Job ID = 9161870 sra ファイルのダウンロード中... Completed: 333589K bytes transferred in 5 seconds (463327K 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 7841572 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1181996/SRR2239564.sra Written 7841572 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: 00:01:28 7841572 reads; of these: 7841572 (100.00%) were unpaired; of these: 210511 (2.68%) aligned 0 times 6085053 (77.60%) aligned exactly 1 time 1546008 (19.72%) aligned >1 times 97.32% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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] 3932489 / 7631061 = 0.5153 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 04:52:44: # Command line: callpeak -t SRX1181996.bam -f BAM -g 12100000 -n SRX1181996.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1181996.10 # format = BAM # ChIP-seq file = ['SRX1181996.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 04:52:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:52:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:52:44: # Command line: callpeak -t SRX1181996.bam -f BAM -g 12100000 -n SRX1181996.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1181996.20 # format = BAM # ChIP-seq file = ['SRX1181996.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 04:52:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:52:44: # Command line: callpeak -t SRX1181996.bam -f BAM -g 12100000 -n SRX1181996.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1181996.05 # format = BAM # ChIP-seq file = ['SRX1181996.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 04:52:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:52:44: #1 read tag files... INFO @ Wed, 28 Jun 2017 04:52:44: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 04:52:52: 1000000 INFO @ Wed, 28 Jun 2017 04:52:52: 1000000 INFO @ Wed, 28 Jun 2017 04:52:52: 1000000 INFO @ Wed, 28 Jun 2017 04:53:00: 2000000 INFO @ Wed, 28 Jun 2017 04:53:00: 2000000 INFO @ Wed, 28 Jun 2017 04:53:00: 2000000 INFO @ Wed, 28 Jun 2017 04:53:07: 3000000 INFO @ Wed, 28 Jun 2017 04:53:07: 3000000 INFO @ Wed, 28 Jun 2017 04:53:07: 3000000 INFO @ Wed, 28 Jun 2017 04:53:13: #1 tag size is determined as 49 bps INFO @ Wed, 28 Jun 2017 04:53:13: #1 tag size = 49 INFO @ Wed, 28 Jun 2017 04:53:13: #1 total tags in treatment: 3698572 INFO @ Wed, 28 Jun 2017 04:53:13: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #1 tag size is determined as 49 bps INFO @ Wed, 28 Jun 2017 04:53:13: #1 tag size = 49 INFO @ Wed, 28 Jun 2017 04:53:13: #1 total tags in treatment: 3698572 INFO @ Wed, 28 Jun 2017 04:53:13: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #1 tags after filtering in treatment: 3698572 INFO @ Wed, 28 Jun 2017 04:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:53:13: #1 finished! INFO @ Wed, 28 Jun 2017 04:53:13: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:53:13: #1 tag size is determined as 49 bps INFO @ Wed, 28 Jun 2017 04:53:13: #1 tag size = 49 INFO @ Wed, 28 Jun 2017 04:53:13: #1 total tags in treatment: 3698572 INFO @ Wed, 28 Jun 2017 04:53:13: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #1 tags after filtering in treatment: 3698572 INFO @ Wed, 28 Jun 2017 04:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:53:13: #1 finished! INFO @ Wed, 28 Jun 2017 04:53:13: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:53:13: #1 tags after filtering in treatment: 3698572 INFO @ Wed, 28 Jun 2017 04:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 04:53:13: #1 finished! INFO @ Wed, 28 Jun 2017 04:53:13: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 04:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 04:53:13: #2 number of paired peaks: 121 WARNING @ Wed, 28 Jun 2017 04:53:13: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Wed, 28 Jun 2017 04:53:13: start model_add_line... INFO @ Wed, 28 Jun 2017 04:53:13: start X-correlation... INFO @ Wed, 28 Jun 2017 04:53:13: end of X-cor INFO @ Wed, 28 Jun 2017 04:53:13: #2 finished! INFO @ Wed, 28 Jun 2017 04:53:13: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 04:53:13: #2 alternative fragment length(s) may be 0,30,79,126,169,206,249,291,330,388,450,520,564 bps INFO @ Wed, 28 Jun 2017 04:53:13: #2.2 Generate R script for model : SRX1181996.10_model.r WARNING @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #2 You may need to consider one of the other alternative d(s): 0,30,79,126,169,206,249,291,330,388,450,520,564 WARNING @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:53:13: #2 number of paired peaks: 121 WARNING @ Wed, 28 Jun 2017 04:53:13: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Wed, 28 Jun 2017 04:53:13: start model_add_line... INFO @ Wed, 28 Jun 2017 04:53:13: start X-correlation... INFO @ Wed, 28 Jun 2017 04:53:13: end of X-cor INFO @ Wed, 28 Jun 2017 04:53:13: #2 finished! INFO @ Wed, 28 Jun 2017 04:53:13: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 04:53:13: #2 alternative fragment length(s) may be 0,30,79,126,169,206,249,291,330,388,450,520,564 bps INFO @ Wed, 28 Jun 2017 04:53:13: #2.2 Generate R script for model : SRX1181996.05_model.r WARNING @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #2 You may need to consider one of the other alternative d(s): 0,30,79,126,169,206,249,291,330,388,450,520,564 WARNING @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:53:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 04:53:13: #2 number of paired peaks: 121 WARNING @ Wed, 28 Jun 2017 04:53:13: Fewer paired peaks (121) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 121 pairs to build model! INFO @ Wed, 28 Jun 2017 04:53:13: start model_add_line... INFO @ Wed, 28 Jun 2017 04:53:13: start X-correlation... INFO @ Wed, 28 Jun 2017 04:53:13: end of X-cor INFO @ Wed, 28 Jun 2017 04:53:13: #2 finished! INFO @ Wed, 28 Jun 2017 04:53:13: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 04:53:13: #2 alternative fragment length(s) may be 0,30,79,126,169,206,249,291,330,388,450,520,564 bps INFO @ Wed, 28 Jun 2017 04:53:13: #2.2 Generate R script for model : SRX1181996.20_model.r WARNING @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #2 You may need to consider one of the other alternative d(s): 0,30,79,126,169,206,249,291,330,388,450,520,564 WARNING @ Wed, 28 Jun 2017 04:53:13: #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 04:53:13: #3 Call peaks... INFO @ Wed, 28 Jun 2017 04:53:13: #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 SRX1181996.05.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 `SRX1181996.05.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/nt018i/job_scripts/9161870: line 231: 12792 終了しました MACS $i /var/spool/uge/nt018i/job_scripts/9161870: line 231: 12793 終了しました MACS $i /var/spool/uge/nt018i/job_scripts/9161870: line 231: 12794 終了しました MACS $i mv: cannot stat `SRX1181996.05.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 SRX1181996.10.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 `SRX1181996.10.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 `SRX1181996.10.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 SRX1181996.20.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 `SRX1181996.20.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 `SRX1181996.20.bb': そのようなファイルやディレクトリはありません