Job ID = 2641127 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,998,745 reads read : 21,997,490 reads written : 21,997,490 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: 00:16:28 10998745 reads; of these: 10998745 (100.00%) were paired; of these: 6264360 (56.96%) aligned concordantly 0 times 4222304 (38.39%) aligned concordantly exactly 1 time 512081 (4.66%) aligned concordantly >1 times ---- 6264360 pairs aligned concordantly 0 times; of these: 4653406 (74.28%) aligned discordantly 1 time ---- 1610954 pairs aligned 0 times concordantly or discordantly; of these: 3221908 mates make up the pairs; of these: 1814828 (56.33%) aligned 0 times 181998 (5.65%) aligned exactly 1 time 1225082 (38.02%) aligned >1 times 91.75% overall alignment rate Time searching: 00:16:28 Overall time: 00:16:28 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] 704699 / 9386400 = 0.0751 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:11:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.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 22:11:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:11:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:11:24: 1000000 INFO @ Sat, 24 Aug 2019 22:11:36: 2000000 INFO @ Sat, 24 Aug 2019 22:11:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.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 22:11:41: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:11:41: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:11:49: 3000000 INFO @ Sat, 24 Aug 2019 22:11:51: 1000000 INFO @ Sat, 24 Aug 2019 22:12:01: 2000000 INFO @ Sat, 24 Aug 2019 22:12:02: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:12:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.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 22:12:11: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:12:11: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:12:12: 3000000 INFO @ Sat, 24 Aug 2019 22:12:15: 5000000 INFO @ Sat, 24 Aug 2019 22:12:21: 1000000 INFO @ Sat, 24 Aug 2019 22:12:22: 4000000 INFO @ Sat, 24 Aug 2019 22:12:28: 6000000 INFO @ Sat, 24 Aug 2019 22:12:32: 2000000 INFO @ Sat, 24 Aug 2019 22:12:33: 5000000 INFO @ Sat, 24 Aug 2019 22:12:41: 7000000 INFO @ Sat, 24 Aug 2019 22:12:43: 3000000 INFO @ Sat, 24 Aug 2019 22:12:44: 6000000 INFO @ Sat, 24 Aug 2019 22:12:56: 4000000 INFO @ Sat, 24 Aug 2019 22:12:57: 8000000 INFO @ Sat, 24 Aug 2019 22:12:57: 7000000 INFO @ Sat, 24 Aug 2019 22:13:07: 5000000 INFO @ Sat, 24 Aug 2019 22:13:08: 8000000 INFO @ Sat, 24 Aug 2019 22:13:10: 9000000 INFO @ Sat, 24 Aug 2019 22:13:17: 6000000 INFO @ Sat, 24 Aug 2019 22:13:19: 9000000 INFO @ Sat, 24 Aug 2019 22:13:21: 10000000 INFO @ Sat, 24 Aug 2019 22:13:28: 7000000 INFO @ Sat, 24 Aug 2019 22:13:31: 10000000 INFO @ Sat, 24 Aug 2019 22:13:32: 11000000 INFO @ Sat, 24 Aug 2019 22:13:38: 8000000 INFO @ Sat, 24 Aug 2019 22:13:43: 12000000 INFO @ Sat, 24 Aug 2019 22:13:43: 11000000 INFO @ Sat, 24 Aug 2019 22:13:50: 9000000 INFO @ Sat, 24 Aug 2019 22:13:55: 13000000 INFO @ Sat, 24 Aug 2019 22:13:56: 12000000 INFO @ Sat, 24 Aug 2019 22:14:03: 10000000 INFO @ Sat, 24 Aug 2019 22:14:06: 14000000 INFO @ Sat, 24 Aug 2019 22:14:08: 13000000 INFO @ Sat, 24 Aug 2019 22:14:15: 11000000 INFO @ Sat, 24 Aug 2019 22:14:17: 15000000 INFO @ Sat, 24 Aug 2019 22:14:19: 14000000 INFO @ Sat, 24 Aug 2019 22:14:25: 12000000 INFO @ Sat, 24 Aug 2019 22:14:27: 16000000 INFO @ Sat, 24 Aug 2019 22:14:31: 15000000 INFO @ Sat, 24 Aug 2019 22:14:35: 13000000 INFO @ Sat, 24 Aug 2019 22:14:37: 17000000 INFO @ Sat, 24 Aug 2019 22:14:43: 16000000 INFO @ Sat, 24 Aug 2019 22:14:46: 14000000 INFO @ Sat, 24 Aug 2019 22:14:47: 18000000 INFO @ Sat, 24 Aug 2019 22:14:54: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:14:54: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:14:54: #1 total tags in treatment: 4384028 INFO @ Sat, 24 Aug 2019 22:14:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:14:54: #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 22:14:54: #1 tags after filtering in treatment: 3652361 INFO @ Sat, 24 Aug 