Job ID = 11245238 sra ファイルのダウンロード中... Completed: 453917K bytes transferred in 6 seconds (566476K 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 16551221 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717380/SRR7878703.sra Written 16551221 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4717380/SRR7878703.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: 00:03:44 16551221 reads; of these: 16551221 (100.00%) were unpaired; of these: 871744 (5.27%) aligned 0 times 14518644 (87.72%) aligned exactly 1 time 1160833 (7.01%) aligned >1 times 94.73% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 7402235 / 15679477 = 0.4721 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 00:04:42: # Command line: callpeak -t SRX4717380.bam -f BAM -g 12100000 -n SRX4717380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4717380.10 # format = BAM # ChIP-seq file = ['SRX4717380.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 00:04:42: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:42: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:42: # Command line: callpeak -t SRX4717380.bam -f BAM -g 12100000 -n SRX4717380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4717380.20 # format = BAM # ChIP-seq file = ['SRX4717380.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 00:04:42: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:42: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:42: # Command line: callpeak -t SRX4717380.bam -f BAM -g 12100000 -n SRX4717380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4717380.05 # format = BAM # ChIP-seq file = ['SRX4717380.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 00:04:42: #1 read tag files... INFO @ Wed, 10 Oct 2018 00:04:42: #1 read treatment tags... INFO @ Wed, 10 Oct 2018 00:04:52: 1000000 INFO @ Wed, 10 Oct 2018 00:04:52: 1000000 INFO @ Wed, 10 Oct 2018 00:04:52: 1000000 INFO @ Wed, 10 Oct 2018 00:05:02: 2000000 INFO @ Wed, 10 Oct 2018 00:05:03: 2000000 INFO @ Wed, 10 Oct 2018 00:05:03: 2000000 INFO @ Wed, 10 Oct 2018 00:05:12: 3000000 INFO @ Wed, 10 Oct 2018 00:05:14: 3000000 INFO @ Wed, 10 Oct 2018 00:05:14: 3000000 INFO @ Wed, 10 Oct 2018 00:05:22: 4000000 INFO @ Wed, 10 Oct 2018 00:05:24: 4000000 INFO @ Wed, 10 Oct 2018 00:05:24: 4000000 INFO @ Wed, 10 Oct 2018 00:05:31: 5000000 INFO @ Wed, 10 Oct 2018 00:05:35: 5000000 INFO @ Wed, 10 Oct 2018 00:05:35: 5000000 INFO @ Wed, 10 Oct 2018 00:05:40: 6000000 INFO @ Wed, 10 Oct 2018 00:05:44: 6000000 INFO @ Wed, 10 Oct 2018 00:05:45: 6000000 INFO @ Wed, 10 Oct 2018 00:05:51: 7000000 INFO @ Wed, 10 Oct 2018 00:05:54: 7000000 INFO @ Wed, 10 Oct 2018 00:05:57: 7000000 INFO @ Wed, 10 Oct 2018 00:06:01: 8000000 INFO @ Wed, 10 Oct 2018 00:06:03: 8000000 INFO @ Wed, 10 Oct 2018 00:06:03: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:06:03: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:06:03: #1 total tags in treatment: 8277242 INFO @ Wed, 10 Oct 2018 00:06:03: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:03: #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 00:06:03: #1 tags after filtering in treatment: 8277242 INFO @ Wed, 10 Oct 2018 00:06:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:06:03: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:03: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:04: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:04: 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 00:06:04: Process for pairing-model is terminated! cat: SRX4717380.05_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 `SRX4717380.05_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 `SRX4717380.05_*.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 `SRX4717380.05_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 00:06:05: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:06:05: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:06:05: #1 total tags in treatment: 8277242 INFO @ Wed, 10 Oct 2018 00:06:05: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:05: #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 00:06:05: #1 tags after filtering in treatment: 8277242 INFO @ Wed, 10 Oct 2018 00:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:06:05: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:05: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:06: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:06: 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 00:06:06: Process for pairing-model is terminated! cat: SRX4717380.20_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): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX4717380.20_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 `SRX4717380.20_*.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 `SRX4717380.20_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 00:06:08: 8000000 INFO @ Wed, 10 Oct 2018 00:06:10: #1 tag size is determined as 76 bps INFO @ Wed, 10 Oct 2018 00:06:10: #1 tag size = 76 INFO @ Wed, 10 Oct 2018 00:06:10: #1 total tags in treatment: 8277242 INFO @ Wed, 10 Oct 2018 00:06:10: #1 user defined the maximum tags... INFO @ Wed, 10 Oct 2018 00:06:10: #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 00:06:10: #1 tags after filtering in treatment: 8277242 INFO @ Wed, 10 Oct 2018 00:06:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 10 Oct 2018 00:06:10: #1 finished! INFO @ Wed, 10 Oct 2018 00:06:10: #2 Build Peak Model... INFO @ Wed, 10 Oct 2018 00:06:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 10 Oct 2018 00:06:11: #2 number of paired peaks: 0 WARNING @ Wed, 10 Oct 2018 00:06:11: 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 00:06:11: Process for pairing-model is terminated! cat: SRX4717380.10_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 `SRX4717380.10_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 `SRX4717380.10_*.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 `SRX4717380.10_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。