Job ID = 10937423 sra ファイルのダウンロード中... Completed: 253075K bytes transferred in 5 seconds (373911K 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 3471868 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198723/SRR4304453.sra Written 3471868 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198723/SRR4304453.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: 00:02:54 3471868 reads; of these: 3471868 (100.00%) were paired; of these: 1366911 (39.37%) aligned concordantly 0 times 1377827 (39.69%) aligned concordantly exactly 1 time 727130 (20.94%) aligned concordantly >1 times ---- 1366911 pairs aligned concordantly 0 times; of these: 33061 (2.42%) aligned discordantly 1 time ---- 1333850 pairs aligned 0 times concordantly or discordantly; of these: 2667700 mates make up the pairs; of these: 2572114 (96.42%) aligned 0 times 42470 (1.59%) aligned exactly 1 time 53116 (1.99%) aligned >1 times 62.96% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 230844 / 2132910 = 0.1082 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 @ Fri, 10 Aug 2018 02:04:22: # Command line: callpeak -t SRX2198723.bam -f BAM -g 12100000 -n SRX2198723.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198723.20 # format = BAM # ChIP-seq file = ['SRX2198723.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 @ Fri, 10 Aug 2018 02:04:22: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:04:22: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:04:22: # Command line: callpeak -t SRX2198723.bam -f BAM -g 12100000 -n SRX2198723.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198723.05 # format = BAM # ChIP-seq file = ['SRX2198723.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 @ Fri, 10 Aug 2018 02:04:22: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:04:22: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:04:22: # Command line: callpeak -t SRX2198723.bam -f BAM -g 12100000 -n SRX2198723.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198723.10 # format = BAM # ChIP-seq file = ['SRX2198723.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 @ Fri, 10 Aug 2018 02:04:22: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:04:22: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:04:30: 1000000 INFO @ Fri, 10 Aug 2018 02:04:31: 1000000 INFO @ Fri, 10 Aug 2018 02:04:31: 1000000 INFO @ Fri, 10 Aug 2018 02:04:39: 2000000 INFO @ Fri, 10 Aug 2018 02:04:39: 2000000 INFO @ Fri, 10 Aug 2018 02:04:39: 2000000 INFO @ Fri, 10 Aug 2018 02:04:47: 3000000 INFO @ Fri, 10 Aug 2018 02:04:47: 3000000 INFO @ Fri, 10 Aug 2018 02:04:47: 3000000 INFO @ Fri, 10 Aug 2018 02:04:55: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:04:55: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:04:55: #1 total tags in treatment: 1878569 INFO @ Fri, 10 Aug 2018 02:04:55: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:04:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:04:55: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:04:55: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:04:55: #1 total tags in treatment: 1878569 INFO @ Fri, 10 Aug 2018 02:04:55: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:04:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:04:55: #1 tags after filtering in treatment: 1246235 INFO @ Fri, 10 Aug 2018 02:04:55: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 10 Aug 2018 02:04:55: #1 finished! INFO @ Fri, 10 Aug 2018 02:04:55: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:04:55: #1 tags after filtering in treatment: 1246235 INFO @ Fri, 10 Aug 2018 02:04:55: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 10 Aug 2018 02:04:55: #1 finished! INFO @ Fri, 10 Aug 2018 02:04:55: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:04:55: #2 number of paired peaks: 41 WARNING @ Fri, 10 Aug 2018 02:04:55: Too few paired peaks (41) 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 @ Fri, 10 Aug 2018 02:04:55: Process for pairing-model is terminated! INFO @ Fri, 10 Aug 2018 02:04:55: #2 number of paired peaks: 41 WARNING @ Fri, 10 Aug 2018 02:04:55: Too few paired peaks (41) 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 @ Fri, 10 Aug 2018 02:04:55: Process for pairing-model is terminated! cat: SRX2198723.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX2198723.20_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) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198723.05_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 `SRX2198723.05_*.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 `SRX2198723.05_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 rm: cannot remove `SRX2198723.20_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 `SRX2198723.20_*.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 `SRX2198723.20_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 @ Fri, 10 Aug 2018 02:04:55: #1 tag size is determined as 51 bps INFO @ Fri, 10 Aug 2018 02:04:55: #1 tag size = 51 INFO @ Fri, 10 Aug 2018 02:04:55: #1 total tags in treatment: 1878569 INFO @ Fri, 10 Aug 2018 02:04:55: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:04:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:04:55: #1 tags after filtering in treatment: 1246235 INFO @ Fri, 10 Aug 2018 02:04:55: #1 Redundant rate of treatment: 0.34 INFO @ Fri, 10 Aug 2018 02:04:55: #1 finished! INFO @ Fri, 10 Aug 2018 02:04:55: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:04:55: #2 number of paired peaks: 41 WARNING @ Fri, 10 Aug 2018 02:04:55: Too few paired peaks (41) 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 @ Fri, 10 Aug 2018 02:04:55: Process for pairing-model is terminated! cat: SRX2198723.10_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) rm: cannot remove `SRX2198723.10_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 `SRX2198723.10_*.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 `SRX2198723.10_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。