Job ID = 11632743 sra ファイルのダウンロード中... Completed: 449830K bytes transferred in 7 seconds (512423K 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 4226755 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123813/DRR131075.sra Written 4226755 spots for /home/okishinya/chipatlas/results/sacCer3/DRX123813/DRR131075.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: 00:04:19 4226755 reads; of these: 4226755 (100.00%) were paired; of these: 450406 (10.66%) aligned concordantly 0 times 3538899 (83.73%) aligned concordantly exactly 1 time 237450 (5.62%) aligned concordantly >1 times ---- 450406 pairs aligned concordantly 0 times; of these: 144853 (32.16%) aligned discordantly 1 time ---- 305553 pairs aligned 0 times concordantly or discordantly; of these: 611106 mates make up the pairs; of these: 508870 (83.27%) aligned 0 times 74187 (12.14%) aligned exactly 1 time 28049 (4.59%) aligned >1 times 93.98% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 8984 / 3911003 = 0.0023 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 07:39:06: # Command line: callpeak -t DRX123813.bam -f BAM -g 12100000 -n DRX123813.05 -q 1e-05 # ARGUMENTS LIST: # name = DRX123813.05 # format = BAM # ChIP-seq file = ['DRX123813.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 07:39:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:39:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:39:06: # Command line: callpeak -t DRX123813.bam -f BAM -g 12100000 -n DRX123813.20 -q 1e-20 # ARGUMENTS LIST: # name = DRX123813.20 # format = BAM # ChIP-seq file = ['DRX123813.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 07:39:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:39:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:39:06: # Command line: callpeak -t DRX123813.bam -f BAM -g 12100000 -n DRX123813.10 -q 1e-10 # ARGUMENTS LIST: # name = DRX123813.10 # format = BAM # ChIP-seq file = ['DRX123813.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 07:39:06: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:39:06: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:39:12: 1000000 INFO @ Fri, 15 Feb 2019 07:39:12: 1000000 INFO @ Fri, 15 Feb 2019 07:39:13: 1000000 INFO @ Fri, 15 Feb 2019 07:39:18: 2000000 INFO @ Fri, 15 Feb 2019 07:39:18: 2000000 INFO @ Fri, 15 Feb 2019 07:39:19: 2000000 INFO @ Fri, 15 Feb 2019 07:39:24: 3000000 INFO @ Fri, 15 Feb 2019 07:39:24: 3000000 INFO @ Fri, 15 Feb 2019 07:39:25: 3000000 INFO @ Fri, 15 Feb 2019 07:39:30: 4000000 INFO @ Fri, 15 Feb 2019 07:39:31: 4000000 INFO @ Fri, 15 Feb 2019 07:39:32: 4000000 INFO @ Fri, 15 Feb 2019 07:39:36: 5000000 INFO @ Fri, 15 Feb 2019 07:39:37: 5000000 INFO @ Fri, 15 Feb 2019 07:39:38: 5000000 INFO @ Fri, 15 Feb 2019 07:39:43: 6000000 INFO @ Fri, 15 Feb 2019 07:39:43: 6000000 INFO @ Fri, 15 Feb 2019 07:39:45: 6000000 INFO @ Fri, 15 Feb 2019 07:39:49: 7000000 INFO @ Fri, 15 Feb 2019 07:39:49: 7000000 INFO @ Fri, 15 Feb 2019 07:39:51: 7000000 INFO @ Fri, 15 Feb 2019 07:39:55: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:39:55: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:39:55: #1 total tags in treatment: 3767455 INFO @ Fri, 15 Feb 2019 07:39:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:39:55: #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 07:39:55: #1 tags after filtering in treatment: 3283927 INFO @ Fri, 15 Feb 2019 07:39:55: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 07:39:55: #1 finished! INFO @ Fri, 15 Feb 2019 07:39:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:39:55: #2 number of paired peaks: 147 WARNING @ Fri, 15 Feb 2019 07:39:55: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Fri, 15 Feb 2019 07:39:55: start model_add_line... INFO @ Fri, 15 Feb 2019 07:39:55: start X-correlation... INFO @ Fri, 15 Feb 2019 07:39:55: end of X-cor INFO @ Fri, 15 Feb 2019 07:39:55: #2 finished! INFO @ Fri, 15 Feb 2019 07:39:55: #2 predicted fragment length is 0 bps INFO @ Fri, 15 Feb 2019 07:39:55: #2 alternative fragment length(s) may be 0,25,54,73,98,123,135,152,177,194,201,230,249,262,287,291,335,362,382,398,473,519,543,575 bps INFO @ Fri, 15 Feb 2019 07:39:55: #2.2 Generate R script for model : DRX123813.20_model.r WARNING @ Fri, 15 Feb 2019 07:39:55: #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 07:39:55: #2 You may need to consider one of the other alternative d(s): 