Job ID = 2641128 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,150,591 reads read : 20,301,182 reads written : 20,301,182 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: 00:14:53 10150591 reads; of these: 10150591 (100.00%) were paired; of these: 5482204 (54.01%) aligned concordantly 0 times 4150579 (40.89%) aligned concordantly exactly 1 time 517808 (5.10%) aligned concordantly >1 times ---- 5482204 pairs aligned concordantly 0 times; of these: 4003896 (73.03%) aligned discordantly 1 time ---- 1478308 pairs aligned 0 times concordantly or discordantly; of these: 2956616 mates make up the pairs; of these: 1717485 (58.09%) aligned 0 times 157796 (5.34%) aligned exactly 1 time 1081335 (36.57%) aligned >1 times 91.54% overall alignment rate Time searching: 00:14:53 Overall time: 00:14:53 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 8 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] 441971 / 8670899 = 0.0510 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:07:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.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 22:07:32: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:07:32: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:07:42: 1000000 INFO @ Sat, 24 Aug 2019 22:07:51: 2000000 INFO @ Sat, 24 Aug 2019 22:08:01: 3000000 INFO @ Sat, 24 Aug 2019 22:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.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 22:08:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:11: 4000000 INFO @ Sat, 24 Aug 2019 22:08:11: 1000000 INFO @ Sat, 24 Aug 2019 22:08:20: 5000000 INFO @ Sat, 24 Aug 2019 22:08:21: 2000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:08:30: 6000000 INFO @ Sat, 24 Aug 2019 22:08:31: 3000000 INFO @ Sat, 24 Aug 2019 22:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.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 22:08:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:08:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:08:40: 7000000 INFO @ Sat, 24 Aug 2019 22:08:41: 4000000 INFO @ Sat, 24 Aug 2019 22:08:41: 1000000 INFO @ Sat, 24 Aug 2019 22:08:50: 8000000 INFO @ Sat, 24 Aug 2019 22:08:50: 5000000 INFO @ Sat, 24 Aug 2019 22:08:51: 2000000 INFO @ Sat, 24 Aug 2019 22:09:00: 9000000 INFO @ Sat, 24 Aug 2019 22:09:00: 6000000 INFO @ Sat, 24 Aug 2019 22:09:01: 3000000 INFO @ Sat, 24 Aug 2019 22:09:10: 10000000 INFO @ Sat, 24 Aug 2019 22:09:10: 7000000 INFO @ Sat, 24 Aug 2019 22:09:11: 4000000 INFO @ Sat, 24 Aug 2019 22:09:20: 11000000 INFO @ Sat, 24 Aug 2019 22:09:20: 8000000 INFO @ Sat, 24 Aug 2019 22:09:21: 5000000 INFO @ Sat, 24 Aug 2019 22:09:30: 9000000 INFO @ Sat, 24 Aug 2019 22:09:30: 12000000 INFO @ Sat, 24 Aug 2019 22:09:31: 6000000 INFO @ Sat, 24 Aug 2019 22:09:40: 10000000 INFO @ Sat, 24 Aug 2019 22:09:40: 13000000 INFO @ Sat, 24 Aug 2019 22:09:41: 7000000 INFO @ Sat, 24 Aug 2019 22:09:50: 11000000 INFO @ Sat, 24 Aug 2019 22:09:50: 14000000 INFO @ Sat, 24 Aug 2019 22:09:50: 8000000 INFO @ Sat, 24 Aug 2019 22:09:59: 12000000 INFO @ Sat, 24 Aug 2019 22:10:00: 15000000 INFO @ Sat, 24 Aug 2019 22:10:00: 9000000 INFO @ Sat, 24 Aug 2019 22:10:09: 13000000 INFO @ Sat, 24 Aug 2019 22:10:09: 16000000 INFO @ Sat, 24 Aug 2019 22:10:10: 10000000 INFO @ Sat, 24 Aug 2019 22:10:19: 14000000 INFO @ Sat, 24 Aug 2019 22:10:19: 17000000 INFO @ Sat, 24 Aug 2019 22:10:20: 11000000 INFO @ Sat, 24 Aug 2019 22:10:26: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:26: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:26: #1 total tags in treatment: 4418129 INFO @ Sat, 24 Aug 2019 22:10:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:26: #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 22:10:26: #1 tags after filtering in treatment: 3682938 INFO @ Sat, 24 Aug 2019 22:10:26: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 24 Aug 2019 22:10:26: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:27: #2 number of paired peaks: 165 WARNING @ Sat, 24 Aug 2019 22:10:27: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 24 Aug 2019 22:10:27: start model_add_line... INFO @ Sat, 24 Aug 2019 22:10:27: start X-correlation... INFO @ Sat, 24 Aug 2019 22:10:27: end of X-cor INFO @ Sat, 24 Aug 2019 22:10:27: #2 finished! INFO @ Sat, 24 Aug 2019 22:10:27: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:10:27: #2 alternative fragment length(s) may be 0,32,54,79,115,136,148,169,186,218,226,279,297,319,329,372,391,424,446,484,510,529,548,573,598 bps INFO @ Sat, 24 Aug 2019 22:10:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.05_model.r WARNING @ Sat, 24 Aug 2019 22:10:27: #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 22:10:27: #2 You may need to consider one of the other alternative d(s): 0,32,54,79,115,136,148,169,186,218,226,279,297,319,329,372,391,424,446,484,510,529,548,573,598 WARNING @ Sat, 24 Aug 2019 22:10:27: #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 