Job ID = 11633138 sra ファイルのダウンロード中... Completed: 109479K bytes transferred in 4 seconds (206717K 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 1866509 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1174074/ERR1094588.sra Written 1866509 spots for /home/okishinya/chipatlas/results/sacCer3/ERX1174074/ERR1094588.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: 00:01:20 1866509 reads; of these: 1866509 (100.00%) were paired; of these: 283030 (15.16%) aligned concordantly 0 times 1462706 (78.37%) aligned concordantly exactly 1 time 120773 (6.47%) aligned concordantly >1 times ---- 283030 pairs aligned concordantly 0 times; of these: 72291 (25.54%) aligned discordantly 1 time ---- 210739 pairs aligned 0 times concordantly or discordantly; of these: 421478 mates make up the pairs; of these: 398167 (94.47%) aligned 0 times 8961 (2.13%) aligned exactly 1 time 14350 (3.40%) aligned >1 times 89.33% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 31047 / 1653864 = 0.0188 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, 15 Feb 2019 08:22:34: # Command line: callpeak -t ERX1174074.bam -f BAM -g 12100000 -n ERX1174074.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1174074.10 # format = BAM # ChIP-seq file = ['ERX1174074.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, 15 Feb 2019 08:22:34: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:22:34: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:22:34: # Command line: callpeak -t ERX1174074.bam -f BAM -g 12100000 -n ERX1174074.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1174074.20 # format = BAM # ChIP-seq file = ['ERX1174074.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, 15 Feb 2019 08:22:34: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:22:34: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:22:34: # Command line: callpeak -t ERX1174074.bam -f BAM -g 12100000 -n ERX1174074.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1174074.05 # format = BAM # ChIP-seq file = ['ERX1174074.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, 15 Feb 2019 08:22:34: #1 read tag files... INFO @ Fri, 15 Feb 2019 08:22:34: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 08:22:40: 1000000 INFO @ Fri, 15 Feb 2019 08:22:40: 1000000 INFO @ Fri, 15 Feb 2019 08:22:40: 1000000 INFO @ Fri, 15 Feb 2019 08:22:46: 2000000 INFO @ Fri, 15 Feb 2019 08:22:47: 2000000 INFO @ Fri, 15 Feb 2019 08:22:47: 2000000 INFO @ Fri, 15 Feb 2019 08:22:52: 3000000 INFO @ Fri, 15 Feb 2019 08:22:53: 3000000 INFO @ Fri, 15 Feb 2019 08:22:53: 3000000 INFO @ Fri, 15 Feb 2019 08:22:54: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:22:54: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:22:54: #1 total tags in treatment: 1553869 INFO @ Fri, 15 Feb 2019 08:22:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:22:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:22:54: #1 tags after filtering in treatment: 1465662 INFO @ Fri, 15 Feb 2019 08:22:54: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:22:54: #1 finished! INFO @ Fri, 15 Feb 2019 08:22:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:22:54: #2 number of paired peaks: 30 WARNING @ Fri, 15 Feb 2019 08:22:54: Too few paired peaks (30) 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, 15 Feb 2019 08:22:54: Process for pairing-model is terminated! cat: ERX1174074.10_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1174074.10_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 `ERX1174074.10_*.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 `ERX1174074.10_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 INFO @ Fri, 15 Feb 2019 08:22:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:22:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:22:55: #1 total tags in treatment: 1553869 INFO @ Fri, 15 Feb 2019 08:22:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:22:55: #1 tags after filtering in treatment: 1465662 INFO @ Fri, 15 Feb 2019 08:22:55: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:22:55: #1 finished! INFO @ Fri, 15 Feb 2019 08:22:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:22:55: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 08:22:55: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 08:22:55: #1 total tags in treatment: 1553869 INFO @ Fri, 15 Feb 2019 08:22:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 08:22:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 08:22:55: #1 tags after filtering in treatment: 1465662 INFO @ Fri, 15 Feb 2019 08:22:55: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 15 Feb 2019 08:22:55: #1 finished! INFO @ Fri, 15 Feb 2019 08:22:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 08:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 08:22:55: #2 number of paired peaks: 30 WARNING @ Fri, 15 Feb 2019 08:22:55: Too few paired peaks (30) 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, 15 Feb 2019 08:22:55: Process for pairing-model is terminated! cat: ERX1174074.20_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Fri, 15 Feb 2019 08:22:55: #2 number of paired peaks: 30 WARNING @ Fri, 15 Feb 2019 08:22:55: Too few paired peaks (30) 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, 15 Feb 2019 08:22:55: Process for pairing-model is terminated! rm: cannot remove `ERX1174074.20_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 `ERX1174074.20_*.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 `ERX1174074.20_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 cat: ERX1174074.05_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): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `ERX1174074.05_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 `ERX1174074.05_*.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 `ERX1174074.05_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。