2019 22:14:54: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 24 Aug 2019 22:14:54: #1 finished! INFO @ Sat, 24 Aug 2019 22:14:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:14:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:14:54: #2 number of paired peaks: 167 WARNING @ Sat, 24 Aug 2019 22:14:54: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 24 Aug 2019 22:14:54: start model_add_line... INFO @ Sat, 24 Aug 2019 22:14:54: start X-correlation... INFO @ Sat, 24 Aug 2019 22:14:55: end of X-cor INFO @ Sat, 24 Aug 2019 22:14:55: #2 finished! INFO @ Sat, 24 Aug 2019 22:14:55: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:14:55: #2 alternative fragment length(s) may be 0,17,47,64,97,118,152,169,188,231,238,277,318,340,373,392,394,407,413,431,445,483,497,522,530,564,590 bps INFO @ Sat, 24 Aug 2019 22:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.05_model.r WARNING @ Sat, 24 Aug 2019 22:14:55: #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 22:14:55: #2 You may need to consider one of the other alternative d(s): 0,17,47,64,97,118,152,169,188,231,238,277,318,340,373,392,394,407,413,431,445,483,497,522,530,564,590 WARNING @ Sat, 24 Aug 2019 22:14:55: #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 22:14:55: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:14:55: 17000000 INFO @ Sat, 24 Aug 2019 22:14:56: 15000000 INFO @ Sat, 24 Aug 2019 22:15:07: 16000000 INFO @ Sat, 24 Aug 2019 22:15:08: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 24 Aug 2019 22:15:17: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:15:17: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:15:17: #1 total tags in treatment: 4384028 INFO @ Sat, 24 Aug 2019 22:15:17: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:17: #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 22:15:17: #1 tags after filtering in treatment: 3652361 INFO @ Sat, 24 Aug 2019 22:15:17: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 24 Aug 2019 22:15:17: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:17: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:18: #2 number of paired peaks: 167 WARNING @ Sat, 24 Aug 2019 22:15:18: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 24 Aug 2019 22:15:18: start model_add_line... INFO @ Sat, 24 Aug 2019 22:15:18: start X-correlation... INFO @ Sat, 24 Aug 2019 22:15:18: end of X-cor INFO @ Sat, 24 Aug 2019 22:15:18: #2 finished! INFO @ Sat, 24 Aug 2019 22:15:18: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:15:18: #2 alternative fragment length(s) may be 0,17,47,64,97,118,152,169,188,231,238,277,318,340,373,392,394,407,413,431,445,483,497,522,530,564,590 bps INFO @ Sat, 24 Aug 2019 22:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546564/SRX5546564.10_model.r WARNING @ Sat, 24 Aug 2019 22:15:18: #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 22:15:18: #2 You may need to consider one of the other alternative d(s): 0,17,47,64,97,118,152,169,188,231,238,277,318,340,373,392,394,407,413,431,445,483,497,522,530,564,590 WARNING @ Sat, 24 Aug 2019 22:15:18: #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 22:15:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:15:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:15:18: 17000000 BigWig に変換しました。 /var/spool/uge/at039/job_scripts/2641127: line 336: 22517 Terminated MACS $i /var/spool/uge/at039/job_scripts/2641127: line 336: 23446 Terminated MACS $i /var/spool/uge/at039/job_scripts/2641127: line 336: 24667 Terminated MACS $i ls: cannot access SRX5546564.05.bed: No such file or directory mv: cannot stat ‘SRX5546564.05.bed’: No such file or directory mv: cannot stat ‘SRX5546564.05.bb’: No such file or directory ls: cannot access SRX5546564.10.bed: No such file or directory mv: cannot stat ‘SRX5546564.10.bed’: No such file or directory mv: cannot stat ‘SRX5546564.10.bb’: No such file or directory ls: cannot access SRX5546564.20.bed: No such file or directory mv: cannot stat ‘SRX5546564.20.bed’: No such file or directory mv: cannot stat ‘SRX5546564.20.bb’: No such file or directory