Job ID = 10937733 sra ファイルのダウンロード中... Completed: 522330K bytes transferred in 669 seconds (6389K 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 15268714 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3557774/SRR6467843.sra Written 15268714 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3557774/SRR6467843.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: 00:03:06 15268714 reads; of these: 15268714 (100.00%) were unpaired; of these: 1134179 (7.43%) aligned 0 times 12630949 (82.72%) aligned exactly 1 time 1503586 (9.85%) aligned >1 times 92.57% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 4428323 / 14134535 = 0.3133 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 03:12:07: # Command line: callpeak -t SRX3557774.bam -f BAM -g 12100000 -n SRX3557774.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3557774.05 # format = BAM # ChIP-seq file = ['SRX3557774.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 03:12:07: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:12:07: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:12:07: # Command line: callpeak -t SRX3557774.bam -f BAM -g 12100000 -n SRX3557774.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3557774.10 # format = BAM # ChIP-seq file = ['SRX3557774.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 03:12:07: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:12:07: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:12:07: # Command line: callpeak -t SRX3557774.bam -f BAM -g 12100000 -n SRX3557774.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3557774.20 # format = BAM # ChIP-seq file = ['SRX3557774.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 03:12:07: #1 read tag files... INFO @ Fri, 10 Aug 2018 03:12:07: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 03:12:14: 1000000 INFO @ Fri, 10 Aug 2018 03:12:14: 1000000 INFO @ Fri, 10 Aug 2018 03:12:14: 1000000 INFO @ Fri, 10 Aug 2018 03:12:21: 2000000 INFO @ Fri, 10 Aug 2018 03:12:21: 2000000 INFO @ Fri, 10 Aug 2018 03:12:21: 2000000 INFO @ Fri, 10 Aug 2018 03:12:28: 3000000 INFO @ Fri, 10 Aug 2018 03:12:28: 3000000 INFO @ Fri, 10 Aug 2018 03:12:28: 3000000 INFO @ Fri, 10 Aug 2018 03:12:35: 4000000 INFO @ Fri, 10 Aug 2018 03:12:35: 4000000 INFO @ Fri, 10 Aug 2018 03:12:35: 4000000 INFO @ Fri, 10 Aug 2018 03:12:41: 5000000 INFO @ Fri, 10 Aug 2018 03:12:42: 5000000 INFO @ Fri, 10 Aug 2018 03:12:42: 5000000 INFO @ Fri, 10 Aug 2018 03:12:48: 6000000 INFO @ Fri, 10 Aug 2018 03:12:49: 6000000 INFO @ Fri, 10 Aug 2018 03:12:49: 6000000 INFO @ Fri, 10 Aug 2018 03:12:55: 7000000 INFO @ Fri, 10 Aug 2018 03:12:56: 7000000 INFO @ Fri, 10 Aug 2018 03:12:56: 7000000 INFO @ Fri, 10 Aug 2018 03:13:02: 8000000 INFO @ Fri, 10 Aug 2018 03:13:03: 8000000 INFO @ Fri, 10 Aug 2018 03:13:04: 8000000 INFO @ Fri, 10 Aug 2018 03:13:08: 9000000 INFO @ Fri, 10 Aug 2018 03:13:10: 9000000 INFO @ Fri, 10 Aug 2018 03:13:11: 9000000 INFO @ Fri, 10 Aug 2018 03:13:13: #1 tag size is determined as 65 bps INFO @ Fri, 10 Aug 2018 03:13:13: #1 tag size = 65 INFO @ Fri, 10 Aug 2018 03:13:13: #1 total tags in treatment: 9706212 INFO @ Fri, 10 Aug 2018 03:13:13: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:13:13: #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 03:13:14: #1 tags after filtering in treatment: 9706212 INFO @ Fri, 10 Aug 2018 03:13:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:13:14: #1 finished! INFO @ Fri, 10 Aug 2018 03:13:14: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:13:14: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 03:13:14: 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 03:13:14: Process for pairing-model is terminated! cat: SRX3557774.05_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 `SRX3557774.05_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 `SRX3557774.05_*.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 `SRX3557774.05_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 @ Fri, 10 Aug 2018 03:13:15: #1 tag size is determined as 65 bps INFO @ Fri, 10 Aug 2018 03:13:15: #1 tag size = 65 INFO @ Fri, 10 Aug 2018 03:13:15: #1 total tags in treatment: 9706212 INFO @ Fri, 10 Aug 2018 03:13:15: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:13:15: #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 03:13:15: #1 tags after filtering in treatment: 9706212 INFO @ Fri, 10 Aug 2018 03:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:13:15: #1 finished! INFO @ Fri, 10 Aug 2018 03:13:15: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:13:16: #1 tag size is determined as 65 bps INFO @ Fri, 10 Aug 2018 03:13:16: #1 tag size = 65 INFO @ Fri, 10 Aug 2018 03:13:16: #1 total tags in treatment: 9706212 INFO @ Fri, 10 Aug 2018 03:13:16: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 03:13:16: #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 03:13:16: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 03:13:16: 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 03:13:16: Process for pairing-model is terminated! cat: SRX3557774.20_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 `SRX3557774.20_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 `SRX3557774.20_*.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 `SRX3557774.20_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 03:13:16: #1 tags after filtering in treatment: 9706212 INFO @ Fri, 10 Aug 2018 03:13:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 03:13:16: #1 finished! INFO @ Fri, 10 Aug 2018 03:13:16: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 03:13:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 03:13:16: #2 number of paired peaks: 0 WARNING @ Fri, 10 Aug 2018 03:13:16: 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 03:13:16: Process for pairing-model is terminated! cat: SRX3557774.10_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 `SRX3557774.10_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 `SRX3557774.10_*.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 `SRX3557774.10_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。