Job ID = 9157327 sra ファイルのダウンロード中... Completed: 448795K bytes transferred in 6 seconds (552502K bits/sec), in 4 files, 5 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 5759844 spots for /home/okishinya/chipatlas/results/ce10/SRX002676/SRR013616.sra Written 5759844 spots total Written 6260093 spots for /home/okishinya/chipatlas/results/ce10/SRX002676/SRR013615.sra Written 6260093 spots total Written 6460060 spots for /home/okishinya/chipatlas/results/ce10/SRX002676/SRR013614.sra Written 6460060 spots total Written 6544503 spots for /home/okishinya/chipatlas/results/ce10/SRX002676/SRR013613.sra Written 6544503 spots total 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: 00:03:27 25024500 reads; of these: 25024500 (100.00%) were unpaired; of these: 7644849 (30.55%) aligned 0 times 14735659 (58.88%) aligned exactly 1 time 2643992 (10.57%) aligned >1 times 69.45% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1629451 / 17379651 = 0.0938 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 @ Tue, 27 Jun 2017 11:29:31: # Command line: callpeak -t SRX002676.bam -f BAM -g ce -n SRX002676.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX002676.20 # format = BAM # ChIP-seq file = ['SRX002676.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:29:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:29:31: # Command line: callpeak -t SRX002676.bam -f BAM -g ce -n SRX002676.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX002676.10 # format = BAM # ChIP-seq file = ['SRX002676.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:29:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:29:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:29:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:29:31: # Command line: callpeak -t SRX002676.bam -f BAM -g ce -n SRX002676.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX002676.05 # format = BAM # ChIP-seq file = ['SRX002676.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 27 Jun 2017 11:29:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 11:29:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 11:29:37: 1000000 INFO @ Tue, 27 Jun 2017 11:29:37: 1000000 INFO @ Tue, 27 Jun 2017 11:29:37: 1000000 INFO @ Tue, 27 Jun 2017 11:29:42: 2000000 INFO @ Tue, 27 Jun 2017 11:29:43: 2000000 INFO @ Tue, 27 Jun 2017 11:29:43: 2000000 INFO @ Tue, 27 Jun 2017 11:29:48: 3000000 INFO @ Tue, 27 Jun 2017 11:29:49: 3000000 INFO @ Tue, 27 Jun 2017 11:29:49: 3000000 INFO @ Tue, 27 Jun 2017 11:29:55: 4000000 INFO @ Tue, 27 Jun 2017 11:29:55: 4000000 INFO @ Tue, 27 Jun 2017 11:29:55: 4000000 INFO @ Tue, 27 Jun 2017 11:30:01: 5000000 INFO @ Tue, 27 Jun 2017 11:30:01: 5000000 INFO @ Tue, 27 Jun 2017 11:30:02: 5000000 INFO @ Tue, 27 Jun 2017 11:30:07: 6000000 INFO @ Tue, 27 Jun 2017 11:30:07: 6000000 INFO @ Tue, 27 Jun 2017 11:30:08: 6000000 INFO @ Tue, 27 Jun 2017 11:30:13: 7000000 INFO @ Tue, 27 Jun 2017 11:30:14: 7000000 INFO @ Tue, 27 Jun 2017 11:30:15: 7000000 INFO @ Tue, 27 Jun 2017 11:30:19: 8000000 INFO @ Tue, 27 Jun 2017 11:30:20: 8000000 INFO @ Tue, 27 Jun 2017 11:30:21: 8000000 INFO @ Tue, 27 Jun 2017 11:30:26: 9000000 INFO @ Tue, 27 Jun 2017 11:30:27: 9000000 INFO @ Tue, 27 Jun 2017 11:30:28: 9000000 INFO @ Tue, 27 Jun 2017 11:30:34: 10000000 INFO @ Tue, 27 Jun 2017 11:30:35: 10000000 INFO @ Tue, 27 Jun 2017 11:30:36: 10000000 INFO @ Tue, 27 Jun 2017 11:30:41: 11000000 INFO @ Tue, 27 Jun 2017 11:30:42: 11000000 INFO @ Tue, 27 Jun 2017 11:30:43: 11000000 INFO @ Tue, 27 Jun 2017 11:30:48: 12000000 INFO @ Tue, 27 Jun 2017 11:30:49: 12000000 INFO @ Tue, 27 Jun 2017 11:30:51: 12000000 INFO @ Tue, 27 Jun 2017 11:30:55: 13000000 INFO @ Tue, 27 Jun 2017 11:30:56: 13000000 INFO @ Tue, 27 Jun 2017 11:30:58: 13000000 INFO @ Tue, 27 Jun 2017 11:31:02: 14000000 INFO @ Tue, 27 Jun 2017 11:31:03: 14000000 INFO @ Tue, 27 Jun 2017 11:31:05: 14000000 INFO @ Tue, 27 Jun 2017 11:31:09: 15000000 INFO @ Tue, 27 Jun 2017 11:31:11: 15000000 INFO @ Tue, 27 Jun 2017 11:31:12: 15000000 INFO @ Tue, 27 Jun 2017 11:31:14: #1 tag size is determined as 27 bps INFO @ Tue, 27 Jun 2017 11:31:14: #1 tag size = 27 INFO @ Tue, 27 Jun 2017 11:31:14: #1 total tags in treatment: 15750200 INFO @ Tue, 27 Jun 2017 11:31:14: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:31:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:31:15: #1 tags after filtering in treatment: 15750200 INFO @ Tue, 27 Jun 2017 11:31:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:31:15: #1 finished! INFO @ Tue, 27 Jun 2017 11:31:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:31:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:31:16: #1 tag size is determined as 27 bps INFO @ Tue, 27 Jun 2017 11:31:16: #1 tag size = 27 INFO @ Tue, 27 Jun 2017 