Job ID = 10609017 sra ファイルのダウンロード中... Completed: 224305K bytes transferred in 17 seconds (102870K 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... Written 2315057 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3063104/SRR5901534.sra Written 2315057 spots total 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: 00:02:56 2315057 reads; of these: 2315057 (100.00%) were paired; of these: 178826 (7.72%) aligned concordantly 0 times 1834545 (79.24%) aligned concordantly exactly 1 time 301686 (13.03%) aligned concordantly >1 times ---- 178826 pairs aligned concordantly 0 times; of these: 62595 (35.00%) aligned discordantly 1 time ---- 116231 pairs aligned 0 times concordantly or discordantly; of these: 232462 mates make up the pairs; of these: 150681 (64.82%) aligned 0 times 51806 (22.29%) aligned exactly 1 time 29975 (12.89%) aligned >1 times 96.75% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 52782 / 2170298 = 0.0243 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 @ Thu, 03 May 2018 23:12:59: # Command line: callpeak -t SRX3063104.bam -f BAM -g 12100000 -n SRX3063104.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3063104.20 # format = BAM # ChIP-seq file = ['SRX3063104.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 @ Thu, 03 May 2018 23:12:59: #1 read tag files... INFO @ Thu, 03 May 2018 23:12:59: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:12:59: # Command line: callpeak -t SRX3063104.bam -f BAM -g 12100000 -n SRX3063104.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3063104.05 # format = BAM # ChIP-seq file = ['SRX3063104.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 @ Thu, 03 May 2018 23:12:59: #1 read tag files... INFO @ Thu, 03 May 2018 23:12:59: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:12:59: # Command line: callpeak -t SRX3063104.bam -f BAM -g 12100000 -n SRX3063104.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3063104.10 # format = BAM # ChIP-seq file = ['SRX3063104.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 @ Thu, 03 May 2018 23:12:59: #1 read tag files... INFO @ Thu, 03 May 2018 23:12:59: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:13:06: 1000000 INFO @ Thu, 03 May 2018 23:13:06: 1000000 INFO @ Thu, 03 May 2018 23:13:06: 1000000 INFO @ Thu, 03 May 2018 23:13:13: 2000000 INFO @ Thu, 03 May 2018 23:13:13: 2000000 INFO @ Thu, 03 May 2018 23:13:14: 2000000 INFO @ Thu, 03 May 2018 23:13:21: 3000000 INFO @ Thu, 03 May 2018 23:13:21: 3000000 INFO @ Thu, 03 May 2018 23:13:21: 3000000 INFO @ Thu, 03 May 2018 23:13:28: 4000000 INFO @ Thu, 03 May 2018 23:13:28: 4000000 INFO @ Thu, 03 May 2018 23:13:28: 4000000 INFO @ Thu, 03 May 2018 23:13:31: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:13:31: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:13:31: #1 total tags in treatment: 2083915 INFO @ Thu, 03 May 2018 23:13:31: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:13:31: #1 tags after filtering in treatment: 1853133 INFO @ Thu, 03 May 2018 23:13:31: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 03 May 2018 23:13:31: #1 finished! INFO @ Thu, 03 May 2018 23:13:31: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:13:31: #2 number of paired peaks: 79 WARNING @ Thu, 03 May 2018 23:13:31: Too few paired peaks (79) 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 @ Thu, 03 May 2018 23:13:31: Process for pairing-model is terminated! cat: SRX3063104.05_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 `SRX3063104.05_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 `SRX3063104.05_*.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 `SRX3063104.05_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 @ Thu, 03 May 2018 23:13:31: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:13:31: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:13:31: #1 total tags in treatment: 2083915 INFO @ Thu, 03 May 2018 23:13:31: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:13:31: #1 tags after filtering in treatment: 1853133 INFO @ Thu, 03 May 2018 23:13:31: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 03 May 2018 23:13:31: #1 finished! INFO @ Thu, 03 May 2018 23:13:31: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:13:31: #2 number of paired peaks: 79 WARNING @ Thu, 03 May 2018 23:13:31: Too few paired peaks (79) 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 @ Thu, 03 May 2018 23:13:31: Process for pairing-model is terminated! cat: SRX3063104.20_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 `SRX3063104.20_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 `SRX3063104.20_*.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 `SRX3063104.20_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 @ Thu, 03 May 2018 23:13:31: #1 tag size is determined as 100 bps INFO @ Thu, 03 May 2018 23:13:31: #1 tag size = 100 INFO @ Thu, 03 May 2018 23:13:31: #1 total tags in treatment: 2083915 INFO @ Thu, 03 May 2018 23:13:31: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:13:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:13:31: #1 tags after filtering in treatment: 1853133 INFO @ Thu, 03 May 2018 23:13:31: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 03 May 2018 23:13:31: #1 finished! INFO @ Thu, 03 May 2018 23:13:31: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:13:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:13:31: #2 number of paired peaks: 79 WARNING @ Thu, 03 May 2018 23:13:31: Too few paired peaks (79) 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 @ Thu, 03 May 2018 23:13:31: Process for pairing-model is terminated! cat: SRX3063104.10_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 `SRX3063104.10_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 `SRX3063104.10_*.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 `SRX3063104.10_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。