Job ID = 11634641 sra ファイルのダウンロード中... Completed: 697611K bytes transferred in 12 seconds (472115K 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 20932015 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3933756/SRR7000946.sra Written 20932015 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3933756/SRR7000946.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 Warning: skipping read 'SRR7000946.13626012 13626012 length=1' because length (1) <= # seed mismatches (0) Warning: skipping read 'SRR7000946.13626012 13626012 length=1' because it was < 2 characters long Multiseed full-index search: 00:05:00 20932015 reads; of these: 20932015 (100.00%) were unpaired; of these: 1804034 (8.62%) aligned 0 times 16446943 (78.57%) aligned exactly 1 time 2681038 (12.81%) aligned >1 times 91.38% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 12050723 / 19127981 = 0.6300 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, 15 Feb 2019 10:30:16: # Command line: callpeak -t SRX3933756.bam -f BAM -g 12100000 -n SRX3933756.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3933756.05 # format = BAM # ChIP-seq file = ['SRX3933756.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, 15 Feb 2019 10:30:16: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:30:16: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:30:16: # Command line: callpeak -t SRX3933756.bam -f BAM -g 12100000 -n SRX3933756.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3933756.20 # format = BAM # ChIP-seq file = ['SRX3933756.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, 15 Feb 2019 10:30:16: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:30:16: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:30:16: # Command line: callpeak -t SRX3933756.bam -f BAM -g 12100000 -n SRX3933756.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3933756.10 # format = BAM # ChIP-seq file = ['SRX3933756.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, 15 Feb 2019 10:30:16: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:30:16: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:30:23: 1000000 INFO @ Fri, 15 Feb 2019 10:30:24: 1000000 INFO @ Fri, 15 Feb 2019 10:30:24: 1000000 INFO @ Fri, 15 Feb 2019 10:30:31: 2000000 INFO @ Fri, 15 Feb 2019 10:30:32: 2000000 INFO @ Fri, 15 Feb 2019 10:30:32: 2000000 INFO @ Fri, 15 Feb 2019 10:30:38: 3000000 INFO @ Fri, 15 Feb 2019 10:30:40: 3000000 INFO @ Fri, 15 Feb 2019 10:30:40: 3000000 INFO @ Fri, 15 Feb 2019 10:30:46: 4000000 INFO @ Fri, 15 Feb 2019 10:30:48: 4000000 INFO @ Fri, 15 Feb 2019 10:30:48: 4000000 INFO @ Fri, 15 Feb 2019 10:30:54: 5000000 INFO @ Fri, 15 Feb 2019 10:30:56: 5000000 INFO @ Fri, 15 Feb 2019 10:30:56: 5000000 INFO @ Fri, 15 Feb 2019 10:31:03: 6000000 INFO @ Fri, 15 Feb 2019 10:31:05: 6000000 INFO @ Fri, 15 Feb 2019 10:31:05: 6000000 INFO @ Fri, 15 Feb 2019 10:31:11: 7000000 INFO @ Fri, 15 Feb 2019 10:31:12: #1 tag size is determined as 35 bps INFO @ Fri, 15 Feb 2019 10:31:12: #1 tag size = 35 INFO @ Fri, 15 Feb 2019 10:31:12: #1 total tags in treatment: 7077258 INFO @ Fri, 15 Feb 2019 10:31:12: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:31:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:31:12: #1 tags after filtering in treatment: 7077258 INFO @ Fri, 15 Feb 2019 10:31:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:31:12: #1 finished! INFO @ Fri, 15 Feb 2019 10:31:12: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:31:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:31:12: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:31:12: 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, 15 Feb 2019 10:31:12: Process for pairing-model is terminated! cat: SRX3933756.10_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 `SRX3933756.10_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 `SRX3933756.10_*.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 `SRX3933756.10_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, 15 Feb 2019 10:31:14: 7000000 INFO @ Fri, 15 Feb 2019 10:31:14: 7000000 INFO @ Fri, 15 Feb 2019 10:31:15: #1 tag size is determined as 35 bps INFO @ Fri, 15 Feb 2019 10:31:15: #1 tag size = 35 INFO @ Fri, 15 Feb 2019 10:31:15: #1 total tags in treatment: 7077258 INFO @ Fri, 15 Feb 2019 10:31:15: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:31:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:31:15: #1 tag size is determined as 35 bps INFO @ Fri, 15 Feb 2019 10:31:15: #1 tag size = 35 INFO @ Fri, 15 Feb 2019 10:31:15: #1 total tags in treatment: 7077258 INFO @ Fri, 15 Feb 2019 10:31:15: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:31:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:31:15: #1 tags after filtering in treatment: 7077258 INFO @ Fri, 15 Feb 2019 10:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:31:15: #1 finished! INFO @ Fri, 15 Feb 2019 10:31:15: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:31:15: #1 tags after filtering in treatment: 7077258 INFO @ Fri, 15 Feb 2019 10:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:31:15: #1 finished! INFO @ Fri, 15 Feb 2019 10:31:15: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:31:15: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:31:15: 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, 15 Feb 2019 10:31:15: Process for pairing-model is terminated! cat: SRX3933756.05_peaks.narrowPeak: そのようなファイルやディレクトリはありません INFO @ Fri, 15 Feb 2019 10:31:15: #2 number of paired peaks: 0 WARNING @ Fri, 15 Feb 2019 10:31:15: 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, 15 Feb 2019 10:31:15: Process for pairing-model is terminated! pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3933756.05_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 `SRX3933756.05_*.xls': そのようなファイルやディレクトリはありません cat: SRX3933756.20_peaks.narrowPeak: そのようなファイルやディレクトリはありません rm: cannot remove `SRX3933756.05_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 pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) rm: cannot remove `SRX3933756.20_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 `SRX3933756.20_*.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 `SRX3933756.20_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。