0,25,54,73,98,123,135,152,177,194,201,230,249,262,287,291,335,362,382,398,473,519,543,575 WARNING @ Fri, 15 Feb 2019 07:39:55: #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 07:39:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:39:55: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:39:55: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:39:55: #1 total tags in treatment: 3767455 INFO @ Fri, 15 Feb 2019 07:39:55: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:39:55: #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 07:39:55: #1 tags after filtering in treatment: 3283927 INFO @ Fri, 15 Feb 2019 07:39:55: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 07:39:55: #1 finished! INFO @ Fri, 15 Feb 2019 07:39:55: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:39:55: #2 number of paired peaks: 147 WARNING @ Fri, 15 Feb 2019 07:39:55: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Fri, 15 Feb 2019 07:39:55: start model_add_line... INFO @ Fri, 15 Feb 2019 07:39:55: start X-correlation... INFO @ Fri, 15 Feb 2019 07:39:55: end of X-cor INFO @ Fri, 15 Feb 2019 07:39:55: #2 finished! INFO @ Fri, 15 Feb 2019 07:39:55: #2 predicted fragment length is 0 bps INFO @ Fri, 15 Feb 2019 07:39:55: #2 alternative fragment length(s) may be 0,25,54,73,98,123,135,152,177,194,201,230,249,262,287,291,335,362,382,398,473,519,543,575 bps INFO @ Fri, 15 Feb 2019 07:39:55: #2.2 Generate R script for model : DRX123813.05_model.r WARNING @ Fri, 15 Feb 2019 07:39:55: #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 07:39:55: #2 You may need to consider one of the other alternative d(s): 0,25,54,73,98,123,135,152,177,194,201,230,249,262,287,291,335,362,382,398,473,519,543,575 WARNING @ Fri, 15 Feb 2019 07:39:55: #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 07:39:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:39:57: #1 tag size is determined as 74 bps INFO @ Fri, 15 Feb 2019 07:39:57: #1 tag size = 74 INFO @ Fri, 15 Feb 2019 07:39:57: #1 total tags in treatment: 3767455 INFO @ Fri, 15 Feb 2019 07:39:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:39:57: #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 07:39:57: #1 tags after filtering in treatment: 3283927 INFO @ Fri, 15 Feb 2019 07:39:57: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 15 Feb 2019 07:39:57: #1 finished! INFO @ Fri, 15 Feb 2019 07:39:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:39:57: #2 number of paired peaks: 147 WARNING @ Fri, 15 Feb 2019 07:39:57: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Fri, 15 Feb 2019 07:39:57: start model_add_line... INFO @ Fri, 15 Feb 2019 07:39:57: start X-correlation... INFO @ Fri, 15 Feb 2019 07:39:57: end of X-cor INFO @ Fri, 15 Feb 2019 07:39:57: #2 finished! INFO @ Fri, 15 Feb 2019 07:39:57: #2 predicted fragment length is 0 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2 alternative fragment length(s) may be 0,25,54,73,98,123,135,152,177,194,201,230,249,262,287,291,335,362,382,398,473,519,543,575 bps INFO @ Fri, 15 Feb 2019 07:39:57: #2.2 Generate R script for model : DRX123813.10_model.r WARNING @ Fri, 15 Feb 2019 07:39:57: #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 07:39:57: #2 You may need to consider one of the other alternative d(s): 0,25,54,73,98,123,135,152,177,194,201,230,249,262,287,291,335,362,382,398,473,519,543,575 WARNING @ Fri, 15 Feb 2019 07:39:57: #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 07:39:57: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:39:57: #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 DRX123813.05.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 `DRX123813.05.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/nt015i/job_scripts/11632743: line 286: 41695 終了しました MACS $i /var/spool/uge/nt015i/job_scripts/11632743: line 286: 41696 終了しました MACS $i /var/spool/uge/nt015i/job_scripts/11632743: line 286: 41697 終了しました MACS $i mv: cannot stat `DRX123813.05.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 DRX123813.10.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 `DRX123813.10.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 `DRX123813.10.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 DRX123813.20.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 `DRX123813.20.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 `DRX123813.20.bb': そのようなファイルやディレクトリはありません