22:10:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:10:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:10:29: 15000000 INFO @ Sat, 24 Aug 2019 22:10:30: 12000000 INFO @ Sat, 24 Aug 2019 22:10:39: 16000000 INFO @ Sat, 24 Aug 2019 22:10:40: 13000000 INFO @ Sat, 24 Aug 2019 22:10:48: 17000000 INFO @ Sat, 24 Aug 2019 22:10:49: 14000000 INFO @ Sat, 24 Aug 2019 22:10:55: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:10:55: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:10:55: #1 total tags in treatment: 4418129 INFO @ Sat, 24 Aug 2019 22:10:55: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:10:55: #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 22:10:55: #1 tags after filtering in treatment: 3682938 INFO @ Sat, 24 Aug 2019 22:10:55: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 24 Aug 2019 22:10:55: #1 finished! INFO @ Sat, 24 Aug 2019 22:10:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:10:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:10:56: #2 number of paired peaks: 165 WARNING @ Sat, 24 Aug 2019 22:10:56: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 24 Aug 2019 22:10:56: start model_add_line... INFO @ Sat, 24 Aug 2019 22:10:56: start X-correlation... INFO @ Sat, 24 Aug 2019 22:10:56: end of X-cor INFO @ Sat, 24 Aug 2019 22:10:56: #2 finished! INFO @ Sat, 24 Aug 2019 22:10:56: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:10:56: #2 alternative fragment length(s) may be 0,32,54,79,115,136,148,169,186,218,226,279,297,319,329,372,391,424,446,484,510,529,548,573,598 bps INFO @ Sat, 24 Aug 2019 22:10:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.10_model.r WARNING @ Sat, 24 Aug 2019 22:10:56: #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 22:10:56: #2 You may need to consider one of the other alternative d(s): 0,32,54,79,115,136,148,169,186,218,226,279,297,319,329,372,391,424,446,484,510,529,548,573,598 WARNING @ Sat, 24 Aug 2019 22:10:56: #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 22:10:56: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:10:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:10:59: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:11:08: 16000000 INFO @ Sat, 24 Aug 2019 22:11:18: 17000000 INFO @ Sat, 24 Aug 2019 22:11:24: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:11:24: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:11:24: #1 total tags in treatment: 4418129 INFO @ Sat, 24 Aug 2019 22:11:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:11:24: #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 22:11:24: #1 tags after filtering in treatment: 3682938 INFO @ Sat, 24 Aug 2019 22:11:24: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 24 Aug 2019 22:11:24: #1 finished! INFO @ Sat, 24 Aug 2019 22:11:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:11:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:11:24: #2 number of paired peaks: 165 WARNING @ Sat, 24 Aug 2019 22:11:24: Fewer paired peaks (165) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 165 pairs to build model! INFO @ Sat, 24 Aug 2019 22:11:24: start model_add_line... INFO @ Sat, 24 Aug 2019 22:11:24: start X-correlation... INFO @ Sat, 24 Aug 2019 22:11:24: end of X-cor INFO @ Sat, 24 Aug 2019 22:11:24: #2 finished! INFO @ Sat, 24 Aug 2019 22:11:24: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:11:24: #2 alternative fragment length(s) may be 0,32,54,79,115,136,148,169,186,218,226,279,297,319,329,372,391,424,446,484,510,529,548,573,598 bps INFO @ Sat, 24 Aug 2019 22:11:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546565/SRX5546565.20_model.r WARNING @ Sat, 24 Aug 2019 22:11:24: #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 22:11:24: #2 You may need to consider one of the other alternative d(s): 0,32,54,79,115,136,148,169,186,218,226,279,297,319,329,372,391,424,446,484,510,529,548,573,598 WARNING @ Sat, 24 Aug 2019 22:11:24: #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 22:11:24: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:11:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 /var/spool/uge/at080/job_scripts/2641128: line 336: 42770 Terminated MACS $i /var/spool/uge/at080/job_scripts/2641128: line 336: 42814 Terminated MACS $i /var/spool/uge/at080/job_scripts/2641128: line 336: 43087 Terminated MACS $i ls: cannot access SRX5546565.05.bed: No such file or directory mv: cannot stat ‘SRX5546565.05.bed’: No such file or directory mv: cannot stat ‘SRX5546565.05.bb’: No such file or directory ls: cannot access SRX5546565.10.bed: No such file or directory mv: cannot stat ‘SRX5546565.10.bed’: No such file or directory mv: cannot stat ‘SRX5546565.10.bb’: No such file or directory ls: cannot access SRX5546565.20.bed: No such file or directory mv: cannot stat ‘SRX5546565.20.bed’: No such file or directory mv: cannot stat ‘SRX5546565.20.bb’: No such file or directory