Job ID = 11193000 sra ファイルのダウンロード中... Completed: 127785K bytes transferred in 5 seconds (192059K 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 6526046 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233721/SRR7360828.sra Written 6526046 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233721/SRR7360828.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: 00:01:04 6526046 reads; of these: 6526046 (100.00%) were unpaired; of these: 751216 (11.51%) aligned 0 times 4933993 (75.60%) aligned exactly 1 time 840837 (12.88%) aligned >1 times 88.49% overall alignment rate Time searching: 00:01:04 Overall time: 00:01:04 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] 2345606 / 5774830 = 0.4062 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 10:46:48: # Command line: callpeak -t SRX4233721.bam -f BAM -g 12100000 -n SRX4233721.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4233721.05 # format = BAM # ChIP-seq file = ['SRX4233721.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 10:46:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:46:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:46:48: # Command line: callpeak -t SRX4233721.bam -f BAM -g 12100000 -n SRX4233721.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4233721.10 # format = BAM # ChIP-seq file = ['SRX4233721.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 10:46:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:46:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:46:48: # Command line: callpeak -t SRX4233721.bam -f BAM -g 12100000 -n SRX4233721.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4233721.20 # format = BAM # ChIP-seq file = ['SRX4233721.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 10:46:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:46:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:46:54: 1000000 INFO @ Sat, 15 Sep 2018 10:46:54: 1000000 INFO @ Sat, 15 Sep 2018 10:46:54: 1000000 INFO @ Sat, 15 Sep 2018 10:47:00: 2000000 INFO @ Sat, 15 Sep 2018 10:47:00: 2000000 INFO @ Sat, 15 Sep 2018 10:47:01: 2000000 INFO @ Sat, 15 Sep 2018 10:47:07: 3000000 INFO @ Sat, 15 Sep 2018 10:47:07: 3000000 INFO @ Sat, 15 Sep 2018 10:47:08: 3000000 INFO @ Sat, 15 Sep 2018 10:47:09: #1 tag size is determined as 48 bps INFO @ Sat, 15 Sep 2018 10:47:09: #1 tag size = 48 INFO @ Sat, 15 Sep 2018 10:47:09: #1 total tags in treatment: 3429224 INFO @ Sat, 15 Sep 2018 10:47:09: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:47:09: #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 10:47:09: #1 tags after filtering in treatment: 3429224 INFO @ Sat, 15 Sep 2018 10:47:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:47:09: #1 finished! INFO @ Sat, 15 Sep 2018 10:47:09: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:47:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:47:10: #2 number of paired peaks: 52 WARNING @ Sat, 15 Sep 2018 10:47:10: Too few paired peaks (52) 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 10:47:10: Process for pairing-model is terminated! cat: SRX4233721.10_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 `SRX4233721.10_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 `SRX4233721.10_*.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 `SRX4233721.10_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 @ Sat, 15 Sep 2018 10:47:10: #1 tag size is determined as 48 bps INFO @ Sat, 15 Sep 2018 10:47:10: #1 tag size = 48 INFO @ Sat, 15 Sep 2018 10:47:10: #1 total tags in treatment: 3429224 INFO @ Sat, 15 Sep 2018 10:47:10: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:47:10: #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 10:47:10: #1 tags after filtering in treatment: 3429224 INFO @ Sat, 15 Sep 2018 10:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:47:10: #1 finished! INFO @ Sat, 15 Sep 2018 10:47:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:47:10: #2 number of paired peaks: 52 WARNING @ Sat, 15 Sep 2018 10:47:10: Too few paired peaks (52) 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 10:47:10: Process for pairing-model is terminated! cat: SRX4233721.20_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 `SRX4233721.20_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 `SRX4233721.20_*.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 `SRX4233721.20_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 10:47:11: #1 tag size is determined as 48 bps INFO @ Sat, 15 Sep 2018 10:47:11: #1 tag size = 48 INFO @ Sat, 15 Sep 2018 10:47:11: #1 total tags in treatment: 3429224 INFO @ Sat, 15 Sep 2018 10:47:11: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:47:11: #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 10:47:11: #1 tags after filtering in treatment: 3429224 INFO @ Sat, 15 Sep 2018 10:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:47:11: #1 finished! INFO @ Sat, 15 Sep 2018 10:47:11: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:47:12: #2 number of paired peaks: 52 WARNING @ Sat, 15 Sep 2018 10:47:12: Too few paired peaks (52) 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 10:47:12: Process for pairing-model is terminated! cat: SRX4233721.05_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): 5 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4233721.05_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 `SRX4233721.05_*.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 `SRX4233721.05_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。