Job ID = 11245147 sra ファイルのダウンロード中... Completed: 21632K bytes transferred in 3 seconds (57330K bits/sec), in 1 file. Completed: 179412K bytes transferred in 5 seconds (287290K 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 457177 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669597/SRR7818174.sra Written 457177 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669597/SRR7818174.sra Read 4801509 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669597/SRR7818175.sra Written 4801509 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4669597/SRR7818175.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 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: 00:04:07 5258686 reads; of these: 5258686 (100.00%) were paired; of these: 475846 (9.05%) aligned concordantly 0 times 4000698 (76.08%) aligned concordantly exactly 1 time 782142 (14.87%) aligned concordantly >1 times ---- 475846 pairs aligned concordantly 0 times; of these: 16129 (3.39%) aligned discordantly 1 time ---- 459717 pairs aligned 0 times concordantly or discordantly; of these: 919434 mates make up the pairs; of these: 772387 (84.01%) aligned 0 times 80246 (8.73%) aligned exactly 1 time 66801 (7.27%) aligned >1 times 92.66% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 945211 / 4795837 = 0.1971 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 @ Tue, 09 Oct 2018 23:40:34: # Command line: callpeak -t SRX4669597.bam -f BAM -g 12100000 -n SRX4669597.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669597.05 # format = BAM # ChIP-seq file = ['SRX4669597.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 @ Tue, 09 Oct 2018 23:40:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:40:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:40:34: # Command line: callpeak -t SRX4669597.bam -f BAM -g 12100000 -n SRX4669597.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669597.10 # format = BAM # ChIP-seq file = ['SRX4669597.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 @ Tue, 09 Oct 2018 23:40:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:40:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:40:34: # Command line: callpeak -t SRX4669597.bam -f BAM -g 12100000 -n SRX4669597.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669597.20 # format = BAM # ChIP-seq file = ['SRX4669597.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 @ Tue, 09 Oct 2018 23:40:34: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:40:34: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:40:41: 1000000 INFO @ Tue, 09 Oct 2018 23:40:42: 1000000 INFO @ Tue, 09 Oct 2018 23:40:42: 1000000 INFO @ Tue, 09 Oct 2018 23:40:48: 2000000 INFO @ Tue, 09 Oct 2018 23:40:50: 2000000 INFO @ Tue, 09 Oct 2018 23:40:50: 2000000 INFO @ Tue, 09 Oct 2018 23:40:54: 3000000 INFO @ Tue, 09 Oct 2018 23:40:59: 3000000 INFO @ Tue, 09 Oct 2018 23:40:59: 3000000 INFO @ Tue, 09 Oct 2018 23:41:01: 4000000 INFO @ Tue, 09 Oct 2018 23:41:07: 4000000 INFO @ Tue, 09 Oct 2018 23:41:07: 4000000 INFO @ Tue, 09 Oct 2018 23:41:08: 5000000 INFO @ Tue, 09 Oct 2018 23:41:14: 6000000 INFO @ Tue, 09 Oct 2018 23:41:15: 5000000 INFO @ Tue, 09 Oct 2018 23:41:15: 5000000 INFO @ Tue, 09 Oct 2018 23:41:21: 7000000 INFO @ Tue, 09 Oct 2018 23:41:23: 6000000 INFO @ Tue, 09 Oct 2018 23:41:23: 6000000 INFO @ Tue, 09 Oct 2018 23:41:27: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:41:27: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:41:27: #1 total tags in treatment: 3840578 INFO @ Tue, 09 Oct 2018 23:41:27: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:41:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:41:27: #1 tags after filtering in treatment: 3079838 INFO @ Tue, 09 Oct 2018 23:41:27: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:41:27: #1 finished! INFO @ Tue, 09 Oct 2018 23:41:27: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:41:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:41:27: #2 number of paired peaks: 40 WARNING @ Tue, 09 Oct 2018 23:41:27: Too few paired peaks (40) 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 @ Tue, 09 Oct 2018 23:41:27: Process for pairing-model is terminated! cat: SRX4669597.05_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669597.05_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 `SRX4669597.05_*.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 `SRX4669597.05_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 @ Tue, 09 Oct 2018 23:41:31: 7000000 INFO @ Tue, 09 Oct 2018 23:41:31: 7000000 INFO @ Tue, 09 Oct 2018 23:41:38: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:41:38: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:41:38: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:41:38: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:41:38: #1 total tags in treatment: 3840578 INFO @ Tue, 09 Oct 2018 23:41:38: #1 total tags in treatment: 3840578 INFO @ Tue, 09 Oct 2018 23:41:38: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:41:38: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:41:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:41:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:41:38: #1 tags after filtering in treatment: 3079838 INFO @ Tue, 09 Oct 2018 23:41:38: #1 tags after filtering in treatment: 3079838 INFO @ Tue, 09 Oct 2018 23:41:38: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:41:38: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 09 Oct 2018 23:41:38: #1 finished! INFO @ Tue, 09 Oct 2018 23:41:38: #1 finished! INFO @ Tue, 09 Oct 2018 23:41:38: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:41:38: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:41:38: #2 number of paired peaks: 40 WARNING @ Tue, 09 Oct 2018 23:41:38: Too few paired peaks (40) 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 @ Tue, 09 Oct 2018 23:41:38: Process for pairing-model is terminated! INFO @ Tue, 09 Oct 2018 23:41:38: #2 number of paired peaks: 40 WARNING @ Tue, 09 Oct 2018 23:41:38: Too few paired peaks (40) 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 @ Tue, 09 Oct 2018 23:41:38: Process for pairing-model is terminated! cat: SRX4669597.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX4669597.20_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 `SRX4669597.10_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 `SRX4669597.10_*.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 `SRX4669597.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4669597.20_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 `SRX4669597.20_*.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 `SRX4669597.20_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。