 times; of these: 38231 (0.44%) aligned discordantly 1 time ---- 8600668 pairs aligned 0 times concordantly or discordantly; of these: 17201336 mates make up the pairs; of these: 16758879 (97.43%) aligned 0 times 352165 (2.05%) aligned exactly 1 time 90292 (0.52%) aligned >1 times 4.43% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 69729 / 166466 = 0.4189 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, 15 Sep 2018 10:23:41: # Command line: callpeak -t SRX3242026.bam -f BAM -g 12100000 -n SRX3242026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3242026.05 # format = BAM # ChIP-seq file = ['SRX3242026.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, 15 Sep 2018 10:23:41: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:23:41: # Command line: callpeak -t SRX3242026.bam -f BAM -g 12100000 -n SRX3242026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3242026.10 # format = BAM # ChIP-seq file = ['SRX3242026.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, 15 Sep 2018 10:23:41: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:23:41: # Command line: callpeak -t SRX3242026.bam -f BAM -g 12100000 -n SRX3242026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3242026.20 # format = BAM # ChIP-seq file = ['SRX3242026.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, 15 Sep 2018 10:23:41: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:23:41: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:23:41: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:23:41: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:23:45: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:23:45: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:23:45: #1 total tags in treatment: 84547 INFO @ Sat, 15 Sep 2018 10:23:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:23:45: #1 tags after filtering in treatment: 80876 INFO @ Sat, 15 Sep 2018 10:23:45: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 10:23:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:23:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:23:45: #2 number of paired peaks: 87 WARNING @ Sat, 15 Sep 2018 10:23:45: Too few paired peaks (87) 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, 15 Sep 2018 10:23:45: Process for pairing-model is terminated! cat: SRX3242026.05_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, 15 Sep 2018 10:23:45: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:23:45: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:23:45: #1 total tags in treatment: 84547 INFO @ Sat, 15 Sep 2018 10:23:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:23:45: #1 tag size is determined as 45 bps INFO @ Sat, 15 Sep 2018 10:23:45: #1 tag size = 45 INFO @ Sat, 15 Sep 2018 10:23:45: #1 total tags in treatment: 84547 INFO @ Sat, 15 Sep 2018 10:23:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:23:45: #1 tags after filtering in treatment: 80876 INFO @ Sat, 15 Sep 2018 10:23:45: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 10:23:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:23:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:23:45: #1 tags after filtering in treatment: 80876 INFO @ Sat, 15 Sep 2018 10:23:45: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 15 Sep 2018 10:23:45: #1 finished! INFO @ Sat, 15 Sep 2018 10:23:45: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:23:45: #2 number of paired peaks: 87 WARNING @ Sat, 15 Sep 2018 10:23:45: Too few paired peaks (87) 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, 15 Sep 2018 10:23:45: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 10:23:45: #2 number of paired peaks: 87 WARNING @ Sat, 15 Sep 2018 10:23:45: Too few paired peaks (87) 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, 15 Sep 2018 10:23:45: Process for pairing-model is terminated! cat: SRX3242026.20_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: SRX3242026.10_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) pass1 - making usageList (0 chroms)pass1 - making usageList (0 chroms): 1 millis : 0 millis rm: cannot remove `SRX3242026.05_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 `SRX3242026.05_*.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 `SRX3242026.05_peaks.narrowPeak'needLargeMem: trying to allocate 0 bytes (limit: 17179869184): そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling rm: cannot remove `SRX3242026.20_model.r'rm: cannot remove `SRX3242026.10_model.r': そのようなファイルやディレクトリはありません : 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 `SRX3242026.20_*.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 `SRX3242026.10_*.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 `SRX3242026.20_peaks.narrowPeak': そのようなファイルやディレクトリはありません rm: cannot remove `SRX3242026.10_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 CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。