Job ID = 10937737 sra ファイルのダウンロード中... Completed: 439506K bytes transferred in 38 seconds (93897K 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 12789124 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3557777/SRR6467846.sra Written 12789124 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3557777/SRR6467846.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:23 12789124 reads; of these: 12789124 (100.00%) were unpaired; of these: 374132 (2.93%) aligned 0 times 11083457 (86.66%) aligned exactly 1 time 1331535 (10.41%) aligned >1 times 97.07% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 3142795 / 12414992 = 0.2531 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 @ Fri, 10 Aug 2018 03:02:16: # Command line: callpeak -t SRX3557777.bam -f BAM -g 12100000 -n SRX3557777.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3557777.05 # format = BAM # ChIP-seq file = ['SRX3557777.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 @ Fri, 10 Aug 2018 03:02:16: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:02:16: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:02:16: # Command line: callpeak -t SRX3557777.bam -f BAM -g 12100000 -n SRX3557777.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3557777.10 # format = BAM # ChIP-seq file = ['SRX3557777.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 @ Fri, 10 Aug 2018 03:02:16: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:02:16: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:02:16: # Command line: callpeak -t SRX3557777.bam -f BAM -g 12100000 -n SRX3557777.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3557777.20 # format = BAM # ChIP-seq file = ['SRX3557777.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 @ Fri, 10 Aug 2018 03:02:16: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:02:16: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:02:25: 1000000 INFO @ Fri, 10 Aug 2018 03:02:26: 1000000 INFO @ Fri, 10 Aug 2018 03:02:26: 1000000 INFO @ Fri, 10 Aug 2018 03:02:34: 2000000 INFO @ Fri, 10 Aug 2018 03:02:35: 2000000 INFO @ Fri, 10 Aug 2018 03:02:35: 2000000 INFO @ Fri, 10 Aug 2018 03:02:43: 3000000 INFO @ Fri, 10 Aug 2018 03:02:45: 3000000 INFO @ Fri, 10 Aug 2018 03:02:45: 3000000 INFO @ Fri, 10 Aug 2018 03:02:51: 4000000 INFO @ Fri, 10 Aug 2018 03:02:54: 4000000 INFO @ Fri, 10 Aug 2018 03:02:54: 4000000 INFO @ Fri, 10 Aug 2018 03:03:00: 5000000 INFO @ Fri, 10 Aug 2018 03:03:04: 5000000 INFO @ Fri, 10 Aug 2018 03:03:04: 5000000 INFO @ Fri, 10 Aug 2018 03:03:09: 6000000 INFO @ Fri, 10 Aug 2018 03:03:13: 6000000 INFO @ Fri, 10 Aug 2018 03:03:13: 6000000 INFO @ Fri, 10 Aug 2018 03:03:18: 7000000 INFO @ Fri, 10 Aug 2018 03:03:23: 7000000 INFO @ Fri, 10 Aug 2018 03:03:23: 7000000 INFO @ Fri, 10 Aug 2018 03:03:27: 8000000 INFO @ Fri, 10 Aug 2018 03:03:33: 8000000 INFO @ Fri, 10 Aug 2018 03:03:33: 8000000 INFO @ Fri, 10 Aug 2018 03:03:35: 9000000 INFO @ Fri, 10 Aug 2018 03:03:38: #1 tag size is determined as 65 bps INFO @ Fri, 10 Aug 2018 03:03:38: #1 tag size = 65 INFO @ Fri, 10 Aug 2018 03:03:38: #1 total tags in treatment: 9272197 INFO @ Fri, 10 Aug 2018 03:03:38: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:03:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:03:38: #1 tags after filtering in treatment: 9272197 INFO @ Fri, 10 Aug 2018 03:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:03:38: #1 finished! INFO @ Fri, 10 Aug 2018 03:03:38: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:03:38: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 03:03:38: 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 @ Fri, 10 Aug 2018 03:03:38: Process for pairing-model is terminated! cat: SRX3557777.20_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 `SRX3557777.20_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 `SRX3557777.20_*.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 `SRX3557777.20_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 @ Fri, 10 Aug 2018 03:03:42: 9000000 INFO @ Fri, 10 Aug 2018 03:03:42: 9000000 INFO @ Fri, 10 Aug 2018 03:03:44: #1 tag size is determined as 65 bps INFO @ Fri, 10 Aug 2018 03:03:44: #1 tag size = 65 INFO @ Fri, 10 Aug 2018 03:03:44: #1 total tags in treatment: 9272197 INFO @ Fri, 10 Aug 2018 03:03:44: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:03:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:03:45: #1 tags after filtering in treatment: 9272197 INFO @ Fri, 10 Aug 2018 03:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:03:45: #1 finished! INFO @ Fri, 10 Aug 2018 03:03:45: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:03:45: #1 tag size is determined as 65 bps INFO @ Fri, 10 Aug 2018 03:03:45: #1 tag size = 65 INFO @ Fri, 10 Aug 2018 03:03:45: #1 total tags in treatment: 9272197 INFO @ Fri, 10 Aug 2018 03:03:45: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:03:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 03:03:45: #1 tags after filtering in treatment: 9272197 INFO @ Fri, 10 Aug 2018 03:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:03:45: #1 finished! INFO @ Fri, 10 Aug 2018 03:03:45: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:03:45: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 03:03:45: 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 @ Fri, 10 Aug 2018 03:03:45: Process for pairing-model is terminated! cat: SRX3557777.10_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3557777.10_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 `SRX3557777.10_*.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 `SRX3557777.10_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 @ Fri, 10 Aug 2018 03:03:45: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 03:03:45: 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 @ Fri, 10 Aug 2018 03:03:45: Process for pairing-model is terminated! cat: SRX3557777.05_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): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3557777.05_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 `SRX3557777.05_*.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 `SRX3557777.05_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。