Job ID = 11245061 sra ファイルのダウンロード中... Completed: 154038K bytes transferred in 4 seconds (253892K 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 4539950 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554774/SRR7696446.sra Written 4539950 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554774/SRR7696446.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: 00:02:28 4539950 reads; of these: 4539950 (100.00%) were paired; of these: 2501300 (55.10%) aligned concordantly 0 times 1823823 (40.17%) aligned concordantly exactly 1 time 214827 (4.73%) aligned concordantly >1 times ---- 2501300 pairs aligned concordantly 0 times; of these: 5017 (0.20%) aligned discordantly 1 time ---- 2496283 pairs aligned 0 times concordantly or discordantly; of these: 4992566 mates make up the pairs; of these: 3271857 (65.53%) aligned 0 times 1523502 (30.52%) aligned exactly 1 time 197207 (3.95%) aligned >1 times 63.97% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 92706 / 2043162 = 0.0454 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 23:20:33: # Command line: callpeak -t SRX4554774.bam -f BAM -g 12100000 -n SRX4554774.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554774.10 # format = BAM # ChIP-seq file = ['SRX4554774.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 23:20:33: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:33: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:33: # Command line: callpeak -t SRX4554774.bam -f BAM -g 12100000 -n SRX4554774.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554774.05 # format = BAM # ChIP-seq file = ['SRX4554774.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 23:20:33: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:33: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:33: # Command line: callpeak -t SRX4554774.bam -f BAM -g 12100000 -n SRX4554774.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554774.20 # format = BAM # ChIP-seq file = ['SRX4554774.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 23:20:33: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:20:33: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:20:38: 1000000 INFO @ Tue, 09 Oct 2018 23:20:38: 1000000 INFO @ Tue, 09 Oct 2018 23:20:38: 1000000 INFO @ Tue, 09 Oct 2018 23:20:43: 2000000 INFO @ Tue, 09 Oct 2018 23:20:43: 2000000 INFO @ Tue, 09 Oct 2018 23:20:43: 2000000 INFO @ Tue, 09 Oct 2018 23:20:47: 3000000 INFO @ Tue, 09 Oct 2018 23:20:47: 3000000 INFO @ Tue, 09 Oct 2018 23:20:47: 3000000 INFO @ Tue, 09 Oct 2018 23:20:52: 4000000 INFO @ Tue, 09 Oct 2018 23:20:52: 4000000 INFO @ Tue, 09 Oct 2018 23:20:52: 4000000 INFO @ Tue, 09 Oct 2018 23:20:57: 5000000 INFO @ Tue, 09 Oct 2018 23:20:57: 5000000 INFO @ Tue, 09 Oct 2018 23:20:57: 5000000 INFO @ Tue, 09 Oct 2018 23:21:00: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:21:00: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:21:00: #1 total tags in treatment: 1945974 INFO @ Tue, 09 Oct 2018 23:21:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:21:00: #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 23:21:00: #1 tags after filtering in treatment: 1470796 INFO @ Tue, 09 Oct 2018 23:21:00: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 09 Oct 2018 23:21:00: #1 finished! INFO @ Tue, 09 Oct 2018 23:21:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:21:00: #2 number of paired peaks: 45 WARNING @ Tue, 09 Oct 2018 23:21:00: Too few paired peaks (45) 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 23:21:00: Process for pairing-model is terminated! cat: SRX4554774.20_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 `SRX4554774.20_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 `SRX4554774.20_*.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 `SRX4554774.20_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 @ Tue, 09 Oct 2018 23:21:00: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:21:00: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:21:00: #1 total tags in treatment: 1945974 INFO @ Tue, 09 Oct 2018 23:21:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:21:00: #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 23:21:00: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:21:00: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:21:00: #1 total tags in treatment: 1945974 INFO @ Tue, 09 Oct 2018 23:21:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:21:00: #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 23:21:00: #1 tags after filtering in treatment: 1470796 INFO @ Tue, 09 Oct 2018 23:21:00: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 09 Oct 2018 23:21:00: #1 finished! INFO @ Tue, 09 Oct 2018 23:21:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:21:00: #1 tags after filtering in treatment: 1470796 INFO @ Tue, 09 Oct 2018 23:21:00: #1 Redundant rate of treatment: 0.24 INFO @ Tue, 09 Oct 2018 23:21:00: #1 finished! INFO @ Tue, 09 Oct 2018 23:21:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:21:00: #2 number of paired peaks: 45 WARNING @ Tue, 09 Oct 2018 23:21:00: Too few paired peaks (45) 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 23:21:00: Process for pairing-model is terminated! cat: SRX4554774.10_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 `SRX4554774.10_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 `SRX4554774.10_*.xls': そのようなファイルやディレクトリはありません INFO @ Tue, 09 Oct 2018 23:21:00: #2 number of paired peaks: 45 rm: cannot remove `SRX4554774.10_peaks.narrowPeak': そのようなファイルやディレクトリはありません WARNING @ Tue, 09 Oct 2018 23:21:00: Too few paired peaks (45) 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 23:21:00: Process for pairing-model is terminated! CompletedMACS2peakCalling cat: SRX4554774.05_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 `SRX4554774.05_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 `SRX4554774.05_*.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 `SRX4554774.05_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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。