Job ID = 9162224 sra ファイルのダウンロード中... Completed: 185271K bytes transferred in 4 seconds (319546K bits/sec), in 1 file, 2 directories. 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 8626257 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1738697/SRR3471228.sra Written 8626257 spots total 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: 00:01:40 8626257 reads; of these: 8626257 (100.00%) were unpaired; of these: 733171 (8.50%) aligned 0 times 4927317 (57.12%) aligned exactly 1 time 2965769 (34.38%) aligned >1 times 91.50% overall alignment rate Time searching: 00:01:40 Overall time: 00:01:40 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_rmdupse_core] 5009207 / 7893086 = 0.6346 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, 28 Jun 2017 06:55:24: # Command line: callpeak -t SRX1738697.bam -f BAM -g 12100000 -n SRX1738697.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1738697.05 # format = BAM # ChIP-seq file = ['SRX1738697.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, 28 Jun 2017 06:55:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:55:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:55:24: # Command line: callpeak -t SRX1738697.bam -f BAM -g 12100000 -n SRX1738697.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1738697.20 # format = BAM # ChIP-seq file = ['SRX1738697.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, 28 Jun 2017 06:55:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:55:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:55:24: # Command line: callpeak -t SRX1738697.bam -f BAM -g 12100000 -n SRX1738697.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1738697.10 # format = BAM # ChIP-seq file = ['SRX1738697.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, 28 Jun 2017 06:55:24: #1 read tag files... INFO @ Wed, 28 Jun 2017 06:55:24: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 06:55:30: 1000000 INFO @ Wed, 28 Jun 2017 06:55:30: 1000000 INFO @ Wed, 28 Jun 2017 06:55:31: 1000000 INFO @ Wed, 28 Jun 2017 06:55:37: 2000000 INFO @ Wed, 28 Jun 2017 06:55:37: 2000000 INFO @ Wed, 28 Jun 2017 06:55:37: 2000000 INFO @ Wed, 28 Jun 2017 06:55:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:55:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:55:43: #1 total tags in treatment: 2883879 INFO @ Wed, 28 Jun 2017 06:55:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:55:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 06:55:43: #1 tags after filtering in treatment: 2883879 INFO @ Wed, 28 Jun 2017 06:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 06:55:43: #1 finished! INFO @ Wed, 28 Jun 2017 06:55:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:55:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:55:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:55:43: #1 total tags in treatment: 2883879 INFO @ Wed, 28 Jun 2017 06:55:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:55:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 06:55:43: #1 tags after filtering in treatment: 2883879 INFO @ Wed, 28 Jun 2017 06:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 06:55:43: #1 finished! INFO @ Wed, 28 Jun 2017 06:55:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:55:43: #2 number of paired peaks: 319 WARNING @ Wed, 28 Jun 2017 06:55:43: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Wed, 28 Jun 2017 06:55:43: start model_add_line... INFO @ Wed, 28 Jun 2017 06:55:43: start X-correlation... INFO @ Wed, 28 Jun 2017 06:55:43: end of X-cor INFO @ Wed, 28 Jun 2017 06:55:43: #2 finished! INFO @ Wed, 28 Jun 2017 06:55:43: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 06:55:43: #2 alternative fragment length(s) may be 0,28,83,109,156,170,208,255,293,375 bps INFO @ Wed, 28 Jun 2017 06:55:43: #2.2 Generate R script for model : SRX1738697.10_model.r WARNING @ Wed, 28 Jun 2017 06:55:43: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 06:55:43: #2 You may need to consider one of the other alternative d(s): 0,28,83,109,156,170,208,255,293,375 WARNING @ Wed, 28 Jun 2017 06:55:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 06:55:43: #3 Call peaks... INFO @ Wed, 28 Jun 2017 06:55:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 06:55:43: #2 number of paired peaks: 319 WARNING @ Wed, 28 Jun 2017 06:55:43: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Wed, 28 Jun 2017 06:55:43: start model_add_line... INFO @ Wed, 28 Jun 2017 06:55:43: start X-correlation... INFO @ Wed, 28 Jun 2017 06:55:43: end of X-cor INFO @ Wed, 28 Jun 2017 06:55:43: #2 finished! INFO @ Wed, 28 Jun 2017 06:55:43: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 06:55:43: #2 alternative fragment length(s) may be 0,28,83,109,156,170,208,255,293,375 bps INFO @ Wed, 28 Jun 2017 06:55:43: #2.2 Generate R script for model : SRX1738697.20_model.r WARNING @ Wed, 28 Jun 2017 06:55:43: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 06:55:43: #2 You may need to consider one of the other alternative d(s): 0,28,83,109,156,170,208,255,293,375 WARNING @ Wed, 28 Jun 2017 06:55:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 06:55:43: #3 Call peaks... INFO @ Wed, 28 Jun 2017 06:55:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 06:55:43: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 06:55:43: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 06:55:43: #1 total tags in treatment: 2883879 INFO @ Wed, 28 Jun 2017 06:55:43: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 06:55:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 06:55:43: #1 tags after filtering in treatment: 2883879 INFO @ Wed, 28 Jun 2017 06:55:43: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 06:55:43: #1 finished! INFO @ Wed, 28 Jun 2017 06:55:43: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 06:55:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 06:55:44: #2 number of paired peaks: 319 WARNING @ Wed, 28 Jun 2017 06:55:44: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Wed, 28 Jun 2017 06:55:44: start model_add_line... INFO @ Wed, 28 Jun 2017 06:55:44: start X-correlation... INFO @ Wed, 28 Jun 2017 06:55:44: end of X-cor INFO @ Wed, 28 Jun 2017 06:55:44: #2 finished! INFO @ Wed, 28 Jun 2017 06:55:44: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 06:55:44: #2 alternative fragment length(s) may be 0,28,83,109,156,170,208,255,293,375 bps INFO @ Wed, 28 Jun 2017 06:55:44: #2.2 Generate R script for model : SRX1738697.05_model.r WARNING @ Wed, 28 Jun 2017 06:55:44: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 06:55:44: #2 You may need to consider one of the other alternative d(s): 0,28,83,109,156,170,208,255,293,375 WARNING @ Wed, 28 Jun 2017 06:55:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 06:55:44: #3 Call peaks... INFO @ Wed, 28 Jun 2017 06:55:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 ls: cannot access SRX1738697.05.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1738697.05.bed': そのようなファイルやディレクトリはありません /var/spool/uge/nt013i/job_scripts/9162224: line 231: 57889 終了しました MACS $i /var/spool/uge/nt013i/job_scripts/9162224: line 231: 57890 終了しました MACS $i /var/spool/uge/nt013i/job_scripts/9162224: line 231: 57891 終了しました MACS $i mv: cannot stat `SRX1738697.05.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX1738697.10.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1738697.10.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX1738697.10.bb': そのようなファイルやディレクトリはありません ls: cannot access SRX1738697.20.bed: そのようなファイルやディレクトリはありません mv: cannot stat `SRX1738697.20.bed': そのようなファイルやディレクトリはありません mv: cannot stat `SRX1738697.20.bb': そのようなファイルやディレクトリはありません