Job ID = 11245233 sra ファイルのダウンロード中... Completed: 463711K bytes transferred in 10 seconds (359096K 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: SINGLE fastq に変換中... Read 16944658 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717375/SRR7878698.sra Written 16944658 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717375/SRR7878698.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: 00:03:35 16944658 reads; of these: 16944658 (100.00%) were unpaired; of these: 2197231 (12.97%) aligned 0 times 10449278 (61.67%) aligned exactly 1 time 4298149 (25.37%) aligned >1 times 87.03% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9206631 / 14747427 = 0.6243 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, 10 Oct 2018 00:01:49: # Command line: callpeak -t SRX4717375.bam -f BAM -g 12100000 -n SRX4717375.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4717375.05 # format = BAM # ChIP-seq file = ['SRX4717375.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, 10 Oct 2018 00:01:49: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:49: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:49: # Command line: callpeak -t SRX4717375.bam -f BAM -g 12100000 -n SRX4717375.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4717375.20 # format = BAM # ChIP-seq file = ['SRX4717375.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, 10 Oct 2018 00:01:49: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:49: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:49: # Command line: callpeak -t SRX4717375.bam -f BAM -g 12100000 -n SRX4717375.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4717375.10 # format = BAM # ChIP-seq file = ['SRX4717375.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, 10 Oct 2018 00:01:49: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:01:49: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:01:56: 1000000 INFO @ Wed, 10 Oct 2018 00:01:57: 1000000 INFO @ Wed, 10 Oct 2018 00:01:57: 1000000 INFO @ Wed, 10 Oct 2018 00:02:04: 2000000 INFO @ Wed, 10 Oct 2018 00:02:04: 2000000 INFO @ Wed, 10 Oct 2018 00:02:04: 2000000 INFO @ Wed, 10 Oct 2018 00:02:11: 3000000 INFO @ Wed, 10 Oct 2018 00:02:11: 3000000 INFO @ Wed, 10 Oct 2018 00:02:11: 3000000 INFO @ Wed, 10 Oct 2018 00:02:18: 4000000 INFO @ Wed, 10 Oct 2018 00:02:18: 4000000 INFO @ Wed, 10 Oct 2018 00:02:18: 4000000 INFO @ Wed, 10 Oct 2018 00:02:25: 5000000 INFO @ Wed, 10 Oct 2018 00:02:25: 5000000 INFO @ Wed, 10 Oct 2018 00:02:26: 5000000 INFO @ Wed, 10 Oct 2018 00:02:29: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:02:29: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:02:29: #1 total tags in treatment: 5540796 INFO @ Wed, 10 Oct 2018 00:02:29: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:02:29: #1 tags after filtering in treatment: 5540796 INFO @ Wed, 10 Oct 2018 00:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:02:29: #1 finished! INFO @ Wed, 10 Oct 2018 00:02:29: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:02:29: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:02:29: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:02:29: #1 total tags in treatment: 5540796 INFO @ Wed, 10 Oct 2018 00:02:29: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:02:29: #1 tags after filtering in treatment: 5540796 INFO @ Wed, 10 Oct 2018 00:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:02:29: #1 finished! INFO @ Wed, 10 Oct 2018 00:02:29: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:02:29: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:02:29: Too few paired peaks (0) 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, 10 Oct 2018 00:02:29: Process for pairing-model is terminated! cat: SRX4717375.20_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 `SRX4717375.20_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 `SRX4717375.20_*.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 `SRX4717375.20_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, 10 Oct 2018 00:02:30: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:02:30: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:02:30: #1 total tags in treatment: 5540796 INFO @ Wed, 10 Oct 2018 00:02:30: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:02:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 10 Oct 2018 00:02:30: #1 tags after filtering in treatment: 5540796 INFO @ Wed, 10 Oct 2018 00:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:02:30: #1 finished! INFO @ Wed, 10 Oct 2018 00:02:30: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:02:30: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:02:30: Too few paired peaks (0) 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, 10 Oct 2018 00:02:30: Process for pairing-model is terminated! cat: SRX4717375.05_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 `SRX4717375.05_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 `SRX4717375.05_*.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 `SRX4717375.05_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, 10 Oct 2018 00:02:30: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:02:30: Too few paired peaks (0) 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, 10 Oct 2018 00:02:30: Process for pairing-model is terminated! cat: SRX4717375.10_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 `SRX4717375.10_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 `SRX4717375.10_*.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 `SRX4717375.10_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。