Job ID = 9161649 sra ファイルのダウンロード中... Completed: 35462K bytes transferred in 3 seconds (78356K 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 415128 spots for /home/okishinya/chipatlas/results/sacCer3/SRX043833/SRR107288.sra Written 415128 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: 00:00:11 415128 reads; of these: 415128 (100.00%) were paired; of these: 391675 (94.35%) aligned concordantly 0 times 22958 (5.53%) aligned concordantly exactly 1 time 495 (0.12%) aligned concordantly >1 times ---- 391675 pairs aligned concordantly 0 times; of these: 156 (0.04%) aligned discordantly 1 time ---- 391519 pairs aligned 0 times concordantly or discordantly; of these: 783038 mates make up the pairs; of these: 644692 (82.33%) aligned 0 times 125205 (15.99%) aligned exactly 1 time 13141 (1.68%) aligned >1 times 22.35% overall alignment rate Time searching: 00:00:11 Overall time: 00:00:11 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] 22112 / 23462 = 0.9425 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 04:15:02: # Command line: callpeak -t SRX043833.bam -f BAM -g 12100000 -n SRX043833.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX043833.10 # format = BAM # ChIP-seq file = ['SRX043833.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 04:15:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:15:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:15:02: # Command line: callpeak -t SRX043833.bam -f BAM -g 12100000 -n SRX043833.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX043833.20 # format = BAM # ChIP-seq file = ['SRX043833.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 04:15:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:15:02: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:15:02: # Command line: callpeak -t SRX043833.bam -f BAM -g 12100000 -n SRX043833.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX043833.05 # format = BAM # ChIP-seq file = ['SRX043833.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 04:15:02: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:15:02: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 28 Jun 2017 04:15:03: #1 tag size is determined as 60 bps INFO @ Wed, 28 Jun 2017 04:15:03: #1 tag size = 60 INFO @ Wed, 28 Jun 2017 04:15:03: #1 total tags in treatment: 1342 INFO @ Wed, 28 Jun 2017 04:15:03: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:15:03: #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 04:15:03: #1 tags after filtering in treatment: 1217 INFO @ Wed, 28 Jun 2017 04:15:03: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 04:15:03: #1 finished! INFO @ Wed, 28 Jun 2017 04:15:03: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:15:03: #2 number of paired peaks: 23 WARNING @ Wed, 28 Jun 2017 04:15:03: Too few paired peaks (23) 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 04:15:03: Process for pairing-model is terminated! cat: SRX043833.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません BigWig に変換しました。 INFO @ Wed, 28 Jun 2017 04:15:03: #1 tag size is determined as 60 bps INFO @ Wed, 28 Jun 2017 04:15:03: #1 tag size = 60 INFO @ Wed, 28 Jun 2017 04:15:03: #1 total tags in treatment: 1342 INFO @ Wed, 28 Jun 2017 04:15:03: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:15:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) INFO @ Wed, 28 Jun 2017 04:15:03: #1 tag size is determined as 60 bps INFO @ Wed, 28 Jun 2017 04:15:03: #1 tag size = 60 INFO @ Wed, 28 Jun 2017 04:15:03: #1 total tags in treatment: 1342 INFO @ Wed, 28 Jun 2017 04:15:03: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:15:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) rm: cannot remove `SRX043833.05_model.r'INFO @ Wed, 28 Jun 2017 04:15:03: #1 tags after filtering in treatment: 1217 : そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 04:15:03: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 04:15:03: #1 finished! rm: cannot remove `SRX043833.05_*.xls'INFO @ Wed, 28 Jun 2017 04:15:03: #2 Build Peak Model... : そのようなファイルやディレクトリはありません INFO @ Wed, 28 Jun 2017 04:15:03: #2 looking for paired plus/minus strand peaks... rm: cannot remove `SRX043833.05_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 @ Wed, 28 Jun 2017 04:15:03: #1 tags after filtering in treatment: 1217 INFO @ Wed, 28 Jun 2017 04:15:03: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 28 Jun 2017 04:15:03: #1 finished! INFO @ Wed, 28 Jun 2017 04:15:03: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:15:03: #2 number of paired peaks: 23 WARNING @ Wed, 28 Jun 2017 04:15:03: Too few paired peaks (23) 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 04:15:03: Process for pairing-model is terminated! INFO @ Wed, 28 Jun 2017 04:15:03: #2 number of paired peaks: 23 WARNING @ Wed, 28 Jun 2017 04:15:03: Too few paired peaks (23) 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 04:15:03: Process for pairing-model is terminated! cat: SRX043833.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません cat: SRX043833.10_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 `SRX043833.20_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 `SRX043833.20_*.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 `SRX043833.20_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 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX043833.10_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 `SRX043833.10_*.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 `SRX043833.10_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