Job ID = 11193091 sra ファイルのダウンロード中... Completed: 127556K bytes transferred in 4 seconds (234250K 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 6739165 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234061/SRR7361040.sra Written 6739165 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234061/SRR7361040.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: 00:01:32 6739165 reads; of these: 6739165 (100.00%) were unpaired; of these: 361612 (5.37%) aligned 0 times 5589831 (82.95%) aligned exactly 1 time 787722 (11.69%) aligned >1 times 94.63% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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_rmdupse_core] 2159591 / 6377553 = 0.3386 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 @ Sat, 15 Sep 2018 10:57:49: # Command line: callpeak -t SRX4234061.bam -f BAM -g 12100000 -n SRX4234061.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4234061.10 # format = BAM # ChIP-seq file = ['SRX4234061.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 @ Sat, 15 Sep 2018 10:57:49: # Command line: callpeak -t SRX4234061.bam -f BAM -g 12100000 -n SRX4234061.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4234061.20 # format = BAM # ChIP-seq file = ['SRX4234061.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 @ Sat, 15 Sep 2018 10:57:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:57:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:57:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:57:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:57:49: # Command line: callpeak -t SRX4234061.bam -f BAM -g 12100000 -n SRX4234061.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4234061.05 # format = BAM # ChIP-seq file = ['SRX4234061.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 @ Sat, 15 Sep 2018 10:57:49: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:57:49: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:57:57: 1000000 INFO @ Sat, 15 Sep 2018 10:57:59: 1000000 INFO @ Sat, 15 Sep 2018 10:57:59: 1000000 INFO @ Sat, 15 Sep 2018 10:58:05: 2000000 INFO @ Sat, 15 Sep 2018 10:58:09: 2000000 INFO @ Sat, 15 Sep 2018 10:58:09: 2000000 INFO @ Sat, 15 Sep 2018 10:58:14: 3000000 INFO @ Sat, 15 Sep 2018 10:58:18: 3000000 INFO @ Sat, 15 Sep 2018 10:58:18: 3000000 INFO @ Sat, 15 Sep 2018 10:58:22: 4000000 INFO @ Sat, 15 Sep 2018 10:58:23: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:58:23: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:58:23: #1 total tags in treatment: 4217962 INFO @ Sat, 15 Sep 2018 10:58:23: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:58:23: #1 tags after filtering in treatment: 4217962 INFO @ Sat, 15 Sep 2018 10:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:23: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:23: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:24: #2 number of paired peaks: 56 WARNING @ Sat, 15 Sep 2018 10:58:24: Too few paired peaks (56) 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 @ Sat, 15 Sep 2018 10:58:24: Process for pairing-model is terminated! cat: SRX4234061.20_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 `SRX4234061.20_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 `SRX4234061.20_*.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 `SRX4234061.20_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 @ Sat, 15 Sep 2018 10:58:27: 4000000 INFO @ Sat, 15 Sep 2018 10:58:27: 4000000 INFO @ Sat, 15 Sep 2018 10:58:29: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:58:29: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:58:29: #1 total tags in treatment: 4217962 INFO @ Sat, 15 Sep 2018 10:58:29: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:58:29: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:58:29: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:58:29: #1 total tags in treatment: 4217962 INFO @ Sat, 15 Sep 2018 10:58:29: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:58:29: #1 tags after filtering in treatment: 4217962 INFO @ Sat, 15 Sep 2018 10:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:29: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:29: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:29: #1 tags after filtering in treatment: 4217962 INFO @ Sat, 15 Sep 2018 10:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:29: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:29: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:29: #2 number of paired peaks: 56 WARNING @ Sat, 15 Sep 2018 10:58:29: Too few paired peaks (56) 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 @ Sat, 15 Sep 2018 10:58:29: Process for pairing-model is terminated! INFO @ Sat, 15 Sep 2018 10:58:29: #2 number of paired peaks: 56 WARNING @ Sat, 15 Sep 2018 10:58:29: Too few paired peaks (56) 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 @ Sat, 15 Sep 2018 10:58:29: Process for pairing-model is terminated! cat: SRX4234061.10_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 cat: SRX4234061.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4234061.10_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 `SRX4234061.10_*.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 `SRX4234061.10_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 `SRX4234061.05_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 `SRX4234061.05_*.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 `SRX4234061.05_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。