Job ID = 11244912 sra ファイルのダウンロード中... Completed: 400500K bytes transferred in 13 seconds (240802K 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: PAIRED fastq に変換中... Read 12371500 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554656/SRR7696330.sra Written 12371500 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554656/SRR7696330.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 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: 00:03:16 12371500 reads; of these: 12371500 (100.00%) were paired; of these: 9136084 (73.85%) aligned concordantly 0 times 2363744 (19.11%) aligned concordantly exactly 1 time 871672 (7.05%) aligned concordantly >1 times ---- 9136084 pairs aligned concordantly 0 times; of these: 101693 (1.11%) aligned discordantly 1 time ---- 9034391 pairs aligned 0 times concordantly or discordantly; of these: 18068782 mates make up the pairs; of these: 17887606 (99.00%) aligned 0 times 79388 (0.44%) aligned exactly 1 time 101788 (0.56%) aligned >1 times 27.71% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 122080 / 3316322 = 0.0368 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 22:51:26: # Command line: callpeak -t SRX4554656.bam -f BAM -g 12100000 -n SRX4554656.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554656.05 # format = BAM # ChIP-seq file = ['SRX4554656.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 22:51:26: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:51:26: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:51:26: # Command line: callpeak -t SRX4554656.bam -f BAM -g 12100000 -n SRX4554656.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554656.10 # format = BAM # ChIP-seq file = ['SRX4554656.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 22:51:26: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:51:26: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:51:26: # Command line: callpeak -t SRX4554656.bam -f BAM -g 12100000 -n SRX4554656.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554656.20 # format = BAM # ChIP-seq file = ['SRX4554656.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 22:51:26: #1 read tag files... INFO @ Tue, 09 Oct 2018 22:51:26: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 22:51:31: 1000000 INFO @ Tue, 09 Oct 2018 22:51:31: 1000000 INFO @ Tue, 09 Oct 2018 22:51:31: 1000000 INFO @ Tue, 09 Oct 2018 22:51:36: 2000000 INFO @ Tue, 09 Oct 2018 22:51:36: 2000000 INFO @ Tue, 09 Oct 2018 22:51:36: 2000000 INFO @ Tue, 09 Oct 2018 22:51:41: 3000000 INFO @ Tue, 09 Oct 2018 22:51:41: 3000000 INFO @ Tue, 09 Oct 2018 22:51:41: 3000000 INFO @ Tue, 09 Oct 2018 22:51:46: 4000000 INFO @ Tue, 09 Oct 2018 22:51:46: 4000000 INFO @ Tue, 09 Oct 2018 22:51:46: 4000000 INFO @ Tue, 09 Oct 2018 22:51:51: 5000000 INFO @ Tue, 09 Oct 2018 22:51:51: 5000000 INFO @ Tue, 09 Oct 2018 22:51:51: 5000000 INFO @ Tue, 09 Oct 2018 22:51:56: 6000000 INFO @ Tue, 09 Oct 2018 22:51:56: 6000000 INFO @ Tue, 09 Oct 2018 22:51:56: 6000000 INFO @ Tue, 09 Oct 2018 22:51:59: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:51:59: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:51:59: #1 total tags in treatment: 3115498 INFO @ Tue, 09 Oct 2018 22:51:59: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:51:59: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:51:59: #1 total tags in treatment: 3115498 INFO @ Tue, 09 Oct 2018 22:51:59: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #1 tags after filtering in treatment: 2207055 INFO @ Tue, 09 Oct 2018 22:51:59: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 09 Oct 2018 22:51:59: #1 finished! INFO @ Tue, 09 Oct 2018 22:51:59: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:51:59: #1 tags after filtering in treatment: 2207055 INFO @ Tue, 09 Oct 2018 22:51:59: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 09 Oct 2018 22:51:59: #1 finished! INFO @ Tue, 09 Oct 2018 22:51:59: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:51:59: #2 number of paired peaks: 302 WARNING @ Tue, 09 Oct 2018 22:51:59: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 09 Oct 2018 22:51:59: start model_add_line... INFO @ Tue, 09 Oct 2018 22:51:59: #2 number of paired peaks: 302 WARNING @ Tue, 09 Oct 2018 22:51:59: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 09 Oct 2018 22:51:59: start model_add_line... INFO @ Tue, 09 Oct 2018 22:51:59: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 22:51:59: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 22:51:59: #1 total tags in treatment: 3115498 INFO @ Tue, 09 Oct 2018 22:51:59: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: start X-correlation... INFO @ Tue, 09 Oct 2018 22:51:59: end of X-cor INFO @ Tue, 09 Oct 2018 22:51:59: #2 finished! INFO @ Tue, 09 Oct 2018 22:51:59: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:51:59: #2 alternative fragment length(s) may be 0,46,79,85,93,120,153,562 bps INFO @ Tue, 09 Oct 2018 22:51:59: #2.2 Generate R script for model : SRX4554656.10_model.r INFO @ Tue, 09 Oct 2018 22:51:59: start X-correlation... INFO @ Tue, 09 Oct 2018 22:51:59: end of X-cor INFO @ Tue, 09 Oct 2018 22:51:59: #2 finished! INFO @ Tue, 09 Oct 2018 22:51:59: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:51:59: #2 alternative fragment length(s) may be 0,46,79,85,93,120,153,562 bps INFO @ Tue, 09 Oct 2018 22:51:59: #2.2 Generate R script for model : SRX4554656.20_model.r WARNING @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #2 You may need to consider one of the other alternative d(s): 0,46,79,85,93,120,153,562 WARNING @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:51:59: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #2 You may need to consider one of the other alternative d(s): 0,46,79,85,93,120,153,562 WARNING @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 22:51:59: #1 tags after filtering in treatment: 2207055 INFO @ Tue, 09 Oct 2018 22:51:59: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 09 Oct 2018 22:51:59: #1 finished! INFO @ Tue, 09 Oct 2018 22:51:59: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 22:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 22:51:59: #2 number of paired peaks: 302 WARNING @ Tue, 09 Oct 2018 22:51:59: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Tue, 09 Oct 2018 22:51:59: start model_add_line... INFO @ Tue, 09 Oct 2018 22:51:59: start X-correlation... INFO @ Tue, 09 Oct 2018 22:51:59: end of X-cor INFO @ Tue, 09 Oct 2018 22:51:59: #2 finished! INFO @ Tue, 09 Oct 2018 22:51:59: #2 predicted fragment length is 0 bps INFO @ Tue, 09 Oct 2018 22:51:59: #2 alternative fragment length(s) may be 0,46,79,85,93,120,153,562 bps INFO @ Tue, 09 Oct 2018 22:51:59: #2.2 Generate R script for model : SRX4554656.05_model.r WARNING @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #2 You may need to consider one of the other alternative d(s): 0,46,79,85,93,120,153,562 WARNING @ Tue, 09 Oct 2018 22:51:59: #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 22:51:59: #3 Call peaks... INFO @ Tue, 09 Oct 2018 22:51:59: #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 SRX4554656.05.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 `SRX4554656.05.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/nt143i/job_scripts/11244912: line 254: 41234 終了しました MACS $i /var/spool/uge/nt143i/job_scripts/11244912: line 254: 41235 終了しました MACS $i /var/spool/uge/nt143i/job_scripts/11244912: line 254: 41236 終了しました MACS $i mv: cannot stat `SRX4554656.05.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 SRX4554656.10.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 `SRX4554656.10.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 `SRX4554656.10.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 SRX4554656.20.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 `SRX4554656.20.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 `SRX4554656.20.bb': そのようなファイルやディレクトリはありません