Job ID = 9163552 sra ファイルのダウンロード中... Completed: 470445K bytes transferred in 7 seconds (487309K 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 16888105 spots for /home/okishinya/chipatlas/results/sacCer3/SRX876302/SRR1802405.sra Written 16888105 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: 00:02:49 16888105 reads; of these: 16888105 (100.00%) were unpaired; of these: 2058225 (12.19%) aligned 0 times 11517401 (68.20%) aligned exactly 1 time 3312479 (19.61%) aligned >1 times 87.81% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 13083377 / 14829880 = 0.8822 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 10:58:31: # Command line: callpeak -t SRX876302.bam -f BAM -g 12100000 -n SRX876302.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX876302.05 # format = BAM # ChIP-seq file = ['SRX876302.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 10:58:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:58:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:58:31: # Command line: callpeak -t SRX876302.bam -f BAM -g 12100000 -n SRX876302.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX876302.20 # format = BAM # ChIP-seq file = ['SRX876302.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 10:58:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:58:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:58:31: # Command line: callpeak -t SRX876302.bam -f BAM -g 12100000 -n SRX876302.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX876302.10 # format = BAM # ChIP-seq file = ['SRX876302.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 10:58:31: #1 read tag files... INFO @ Wed, 28 Jun 2017 10:58:31: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 10:58:37: 1000000 INFO @ Wed, 28 Jun 2017 10:58:37: 1000000 INFO @ Wed, 28 Jun 2017 10:58:37: 1000000 INFO @ Wed, 28 Jun 2017 10:58:41: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 10:58:41: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 10:58:41: #1 total tags in treatment: 1746503 INFO @ Wed, 28 Jun 2017 10:58:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:58:41: #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 10:58:41: #1 tags after filtering in treatment: 1746503 INFO @ Wed, 28 Jun 2017 10:58:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 10:58:41: #1 finished! INFO @ Wed, 28 Jun 2017 10:58:41: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:58:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:58:41: #2 number of paired peaks: 216 WARNING @ Wed, 28 Jun 2017 10:58:41: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Wed, 28 Jun 2017 10:58:41: start model_add_line... INFO @ Wed, 28 Jun 2017 10:58:41: start X-correlation... INFO @ Wed, 28 Jun 2017 10:58:41: end of X-cor INFO @ Wed, 28 Jun 2017 10:58:41: #2 finished! INFO @ Wed, 28 Jun 2017 10:58:41: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 10:58:41: #2 alternative fragment length(s) may be 0,32,52,71,101,123,135,158,176,202,235,270,275,290,362,379,407,434,454,496,528,562,582 bps INFO @ Wed, 28 Jun 2017 10:58:41: #2.2 Generate R script for model : SRX876302.10_model.r WARNING @ Wed, 28 Jun 2017 10:58:41: #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 10:58:41: #2 You may need to consider one of the other alternative d(s): 0,32,52,71,101,123,135,158,176,202,235,270,275,290,362,379,407,434,454,496,528,562,582 WARNING @ Wed, 28 Jun 2017 10:58:41: #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 10:58:41: #3 Call peaks... INFO @ Wed, 28 Jun 2017 10:58:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 10:58:41: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 10:58:41: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 10:58:41: #1 total tags in treatment: 1746503 INFO @ Wed, 28 Jun 2017 10:58:41: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:58:41: #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 10:58:42: #1 tags after filtering in treatment: 1746503 INFO @ Wed, 28 Jun 2017 10:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 10:58:42: #1 finished! INFO @ Wed, 28 Jun 2017 10:58:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:58:42: #1 tag size is determined as 40 bps INFO @ Wed, 28 Jun 2017 10:58:42: #1 tag size = 40 INFO @ Wed, 28 Jun 2017 10:58:42: #1 total tags in treatment: 1746503 INFO @ Wed, 28 Jun 2017 10:58:42: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 10:58:42: #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 10:58:42: #1 tags after filtering in treatment: 1746503 INFO @ Wed, 28 Jun 2017 10:58:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 28 Jun 2017 10:58:42: #1 finished! INFO @ Wed, 28 Jun 2017 10:58:42: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 10:58:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 10:58:42: #2 number of paired peaks: 216 WARNING @ Wed, 28 Jun 2017 10:58:42: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Wed, 28 Jun 2017 10:58:42: start model_add_line... INFO @ Wed, 28 Jun 2017 10:58:42: start X-correlation... INFO @ Wed, 28 Jun 2017 10:58:42: end of X-cor INFO @ Wed, 28 Jun 2017 10:58:42: #2 finished! INFO @ Wed, 28 Jun 2017 10:58:42: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 10:58:42: #2 alternative fragment length(s) may be 0,32,52,71,101,123,135,158,176,202,235,270,275,290,362,379,407,434,454,496,528,562,582 bps INFO @ Wed, 28 Jun 2017 10:58:42: #2.2 Generate R script for model : SRX876302.20_model.r WARNING @ Wed, 28 Jun 2017 10:58:42: #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 10:58:42: #2 You may need to consider one of the other alternative d(s): 0,32,52,71,101,123,135,158,176,202,235,270,275,290,362,379,407,434,454,496,528,562,582 WARNING @ Wed, 28 Jun 2017 10:58:42: #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 10:58:42: #3 Call peaks... INFO @ Wed, 28 Jun 2017 10:58:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 10:58:42: #2 number of paired peaks: 216 WARNING @ Wed, 28 Jun 2017 10:58:42: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Wed, 28 Jun 2017 10:58:42: start model_add_line... INFO @ Wed, 28 Jun 2017 10:58:42: start X-correlation... INFO @ Wed, 28 Jun 2017 10:58:42: end of X-cor INFO @ Wed, 28 Jun 2017 10:58:42: #2 finished! INFO @ Wed, 28 Jun 2017 10:58:42: #2 predicted fragment length is 0 bps INFO @ Wed, 28 Jun 2017 10:58:42: #2 alternative fragment length(s) may be 0,32,52,71,101,123,135,158,176,202,235,270,275,290,362,379,407,434,454,496,528,562,582 bps INFO @ Wed, 28 Jun 2017 10:58:42: #2.2 Generate R script for model : SRX876302.05_model.r WARNING @ Wed, 28 Jun 2017 10:58:42: #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 10:58:42: #2 You may need to consider one of the other alternative d(s): 0,32,52,71,101,123,135,158,176,202,235,270,275,290,362,379,407,434,454,496,528,562,582 WARNING @ Wed, 28 Jun 2017 10:58:42: #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 10:58:42: #3 Call peaks... INFO @ Wed, 28 Jun 2017 10:58:42: #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 SRX876302.05.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 `SRX876302.05.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/9163552: line 231: 37346 終了しました MACS $i /var/spool/uge/nt027i/job_scripts/9163552: line 231: 37347 終了しました MACS $i /var/spool/uge/nt027i/job_scripts/9163552: line 231: 37348 終了しました MACS $i mv: cannot stat `SRX876302.05.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 SRX876302.10.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 `SRX876302.10.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 `SRX876302.10.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 SRX876302.20.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 `SRX876302.20.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 `SRX876302.20.bb': そのようなファイルやディレクトリはありません