Job ID = 2641134 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,030,100 reads read : 22,060,200 reads written : 22,060,200 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:15:39 11030100 reads; of these: 11030100 (100.00%) were paired; of these: 5429621 (49.23%) aligned concordantly 0 times 4912171 (44.53%) aligned concordantly exactly 1 time 688308 (6.24%) aligned concordantly >1 times ---- 5429621 pairs aligned concordantly 0 times; of these: 3988206 (73.45%) aligned discordantly 1 time ---- 1441415 pairs aligned 0 times concordantly or discordantly; of these: 2882830 mates make up the pairs; of these: 1508245 (52.32%) aligned 0 times 161859 (5.61%) aligned exactly 1 time 1212726 (42.07%) aligned >1 times 93.16% overall alignment rate Time searching: 00:15:39 Overall time: 00:15:39 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_sort_core] merging from 12 files... [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] 561065 / 9587568 = 0.0585 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.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 @ Sat, 24 Aug 2019 22:13:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:13:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:13:20: 1000000 INFO @ Sat, 24 Aug 2019 22:13:32: 2000000 INFO @ Sat, 24 Aug 2019 22:13:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.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 @ Sat, 24 Aug 2019 22:13:39: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:13:39: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:13:44: 3000000 INFO @ Sat, 24 Aug 2019 22:13:51: 1000000 INFO @ Sat, 24 Aug 2019 22:13:55: 4000000 INFO @ Sat, 24 Aug 2019 22:14:03: 2000000 INFO @ Sat, 24 Aug 2019 22:14:07: 5000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:14:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.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 @ Sat, 24 Aug 2019 22:14:09: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:14:09: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:14:14: 3000000 INFO @ Sat, 24 Aug 2019 22:14:18: 6000000 INFO @ Sat, 24 Aug 2019 22:14:19: 1000000 INFO @ Sat, 24 Aug 2019 22:14:26: 4000000 INFO @ Sat, 24 Aug 2019 22:14:29: 2000000 INFO @ Sat, 24 Aug 2019 22:14:30: 7000000 INFO @ Sat, 24 Aug 2019 22:14:38: 5000000 INFO @ Sat, 24 Aug 2019 22:14:38: 3000000 INFO @ Sat, 24 Aug 2019 22:14:42: 8000000 INFO @ Sat, 24 Aug 2019 22:14:48: 4000000 INFO @ Sat, 24 Aug 2019 22:14:50: 6000000 INFO @ Sat, 24 Aug 2019 22:14:53: 9000000 INFO @ Sat, 24 Aug 2019 22:14:58: 5000000 INFO @ Sat, 24 Aug 2019 22:15:02: 7000000 INFO @ Sat, 24 Aug 2019 22:15:05: 10000000 INFO @ Sat, 24 Aug 2019 22:15:07: 6000000 INFO @ Sat, 24 Aug 2019 22:15:12: 8000000 INFO @ Sat, 24 Aug 2019 22:15:17: 11000000 INFO @ Sat, 24 Aug 2019 22:15:17: 7000000 INFO @ Sat, 24 Aug 2019 22:15:21: 9000000 INFO @ Sat, 24 Aug 2019 22:15:26: 8000000 INFO @ Sat, 24 Aug 2019 22:15:28: 12000000 INFO @ Sat, 24 Aug 2019 22:15:30: 10000000 INFO @ Sat, 24 Aug 2019 22:15:36: 9000000 INFO @ Sat, 24 Aug 2019 22:15:39: 11000000 INFO @ Sat, 24 Aug 2019 22:15:40: 13000000 INFO @ Sat, 24 Aug 2019 22:15:45: 10000000 INFO @ Sat, 24 Aug 2019 22:15:49: 12000000 INFO @ Sat, 24 Aug 2019 22:15:52: 14000000 INFO @ Sat, 24 Aug 2019 22:15:55: 11000000 INFO @ Sat, 24 Aug 2019 22:15:58: 13000000 INFO @ Sat, 24 Aug 2019 22:16:04: 15000000 INFO @ Sat, 24 Aug 2019 22:16:04: 12000000 INFO @ Sat, 24 Aug 2019 22:16:08: 14000000 INFO @ Sat, 24 Aug 2019 22:16:14: 13000000 INFO @ Sat, 24 Aug 2019 22:16:15: 16000000 INFO @ Sat, 24 Aug 2019 22:16:17: 15000000 INFO @ Sat, 24 Aug 2019 22:16:23: 14000000 INFO @ Sat, 24 Aug 2019 22:16:27: 17000000 INFO @ Sat, 24 Aug 2019 22:16:27: 16000000 INFO @ Sat, 24 Aug 2019 22:16:33: 15000000 INFO @ Sat, 24 Aug 2019 22:16:36: 17000000 INFO @ Sat, 24 Aug 2019 22:16:38: 18000000 INFO @ Sat, 24 Aug 2019 22:16:42: 16000000 INFO @ Sat, 24 Aug 2019 22:16:46: 18000000 INFO @ Sat, 24 Aug 2019 22:16:50: 19000000 INFO @ Sat, 24 Aug 2019 22:16:52: 17000000 INFO @ Sat, 24 Aug 2019 22:16:55: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:16:55: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:16:55: #1 total tags in treatment: 5239895 INFO @ Sat, 24 Aug 2019 22:16:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:16:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:16:55: #1 tags after filtering in treatment: 4231854 INFO @ Sat, 24 Aug 2019 22:16:55: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:16:55: #1 finished! INFO @ Sat, 24 Aug 2019 22:16:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:16:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:16:55: 19000000 INFO @ Sat, 24 Aug 2019 22:16:55: #2 number of paired peaks: 102 WARNING @ Sat, 24 Aug 2019 22:16:55: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 24 Aug 2019 22:16:55: start model_add_line... INFO @ Sat, 24 Aug 2019 22:16:55: start X-correlation... INFO @ Sat, 24 Aug 2019 22:16:55: end of X-cor INFO @ Sat, 24 Aug 2019 22:16:55: #2 finished! INFO @ Sat, 24 Aug 2019 22:16:55: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:16:55: #2 alternative fragment length(s) may be 0,15,30,57,79,83,114,153,188,191,195,204,209,228,236,259,279,308,314,332,365,383,416,453,479,486,504,541,557,581,591 bps INFO @ Sat, 24 Aug 2019 22:16:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.05_model.r WARNING @ Sat, 24 Aug 2019 22:16:55: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:16:55: #2 You may need to consider one of the other alternative d(s): 0,15,30,57,79,83,114,153,188,191,195,204,209,228,236,259,279,308,314,332,365,383,416,453,479,486,504,541,557,581,591 WARNING @ Sat, 24 Aug 2019 22:16:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:16:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:16:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:16:59: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:16:59: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:16:59: #1 total tags in treatment: 5239895 INFO @ Sat, 24 Aug 2019 22:16:59: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:16:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:16:59: #1 tags after filtering in treatment: 4231854 INFO @ Sat, 24 Aug 2019 22:16:59: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:16:59: #1 finished! INFO @ Sat, 24 Aug 2019 22:16:59: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:16:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:16:59: #2 number of paired peaks: 102 WARNING @ Sat, 24 Aug 2019 22:16:59: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 24 Aug 2019 22:16:59: start model_add_line... INFO @ Sat, 24 Aug 2019 22:16:59: start X-correlation... INFO @ Sat, 24 Aug 2019 22:17:00: end of X-cor INFO @ Sat, 24 Aug 2019 22:17:00: #2 finished! INFO @ Sat, 24 Aug 2019 22:17:00: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:17:00: #2 alternative fragment length(s) may be 0,15,30,57,79,83,114,153,188,191,195,204,209,228,236,259,279,308,314,332,365,383,416,453,479,486,504,541,557,581,591 bps INFO @ Sat, 24 Aug 2019 22:17:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.10_model.r WARNING @ Sat, 24 Aug 2019 22:17:00: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:17:00: #2 You may need to consider one of the other alternative d(s): 0,15,30,57,79,83,114,153,188,191,195,204,209,228,236,259,279,308,314,332,365,383,416,453,479,486,504,541,557,581,591 WARNING @ Sat, 24 Aug 2019 22:17:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:17:00: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:17:01: 18000000 INFO @ Sat, 24 Aug 2019 22:17:10: 19000000 INFO @ Sat, 24 Aug 2019 22:17:14: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:17:14: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:17:14: #1 total tags in treatment: 5239895 INFO @ Sat, 24 Aug 2019 22:17:14: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:17:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:17:14: #1 tags after filtering in treatment: 4231854 INFO @ Sat, 24 Aug 2019 22:17:14: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:17:14: #1 finished! INFO @ Sat, 24 Aug 2019 22:17:14: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:17:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:17:14: #2 number of paired peaks: 102 WARNING @ Sat, 24 Aug 2019 22:17:14: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 24 Aug 2019 22:17:14: start model_add_line... INFO @ Sat, 24 Aug 2019 22:17:14: start X-correlation... INFO @ Sat, 24 Aug 2019 22:17:14: end of X-cor INFO @ Sat, 24 Aug 2019 22:17:14: #2 finished! INFO @ Sat, 24 Aug 2019 22:17:14: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:17:14: #2 alternative fragment length(s) may be 0,15,30,57,79,83,114,153,188,191,195,204,209,228,236,259,279,308,314,332,365,383,416,453,479,486,504,541,557,581,591 bps INFO @ Sat, 24 Aug 2019 22:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546569/SRX5546569.20_model.r WARNING @ Sat, 24 Aug 2019 22:17:14: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 22:17:14: #2 You may need to consider one of the other alternative d(s): 0,15,30,57,79,83,114,153,188,191,195,204,209,228,236,259,279,308,314,332,365,383,416,453,479,486,504,541,557,581,591 WARNING @ Sat, 24 Aug 2019 22:17:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 22:17:14: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:17:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at117/job_scripts/2641134: line 336: 40931 Terminated MACS $i /var/spool/uge/at117/job_scripts/2641134: line 336: 41012 Terminated MACS $i /var/spool/uge/at117/job_scripts/2641134: line 336: 41223 Terminated MACS $i ls: cannot access SRX5546569.05.bed: No such file or directory mv: cannot stat ‘SRX5546569.05.bed’: No such file or directory mv: cannot stat ‘SRX5546569.05.bb’: No such file or directory ls: cannot access SRX5546569.10.bed: No such file or directory mv: cannot stat ‘SRX5546569.10.bed’: No such file or directory mv: cannot stat ‘SRX5546569.10.bb’: No such file or directory ls: cannot access SRX5546569.20.bed: No such file or directory mv: cannot stat ‘SRX5546569.20.bed’: No such file or directory mv: cannot stat ‘SRX5546569.20.bb’: No such file or directory