Job ID = 10609024 sra ファイルのダウンロード中... Completed: 407064K bytes transferred in 36 seconds (92459K 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... Written 25373929 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3467375/SRR6372053.sra Written 25373929 spots total 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: 00:07:27 25373929 reads; of these: 25373929 (100.00%) were unpaired; of these: 8528197 (33.61%) aligned 0 times 9856093 (38.84%) aligned exactly 1 time 6989639 (27.55%) aligned >1 times 66.39% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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] 13317215 / 16845732 = 0.7905 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 @ Thu, 03 May 2018 23:20:05: # Command line: callpeak -t SRX3467375.bam -f BAM -g 12100000 -n SRX3467375.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3467375.10 # format = BAM # ChIP-seq file = ['SRX3467375.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 @ Thu, 03 May 2018 23:20:05: #1 read tag files... INFO @ Thu, 03 May 2018 23:20:05: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:20:05: # Command line: callpeak -t SRX3467375.bam -f BAM -g 12100000 -n SRX3467375.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3467375.05 # format = BAM # ChIP-seq file = ['SRX3467375.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 @ Thu, 03 May 2018 23:20:05: #1 read tag files... INFO @ Thu, 03 May 2018 23:20:05: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:20:05: # Command line: callpeak -t SRX3467375.bam -f BAM -g 12100000 -n SRX3467375.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3467375.20 # format = BAM # ChIP-seq file = ['SRX3467375.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 @ Thu, 03 May 2018 23:20:05: #1 read tag files... INFO @ Thu, 03 May 2018 23:20:05: #1 read treatment tags... INFO @ Thu, 03 May 2018 23:20:11: 1000000 INFO @ Thu, 03 May 2018 23:20:12: 1000000 INFO @ Thu, 03 May 2018 23:20:12: 1000000 INFO @ Thu, 03 May 2018 23:20:17: 2000000 INFO @ Thu, 03 May 2018 23:20:18: 2000000 INFO @ Thu, 03 May 2018 23:20:18: 2000000 INFO @ Thu, 03 May 2018 23:20:23: 3000000 INFO @ Thu, 03 May 2018 23:20:24: 3000000 INFO @ Thu, 03 May 2018 23:20:24: 3000000 INFO @ Thu, 03 May 2018 23:20:26: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:20:26: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:20:26: #1 total tags in treatment: 3528517 INFO @ Thu, 03 May 2018 23:20:26: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:20:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:20:26: #1 tags after filtering in treatment: 3528517 INFO @ Thu, 03 May 2018 23:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:20:26: #1 finished! INFO @ Thu, 03 May 2018 23:20:26: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:20:26: #2 number of paired peaks: 29 WARNING @ Thu, 03 May 2018 23:20:26: Too few paired peaks (29) 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 @ Thu, 03 May 2018 23:20:26: Process for pairing-model is terminated! cat: SRX3467375.10_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3467375.10_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 `SRX3467375.10_*.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 `SRX3467375.10_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 @ Thu, 03 May 2018 23:20:27: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:20:27: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:20:27: #1 total tags in treatment: 3528517 INFO @ Thu, 03 May 2018 23:20:27: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:20:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:20:27: #1 tag size is determined as 50 bps INFO @ Thu, 03 May 2018 23:20:27: #1 tag size = 50 INFO @ Thu, 03 May 2018 23:20:27: #1 total tags in treatment: 3528517 INFO @ Thu, 03 May 2018 23:20:27: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 23:20:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 23:20:27: #1 tags after filtering in treatment: 3528517 INFO @ Thu, 03 May 2018 23:20:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:20:27: #1 finished! INFO @ Thu, 03 May 2018 23:20:27: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:20:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:20:27: #1 tags after filtering in treatment: 3528517 INFO @ Thu, 03 May 2018 23:20:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 23:20:27: #1 finished! INFO @ Thu, 03 May 2018 23:20:27: #2 Build Peak Model... INFO @ Thu, 03 May 2018 23:20:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 23:20:27: #2 number of paired peaks: 29 WARNING @ Thu, 03 May 2018 23:20:27: Too few paired peaks (29) 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 @ Thu, 03 May 2018 23:20:27: Process for pairing-model is terminated! cat: SRX3467375.05_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 `SRX3467375.05_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 `SRX3467375.05_*.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 `SRX3467375.05_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 @ Thu, 03 May 2018 23:20:27: #2 number of paired peaks: 29 WARNING @ Thu, 03 May 2018 23:20:27: Too few paired peaks (29) 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 @ Thu, 03 May 2018 23:20:27: Process for pairing-model is terminated! cat: SRX3467375.20_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): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3467375.20_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 `SRX3467375.20_*.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 `SRX3467375.20_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。