Job ID = 11632748 sra ファイルのダウンロード中... Completed: 469081K bytes transferred in 7 seconds (530162K 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 4655433 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123818/DRR131080.sra Written 4655433 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123818/DRR131080.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: 00:04:50 4655433 reads; of these: 4655433 (100.00%) were paired; of these: 443510 (9.53%) aligned concordantly 0 times 3917908 (84.16%) aligned concordantly exactly 1 time 294015 (6.32%) aligned concordantly >1 times ---- 443510 pairs aligned concordantly 0 times; of these: 206431 (46.54%) aligned discordantly 1 time ---- 237079 pairs aligned 0 times concordantly or discordantly; of these: 474158 mates make up the pairs; of these: 392657 (82.81%) aligned 0 times 42715 (9.01%) aligned exactly 1 time 38786 (8.18%) aligned >1 times 95.78% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 11767 / 4406345 = 0.0027 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 @ Fri, 15 Feb 2019 07:40:31: # Command line: callpeak -t DRX123818.bam -f BAM -g 12100000 -n DRX123818.05 -q 1e-05 # ARGUMENTS LIST: # name = DRX123818.05 # format = BAM # ChIP-seq file = ['DRX123818.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 @ Fri, 15 Feb 2019 07:40:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:40:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:40:31: # Command line: callpeak -t DRX123818.bam -f BAM -g 12100000 -n DRX123818.20 -q 1e-20 # ARGUMENTS LIST: # name = DRX123818.20 # format = BAM # ChIP-seq file = ['DRX123818.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 @ Fri, 15 Feb 2019 07:40:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:40:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:40:31: # Command line: callpeak -t DRX123818.bam -f BAM -g 12100000 -n DRX123818.10 -q 1e-10 # ARGUMENTS LIST: # name = DRX123818.10 # format = BAM # ChIP-seq file = ['DRX123818.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 @ Fri, 15 Feb 2019 07:40:31: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:40:31: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:40:38: 1000000 INFO @ Fri, 15 Feb 2019 07:40:38: 1000000 INFO @ Fri, 15 Feb 2019 07:40:38: 1000000 INFO @ Fri, 15 Feb 2019 07:40:45: 2000000 INFO @ Fri, 15 Feb 2019 07:40:46: 2000000 INFO @ Fri, 15 Feb 2019 07:40:46: 2000000 INFO @ Fri, 15 Feb 2019 07:40:52: 3000000 INFO @ Fri, 15 Feb 2019 07:40:53: 3000000 INFO @ Fri, 15 Feb 2019 07:40:53: 3000000 INFO @ Fri, 15 Feb 2019 07:40:59: 4000000 INFO @ Fri, 15 Feb 2019 07:41:00: 4000000 INFO @ Fri, 15 Feb 2019 07:41:01: 4000000 INFO @ Fri, 15 Feb 2019 07:41:07: 5000000 INFO @ Fri, 15 Feb 2019 07:41:08: 5000000 INFO @ Fri, 15 Feb 2019 07:41:08: 5000000 INFO @ Fri, 15 Feb 2019 07:41:14: 6000000 INFO @ Fri, 15 Feb 2019 07:41:16: 6000000 INFO @ Fri, 15 Feb 2019 07:41:16: 6000000 INFO @ Fri, 15 Feb 2019 07:41:21: 7000000 INFO @ Fri, 15 Feb 2019 07:41:23: 7000000 INFO @ Fri, 15 Feb 2019 07:41:24: 7000000 INFO @ Fri, 15 Feb 2019 07:41:28: 8000000 INFO @ Fri, 15 Feb 2019 07:41:31: 8000000 INFO @ Fri, 15 Feb 2019 07:41:31: 8000000 INFO @ Fri, 15 Feb 2019 07:41:34: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 07:41:34: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 07:41:34: #1 total tags in treatment: 4200348 INFO @ Fri, 15 Feb 2019 07:41:34: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:41:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:41:35: #1 tags after filtering in treatment: 3606296 INFO @ Fri, 15 Feb 2019 07:41:35: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 15 Feb 2019 07:41:35: #1 finished! INFO @ Fri, 15 Feb 2019 07:41:35: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:41:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:41:35: #2 number of paired peaks: 144 WARNING @ Fri, 15 Feb 2019 07:41:35: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 15 Feb 2019 07:41:35: start model_add_line... INFO @ Fri, 15 Feb 2019 07:41:35: start X-correlation... INFO @ Fri, 15 Feb 2019 07:41:35: end of X-cor INFO @ Fri, 15 Feb 2019 07:41:35: #2 finished! INFO @ Fri, 15 Feb 2019 07:41:35: #2 predicted fragment length is 0 bps INFO @ Fri, 15 Feb 2019 07:41:35: #2 alternative fragment length(s) may be 0,19,25,75,96,116,129,149,176,200,227,248,262,282,339,402,424,461,490,506,531,539,545,555,577 bps INFO @ Fri, 15 Feb 2019 07:41:35: #2.2 Generate R script for model : DRX123818.10_model.r WARNING @ Fri, 15 Feb 2019 07:41:35: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:41:35: #2 