Job ID = 10937405 sra ファイルのダウンロード中... Completed: 124614K bytes transferred in 4 seconds (231427K 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 2419038 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198720/SRR4304450.sra Written 2419038 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2198720/SRR4304450.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: 00:01:04 2419038 reads; of these: 2419038 (100.00%) were paired; of these: 1384421 (57.23%) aligned concordantly 0 times 838688 (34.67%) aligned concordantly exactly 1 time 195929 (8.10%) aligned concordantly >1 times ---- 1384421 pairs aligned concordantly 0 times; of these: 10295 (0.74%) aligned discordantly 1 time ---- 1374126 pairs aligned 0 times concordantly or discordantly; of these: 2748252 mates make up the pairs; of these: 2446367 (89.02%) aligned 0 times 234512 (8.53%) aligned exactly 1 time 67373 (2.45%) aligned >1 times 49.44% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 9082 / 1042812 = 0.0087 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 02:00:07: # Command line: callpeak -t SRX2198720.bam -f BAM -g 12100000 -n SRX2198720.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2198720.10 # format = BAM # ChIP-seq file = ['SRX2198720.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 02:00:07: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:00:07: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:00:07: # Command line: callpeak -t SRX2198720.bam -f BAM -g 12100000 -n SRX2198720.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2198720.05 # format = BAM # ChIP-seq file = ['SRX2198720.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 02:00:07: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:00:07: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:00:07: # Command line: callpeak -t SRX2198720.bam -f BAM -g 12100000 -n SRX2198720.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2198720.20 # format = BAM # ChIP-seq file = ['SRX2198720.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 02:00:07: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:00:07: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:00:12: 1000000 INFO @ Fri, 10 Aug 2018 02:00:12: 1000000 INFO @ Fri, 10 Aug 2018 02:00:13: 1000000 INFO @ Fri, 10 Aug 2018 02:00:17: 2000000 INFO @ Fri, 10 Aug 2018 02:00:17: 2000000 INFO @ Fri, 10 Aug 2018 02:00:19: 2000000 INFO @ Fri, 10 Aug 2018 02:00:19: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:00:19: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:00:19: #1 total tags in treatment: 1025557 INFO @ Fri, 10 Aug 2018 02:00:19: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:00:19: #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 02:00:19: #1 tags after filtering in treatment: 717647 INFO @ Fri, 10 Aug 2018 02:00:19: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 10 Aug 2018 02:00:19: #1 finished! INFO @ Fri, 10 Aug 2018 02:00:19: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:00:19: #2 number of paired peaks: 62 WARNING @ Fri, 10 Aug 2018 02:00:19: Too few paired peaks (62) 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 02:00:19: Process for pairing-model is terminated! cat: SRX2198720.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198720.10_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 `SRX2198720.10_*.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 `SRX2198720.10_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, 10 Aug 2018 02:00:19: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:00:19: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:00:19: #1 total tags in treatment: 1025557 INFO @ Fri, 10 Aug 2018 02:00:19: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:00:19: #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 02:00:19: #1 tags after filtering in treatment: 717647 INFO @ Fri, 10 Aug 2018 02:00:19: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 10 Aug 2018 02:00:19: #1 finished! INFO @ Fri, 10 Aug 2018 02:00:19: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:00:20: #2 number of paired peaks: 62 WARNING @ Fri, 10 Aug 2018 02:00:20: Too few paired peaks (62) 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 02:00:20: Process for pairing-model is terminated! cat: SRX2198720.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198720.05_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 `SRX2198720.05_*.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 `SRX2198720.05_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 @ Fri, 10 Aug 2018 02:00:21: #1 tag size is determined as 39 bps INFO @ Fri, 10 Aug 2018 02:00:21: #1 tag size = 39 INFO @ Fri, 10 Aug 2018 02:00:21: #1 total tags in treatment: 1025557 INFO @ Fri, 10 Aug 2018 02:00:21: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:00:21: #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 02:00:21: #1 tags after filtering in treatment: 717647 INFO @ Fri, 10 Aug 2018 02:00:21: #1 Redundant rate of treatment: 0.30 INFO @ Fri, 10 Aug 2018 02:00:21: #1 finished! INFO @ Fri, 10 Aug 2018 02:00:21: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:00:21: #2 number of paired peaks: 62 WARNING @ Fri, 10 Aug 2018 02:00:21: Too few paired peaks (62) 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 02:00:21: Process for pairing-model is terminated! cat: SRX2198720.20_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX2198720.20_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 `SRX2198720.20_*.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 `SRX2198720.20_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。