Job ID = 11244839 sra ファイルのダウンロード中... Completed: 71046K bytes transferred in 3 seconds (149691K bits/sec), in 1 file. Completed: 156460K bytes transferred in 4 seconds (271231K 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 2396376 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732400/SRR6759904.sra Written 2396376 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732400/SRR6759904.sra Read 5178930 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732400/SRR6759905.sra Written 5178930 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3732400/SRR6759905.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 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: 00:01:12 7575306 reads; of these: 7575306 (100.00%) were unpaired; of these: 2378705 (31.40%) aligned 0 times 4272755 (56.40%) aligned exactly 1 time 923846 (12.20%) aligned >1 times 68.60% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 2347099 / 5196601 = 0.4517 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, 09 Oct 2018 22:03:41: # Command line: callpeak -t SRX3732400.bam -f BAM -g 12100000 -n SRX3732400.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3732400.20 # format = BAM # ChIP-seq file = ['SRX3732400.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 @ Tue, 09 Oct 2018 22:03:41: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:41: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:41: # Command line: callpeak -t SRX3732400.bam -f BAM -g 12100000 -n SRX3732400.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3732400.10 # format = BAM # ChIP-seq file = ['SRX3732400.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 @ Tue, 09 Oct 2018 22:03:41: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:41: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:41: # Command line: callpeak -t SRX3732400.bam -f BAM -g 12100000 -n SRX3732400.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3732400.05 # format = BAM # ChIP-seq file = ['SRX3732400.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 @ Tue, 09 Oct 2018 22:03:41: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:03:41: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:03:47: 1000000 INFO @ Tue, 09 Oct 2018 22:03:48: 1000000 INFO @ Tue, 09 Oct 2018 22:03:48: 1000000 INFO @ Tue, 09 Oct 2018 22:03:54: 2000000 INFO @ Tue, 09 Oct 2018 22:03:55: 2000000 INFO @ Tue, 09 Oct 2018 22:03:55: 2000000 INFO @ Tue, 09 Oct 2018 22:03:59: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:03:59: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:03:59: #1 total tags in treatment: 2849502 INFO @ Tue, 09 Oct 2018 22:03:59: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:03:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:03:59: #1 tags after filtering in treatment: 2849502 INFO @ Tue, 09 Oct 2018 22:03:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:03:59: #1 finished! INFO @ Tue, 09 Oct 2018 22:03:59: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:04:00: #2 number of paired peaks: 171 WARNING @ Tue, 09 Oct 2018 22:04:00: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 09 Oct 2018 22:04:00: start model_add_line... INFO @ Tue, 09 Oct 2018 22:04:00: start X-correlation... INFO @ Tue, 09 Oct 2018 22:04:00: end of X-cor INFO @ Tue, 09 Oct 2018 22:04:00: #2 finished! INFO @ Tue, 09 Oct 2018 22:04:00: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:04:00: #2 alternative fragment length(s) may be 0,49,150,423,427,472,510 bps INFO @ Tue, 09 Oct 2018 22:04:00: #2.2 Generate R script for model : SRX3732400.05_model.r WARNING @ Tue, 09 Oct 2018 22:04:00: #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, 09 Oct 2018 22:04:00: #2 You may need to consider one of the other alternative d(s): 0,49,150,423,427,472,510 WARNING @ Tue, 09 Oct 2018 22:04:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:04:00: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:04:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:04:00: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:04:00: #1 tag size is determined as 50 bps INFO @ Tue, 09 Oct 2018 22:04:00: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:04:00: #1 tag size = 50 INFO @ Tue, 09 Oct 2018 22:04:00: #1 total tags in treatment: 2849502 INFO @ Tue, 09 Oct 2018 22:04:00: #1 total tags in treatment: 2849502 INFO @ Tue, 09 Oct 2018 22:04:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:04:00: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:04:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:04:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 22:04:00: #1 tags after filtering in treatment: 2849502 INFO @ Tue, 09 Oct 2018 22:04:00: #1 tags after filtering in treatment: 2849502 INFO @ Tue, 09 Oct 2018 22:04:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:04:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 09 Oct 2018 22:04:00: #1 finished! INFO @ Tue, 09 Oct 2018 22:04:00: #1 finished! INFO @ Tue, 09 Oct 2018 22:04:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:04:00: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:04:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:04:01: #2 number of paired peaks: 171 WARNING @ Tue, 09 Oct 2018 22:04:01: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 09 Oct 2018 22:04:01: start model_add_line... INFO @ Tue, 09 Oct 2018 22:04:01: start X-correlation... INFO @ Tue, 09 Oct 2018 22:04:01: end of X-cor INFO @ Tue, 09 Oct 2018 22:04:01: #2 finished! INFO @ Tue, 09 Oct 2018 22:04:01: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:04:01: #2 alternative fragment length(s) may be 0,49,150,423,427,472,510 bps INFO @ Tue, 09 Oct 2018 22:04:01: #2.2 Generate R script for model : SRX3732400.20_model.r WARNING @ Tue, 09 Oct 2018 22:04:01: #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, 09 Oct 2018 22:04:01: #2 You may need to consider one of the other alternative d(s): 0,49,150,423,427,472,510 WARNING @ Tue, 09 Oct 2018 22:04:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:04:01: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:04:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:04:01: #2 number of paired peaks: 171 WARNING @ Tue, 09 Oct 2018 22:04:01: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Tue, 09 Oct 2018 22:04:01: start model_add_line... INFO @ Tue, 09 Oct 2018 22:04:01: start X-correlation... INFO @ Tue, 09 Oct 2018 22:04:01: end of X-cor INFO @ Tue, 09 Oct 2018 22:04:01: #2 finished! INFO @ Tue, 09 Oct 2018 22:04:01: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:04:01: #2 alternative fragment length(s) may be 0,49,150,423,427,472,510 bps INFO @ Tue, 09 Oct 2018 22:04:01: #2.2 Generate R script for model : SRX3732400.10_model.r WARNING @ Tue, 09 Oct 2018 22:04:01: #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, 09 Oct 2018 22:04:01: #2 You may need to consider one of the other alternative d(s): 0,49,150,423,427,472,510 WARNING @ Tue, 09 Oct 2018 22:04:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 09 Oct 2018 22:04:01: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:04:01: #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 SRX3732400.05.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 `SRX3732400.05.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/nt031i/job_scripts/11244839: line 254: 29382 終了しました MACS $i /var/spool/uge/nt031i/job_scripts/11244839: line 254: 29383 終了しました MACS $i /var/spool/uge/nt031i/job_scripts/11244839: line 254: 29385 終了しました MACS $i mv: cannot stat `SRX3732400.05.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 SRX3732400.10.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 `SRX3732400.10.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 `SRX3732400.10.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 SRX3732400.20.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 `SRX3732400.20.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 `SRX3732400.20.bb': そのようなファイルやディレクトリはありません