11:31:16: #1 total tags in treatment: 15750200 INFO @ Tue, 27 Jun 2017 11:31:16: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:31:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:31:16: #2 number of paired peaks: 220 WARNING @ Tue, 27 Jun 2017 11:31:16: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 27 Jun 2017 11:31:16: start model_add_line... INFO @ Tue, 27 Jun 2017 11:31:16: start X-correlation... INFO @ Tue, 27 Jun 2017 11:31:16: end of X-cor INFO @ Tue, 27 Jun 2017 11:31:16: #2 finished! INFO @ Tue, 27 Jun 2017 11:31:16: #2 predicted fragment length is 0 bps INFO @ Tue, 27 Jun 2017 11:31:16: #2 alternative fragment length(s) may be 0,25,582 bps INFO @ Tue, 27 Jun 2017 11:31:16: #2.2 Generate R script for model : SRX002676.20_model.r WARNING @ Tue, 27 Jun 2017 11:31:16: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:31:16: #2 You may need to consider one of the other alternative d(s): 0,25,582 WARNING @ Tue, 27 Jun 2017 11:31:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:31:16: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:31:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:31:16: #1 tags after filtering in treatment: 15750200 INFO @ Tue, 27 Jun 2017 11:31:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:31:16: #1 finished! INFO @ Tue, 27 Jun 2017 11:31:16: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:31:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:31:17: #2 number of paired peaks: 220 WARNING @ Tue, 27 Jun 2017 11:31:17: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 27 Jun 2017 11:31:17: start model_add_line... INFO @ Tue, 27 Jun 2017 11:31:17: #1 tag size is determined as 27 bps INFO @ Tue, 27 Jun 2017 11:31:17: #1 tag size = 27 INFO @ Tue, 27 Jun 2017 11:31:17: #1 total tags in treatment: 15750200 INFO @ Tue, 27 Jun 2017 11:31:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 11:31:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 11:31:17: start X-correlation... INFO @ Tue, 27 Jun 2017 11:31:17: end of X-cor INFO @ Tue, 27 Jun 2017 11:31:17: #2 finished! INFO @ Tue, 27 Jun 2017 11:31:17: #2 predicted fragment length is 0 bps INFO @ Tue, 27 Jun 2017 11:31:17: #2 alternative fragment length(s) may be 0,25,582 bps INFO @ Tue, 27 Jun 2017 11:31:17: #2.2 Generate R script for model : SRX002676.10_model.r WARNING @ Tue, 27 Jun 2017 11:31:17: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:31:17: #2 You may need to consider one of the other alternative d(s): 0,25,582 WARNING @ Tue, 27 Jun 2017 11:31:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:31:17: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:31:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 11:31:18: #1 tags after filtering in treatment: 15750200 INFO @ Tue, 27 Jun 2017 11:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 11:31:18: #1 finished! INFO @ Tue, 27 Jun 2017 11:31:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 11:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 11:31:19: #2 number of paired peaks: 220 WARNING @ Tue, 27 Jun 2017 11:31:19: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 27 Jun 2017 11:31:19: start model_add_line... INFO @ Tue, 27 Jun 2017 11:31:19: start X-correlation... INFO @ Tue, 27 Jun 2017 11:31:19: end of X-cor INFO @ Tue, 27 Jun 2017 11:31:19: #2 finished! INFO @ Tue, 27 Jun 2017 11:31:19: #2 predicted fragment length is 0 bps INFO @ Tue, 27 Jun 2017 11:31:19: #2 alternative fragment length(s) may be 0,25,582 bps INFO @ Tue, 27 Jun 2017 11:31:19: #2.2 Generate R script for model : SRX002676.05_model.r WARNING @ Tue, 27 Jun 2017 11:31:19: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 11:31:19: #2 You may need to consider one of the other alternative d(s): 0,25,582 WARNING @ Tue, 27 Jun 2017 11:31:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 11:31:19: #3 Call peaks... INFO @ Tue, 27 Jun 2017 11:31:19: #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 SRX002676.05.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 `SRX002676.05.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/nt027i/job_scripts/9157327: line 231: 20858 終了しました MACS $i /var/spool/uge/nt027i/job_scripts/9157327: line 231: 20859 終了しました MACS $i /var/spool/uge/nt027i/job_scripts/9157327: line 231: 20860 終了しました MACS $i mv: cannot stat `SRX002676.05.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 SRX002676.10.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 `SRX002676.10.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 `SRX002676.10.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 SRX002676.20.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 `SRX002676.20.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 `SRX002676.20.bb': そのようなファイルやディレクトリはありません