Job ID = 10254462 sra ファイルのダウンロード中... Completed: 328966K bytes transferred in 15 seconds (172819K bits/sec), in 1 file. Completed: 346176K bytes transferred in 15 seconds (185446K 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 9368519 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353399/SRR6246272.sra Written 9368519 spots total Written 9888046 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3353399/SRR6246273.sra Written 9888046 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 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: 00:03:22 19256565 reads; of these: 19256565 (100.00%) were unpaired; of these: 894998 (4.65%) aligned 0 times 16328187 (84.79%) aligned exactly 1 time 2033380 (10.56%) aligned >1 times 95.35% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 7145092 / 18361567 = 0.3891 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, 06 Dec 2017 18:30:55: # Command line: callpeak -t SRX3353399.bam -f BAM -g 12100000 -n SRX3353399.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3353399.20 # format = BAM # ChIP-seq file = ['SRX3353399.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, 06 Dec 2017 18:30:55: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:30:55: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:30:55: # Command line: callpeak -t SRX3353399.bam -f BAM -g 12100000 -n SRX3353399.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3353399.05 # format = BAM # ChIP-seq file = ['SRX3353399.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, 06 Dec 2017 18:30:55: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:30:55: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:30:55: # Command line: callpeak -t SRX3353399.bam -f BAM -g 12100000 -n SRX3353399.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3353399.10 # format = BAM # ChIP-seq file = ['SRX3353399.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, 06 Dec 2017 18:30:55: #1 read tag files... INFO @ Wed, 06 Dec 2017 18:30:55: #1 read treatment tags... INFO @ Wed, 06 Dec 2017 18:31:01: 1000000 INFO @ Wed, 06 Dec 2017 18:31:02: 1000000 INFO @ Wed, 06 Dec 2017 18:31:02: 1000000 INFO @ Wed, 06 Dec 2017 18:31:08: 2000000 INFO @ Wed, 06 Dec 2017 18:31:08: 2000000 INFO @ Wed, 06 Dec 2017 18:31:08: 2000000 INFO @ Wed, 06 Dec 2017 18:31:14: 3000000 INFO @ Wed, 06 Dec 2017 18:31:14: 3000000 INFO @ Wed, 06 Dec 2017 18:31:15: 3000000 INFO @ Wed, 06 Dec 2017 18:31:20: 4000000 INFO @ Wed, 06 Dec 2017 18:31:21: 4000000 INFO @ Wed, 06 Dec 2017 18:31:21: 4000000 INFO @ Wed, 06 Dec 2017 18:31:27: 5000000 INFO @ Wed, 06 Dec 2017 18:31:27: 5000000 INFO @ Wed, 06 Dec 2017 18:31:28: 5000000 INFO @ Wed, 06 Dec 2017 18:31:33: 6000000 INFO @ Wed, 06 Dec 2017 18:31:34: 6000000 INFO @ Wed, 06 Dec 2017 18:31:35: 6000000 INFO @ Wed, 06 Dec 2017 18:31:39: 7000000 INFO @ Wed, 06 Dec 2017 18:31:40: 7000000 INFO @ Wed, 06 Dec 2017 18:31:41: 7000000 INFO @ Wed, 06 Dec 2017 18:31:46: 8000000 INFO @ Wed, 06 Dec 2017 18:31:46: 8000000 INFO @ Wed, 06 Dec 2017 18:31:48: 8000000 INFO @ Wed, 06 Dec 2017 18:31:52: 9000000 INFO @ Wed, 06 Dec 2017 18:31:53: 9000000 INFO @ Wed, 06 Dec 2017 18:31:55: 9000000 INFO @ Wed, 06 Dec 2017 18:31:58: 10000000 INFO @ Wed, 06 Dec 2017 18:31:59: 10000000 INFO @ Wed, 06 Dec 2017 18:32:01: 10000000 INFO @ Wed, 06 Dec 2017 18:32:05: 11000000 INFO @ Wed, 06 Dec 2017 18:32:06: 11000000 INFO @ Wed, 06 Dec 2017 18:32:06: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:32:06: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:32:06: #1 total tags in treatment: 11216475 INFO @ Wed, 06 Dec 2017 18:32:06: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:32:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:32:06: #1 tags after filtering in treatment: 11216475 INFO @ Wed, 06 Dec 2017 18:32:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 18:32:06: #1 finished! INFO @ Wed, 06 Dec 2017 18:32:06: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:32:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:32:07: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:32:07: 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, 06 Dec 2017 18:32:07: Process for pairing-model is terminated! cat: SRX3353399.05_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 `SRX3353399.05_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 `SRX3353399.05_*.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 `SRX3353399.05_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, 06 Dec 2017 18:32:07: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:32:07: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:32:07: #1 total tags in treatment: 11216475 INFO @ Wed, 06 Dec 2017 18:32:07: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:32:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:32:07: #1 tags after filtering in treatment: 11216475 INFO @ Wed, 06 Dec 2017 18:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 18:32:07: #1 finished! INFO @ Wed, 06 Dec 2017 18:32:07: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:32:08: 11000000 INFO @ Wed, 06 Dec 2017 18:32:08: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:32:08: 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, 06 Dec 2017 18:32:08: Process for pairing-model is terminated! cat: SRX3353399.10_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 `SRX3353399.10_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 `SRX3353399.10_*.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 `SRX3353399.10_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 @ Wed, 06 Dec 2017 18:32:09: #1 tag size is determined as 51 bps INFO @ Wed, 06 Dec 2017 18:32:09: #1 tag size = 51 INFO @ Wed, 06 Dec 2017 18:32:09: #1 total tags in treatment: 11216475 INFO @ Wed, 06 Dec 2017 18:32:09: #1 user defined the maximum tags... INFO @ Wed, 06 Dec 2017 18:32:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 06 Dec 2017 18:32:09: #1 tags after filtering in treatment: 11216475 INFO @ Wed, 06 Dec 2017 18:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 06 Dec 2017 18:32:09: #1 finished! INFO @ Wed, 06 Dec 2017 18:32:09: #2 Build Peak Model... INFO @ Wed, 06 Dec 2017 18:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 06 Dec 2017 18:32:10: #2 number of paired peaks: 0 WARNING @ Wed, 06 Dec 2017 18:32:10: 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, 06 Dec 2017 18:32:10: Process for pairing-model is terminated! cat: SRX3353399.20_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 `SRX3353399.20_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 `SRX3353399.20_*.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 `SRX3353399.20_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。