Job ID = 9162512 sra ファイルのダウンロード中... Completed: 82039K bytes transferred in 3 seconds (170743K bits/sec), in 1 file, 2 directories. 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 1222872 spots for /home/okishinya/chipatlas/results/sacCer3/SRX360908/SRR1003630.sra Written 1222872 spots total 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: 00:00:56 1222872 reads; of these: 1222872 (100.00%) were paired; of these: 144409 (11.81%) aligned concordantly 0 times 906174 (74.10%) aligned concordantly exactly 1 time 172289 (14.09%) aligned concordantly >1 times ---- 144409 pairs aligned concordantly 0 times; of these: 2831 (1.96%) aligned discordantly 1 time ---- 141578 pairs aligned 0 times concordantly or discordantly; of these: 283156 mates make up the pairs; of these: 253244 (89.44%) aligned 0 times 24346 (8.60%) aligned exactly 1 time 5566 (1.97%) aligned >1 times 89.65% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 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] 214253 / 1079918 = 0.1984 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 @ Wed, 28 Jun 2017 08:01:08: # Command line: callpeak -t SRX360908.bam -f BAM -g 12100000 -n SRX360908.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX360908.20 # format = BAM # ChIP-seq file = ['SRX360908.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 @ Wed, 28 Jun 2017 08:01:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:01:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:01:08: # Command line: callpeak -t SRX360908.bam -f BAM -g 12100000 -n SRX360908.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX360908.10 # format = BAM # ChIP-seq file = ['SRX360908.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 @ Wed, 28 Jun 2017 08:01:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:01:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:01:08: # Command line: callpeak -t SRX360908.bam -f BAM -g 12100000 -n SRX360908.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX360908.05 # format = BAM # ChIP-seq file = ['SRX360908.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 @ Wed, 28 Jun 2017 08:01:08: #1 read tag files... INFO @ Wed, 28 Jun 2017 08:01:08: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 08:01:14: 1000000 INFO @ Wed, 28 Jun 2017 08:01:15: 1000000 INFO @ Wed, 28 Jun 2017 08:01:15: 1000000 INFO @ Wed, 28 Jun 2017 08:01:19: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:01:19: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:01:19: #1 total tags in treatment: 864275 INFO @ Wed, 28 Jun 2017 08:01:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:01:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:01:19: #1 tags after filtering in treatment: 791275 INFO @ Wed, 28 Jun 2017 08:01:19: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 08:01:19: #1 finished! INFO @ Wed, 28 Jun 2017 08:01:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:01:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:01:19: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 08:01:19: Too few paired peaks (39) 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 @ Wed, 28 Jun 2017 08:01:19: Process for pairing-model is terminated! cat: SRX360908.20_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 `SRX360908.20_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 `SRX360908.20_*.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 `SRX360908.20_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 @ Wed, 28 Jun 2017 08:01:20: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:01:20: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:01:20: #1 total tags in treatment: 864275 INFO @ Wed, 28 Jun 2017 08:01:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:01:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:01:20: #1 tag size is determined as 51 bps INFO @ Wed, 28 Jun 2017 08:01:20: #1 tag size = 51 INFO @ Wed, 28 Jun 2017 08:01:20: #1 total tags in treatment: 864275 INFO @ Wed, 28 Jun 2017 08:01:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 08:01:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 08:01:20: #1 tags after filtering in treatment: 791275 INFO @ Wed, 28 Jun 2017 08:01:20: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 08:01:20: #1 finished! INFO @ Wed, 28 Jun 2017 08:01:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:01:20: #1 tags after filtering in treatment: 791275 INFO @ Wed, 28 Jun 2017 08:01:20: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 08:01:20: #1 finished! INFO @ Wed, 28 Jun 2017 08:01:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 08:01:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 08:01:20: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 08:01:20: Too few paired peaks (39) 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 @ Wed, 28 Jun 2017 08:01:20: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 08:01:20: #2 number of paired peaks: 39 WARNING @ Wed, 28 Jun 2017 08:01:20: Too few paired peaks (39) 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 @ Wed, 28 Jun 2017 08:01:20: Process for pairing-model is terminated! cat: SRX360908.10_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX360908.05_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 `SRX360908.10_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 `SRX360908.10_*.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 `SRX360908.10_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX360908.05_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 `SRX360908.05_*.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 `SRX360908.05_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。