You may need to consider one of the other alternative d(s): 0,19,25,75,96,116,129,149,176,200,227,248,262,282,339,402,424,461,490,506,531,539,545,555,577 WARNING @ Fri, 15 Feb 2019 07:41:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:41:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:41:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:41:38: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 07:41:38: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 07:41:38: #1 total tags in treatment: 4200348 INFO @ Fri, 15 Feb 2019 07:41:38: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:41:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:41:38: #1 tags after filtering in treatment: 3606296 INFO @ Fri, 15 Feb 2019 07:41:38: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 15 Feb 2019 07:41:38: #1 finished! INFO @ Fri, 15 Feb 2019 07:41:38: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:41:38: #2 number of paired peaks: 144 WARNING @ Fri, 15 Feb 2019 07:41:38: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 15 Feb 2019 07:41:38: start model_add_line... INFO @ Fri, 15 Feb 2019 07:41:38: start X-correlation... INFO @ Fri, 15 Feb 2019 07:41:38: end of X-cor INFO @ Fri, 15 Feb 2019 07:41:38: #2 finished! INFO @ Fri, 15 Feb 2019 07:41:38: #2 predicted fragment length is 0 bps INFO @ Fri, 15 Feb 2019 07:41:38: #2 alternative fragment length(s) may be 0,19,25,75,96,116,129,149,176,200,227,248,262,282,339,402,424,461,490,506,531,539,545,555,577 bps INFO @ Fri, 15 Feb 2019 07:41:38: #2.2 Generate R script for model : DRX123818.05_model.r WARNING @ Fri, 15 Feb 2019 07:41:38: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:41:38: #2 You may need to consider one of the other alternative d(s): 0,19,25,75,96,116,129,149,176,200,227,248,262,282,339,402,424,461,490,506,531,539,545,555,577 WARNING @ Fri, 15 Feb 2019 07:41:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:41:38: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:41:38: #1 tag size is determined as 75 bps INFO @ Fri, 15 Feb 2019 07:41:38: #1 tag size = 75 INFO @ Fri, 15 Feb 2019 07:41:38: #1 total tags in treatment: 4200348 INFO @ Fri, 15 Feb 2019 07:41:38: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:41:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:41:38: #1 tags after filtering in treatment: 3606296 INFO @ Fri, 15 Feb 2019 07:41:38: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 15 Feb 2019 07:41:38: #1 finished! INFO @ Fri, 15 Feb 2019 07:41:38: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:41:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:41:38: #2 number of paired peaks: 144 WARNING @ Fri, 15 Feb 2019 07:41:38: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Fri, 15 Feb 2019 07:41:38: start model_add_line... INFO @ Fri, 15 Feb 2019 07:41:38: start X-correlation... INFO @ Fri, 15 Feb 2019 07:41:38: end of X-cor INFO @ Fri, 15 Feb 2019 07:41:38: #2 finished! INFO @ Fri, 15 Feb 2019 07:41:38: #2 predicted fragment length is 0 bps INFO @ Fri, 15 Feb 2019 07:41:38: #2 alternative fragment length(s) may be 0,19,25,75,96,116,129,149,176,200,227,248,262,282,339,402,424,461,490,506,531,539,545,555,577 bps INFO @ Fri, 15 Feb 2019 07:41:38: #2.2 Generate R script for model : DRX123818.20_model.r WARNING @ Fri, 15 Feb 2019 07:41:39: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 15 Feb 2019 07:41:39: #2 You may need to consider one of the other alternative d(s): 0,19,25,75,96,116,129,149,176,200,227,248,262,282,339,402,424,461,490,506,531,539,545,555,577 WARNING @ Fri, 15 Feb 2019 07:41:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 15 Feb 2019 07:41:39: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:41:39: #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 DRX123818.05.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 `DRX123818.05.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/nt010i/job_scripts/11632748: line 286: 41257 終了しました MACS $i /var/spool/uge/nt010i/job_scripts/11632748: line 286: 41258 終了しました MACS $i /var/spool/uge/nt010i/job_scripts/11632748: line 286: 41260 終了しました MACS $i mv: cannot stat `DRX123818.05.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 DRX123818.10.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 `DRX123818.10.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 `DRX123818.10.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 DRX123818.20.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 `DRX123818.20.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 `DRX123818.20.bb': そのようなファイルやディレクトリはありません