Job ID = 2641123 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,523,683 reads read : 23,047,366 reads written : 23,047,366 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: 00:17:05 11523683 reads; of these: 11523683 (100.00%) were paired; of these: 5986367 (51.95%) aligned concordantly 0 times 4883470 (42.38%) aligned concordantly exactly 1 time 653846 (5.67%) aligned concordantly >1 times ---- 5986367 pairs aligned concordantly 0 times; of these: 4368206 (72.97%) aligned discordantly 1 time ---- 1618161 pairs aligned 0 times concordantly or discordantly; of these: 3236322 mates make up the pairs; of these: 1800908 (55.65%) aligned 0 times 174842 (5.40%) aligned exactly 1 time 1260572 (38.95%) aligned >1 times 92.19% overall alignment rate Time searching: 00:17:05 Overall time: 00:17:05 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] 545358 / 9904172 = 0.0551 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:12:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.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 22:12:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:12:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:12:35: 1000000 INFO @ Sat, 24 Aug 2019 22:12:43: 2000000 INFO @ Sat, 24 Aug 2019 22:12:51: 3000000 INFO @ Sat, 24 Aug 2019 22:12:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.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 22:12:58: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:12:58: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:12:58: 4000000 INFO @ Sat, 24 Aug 2019 22:13:06: 1000000 INFO @ Sat, 24 Aug 2019 22:13:06: 5000000 INFO @ Sat, 24 Aug 2019 22:13:13: 6000000 INFO @ Sat, 24 Aug 2019 22:13:13: 2000000 INFO @ Sat, 24 Aug 2019 22:13:21: 7000000 INFO @ Sat, 24 Aug 2019 22:13:21: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:13:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.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 22:13:27: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:13:27: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:13:29: 8000000 INFO @ Sat, 24 Aug 2019 22:13:29: 4000000 INFO @ Sat, 24 Aug 2019 22:13:35: 1000000 INFO @ Sat, 24 Aug 2019 22:13:36: 9000000 INFO @ Sat, 24 Aug 2019 22:13:36: 5000000 INFO @ Sat, 24 Aug 2019 22:13:43: 2000000 INFO @ Sat, 24 Aug 2019 22:13:44: 10000000 INFO @ Sat, 24 Aug 2019 22:13:45: 6000000 INFO @ Sat, 24 Aug 2019 22:13:52: 3000000 INFO @ Sat, 24 Aug 2019 22:13:53: 11000000 INFO @ Sat, 24 Aug 2019 22:13:53: 7000000 INFO @ Sat, 24 Aug 2019 22:14:00: 4000000 INFO @ Sat, 24 Aug 2019 22:14:01: 12000000 INFO @ Sat, 24 Aug 2019 22:14:02: 8000000 INFO @ Sat, 24 Aug 2019 22:14:08: 5000000 INFO @ Sat, 24 Aug 2019 22:14:09: 13000000 INFO @ Sat, 24 Aug 2019 22:14:11: 9000000 INFO @ Sat, 24 Aug 2019 22:14:16: 6000000 INFO @ Sat, 24 Aug 2019 22:14:17: 14000000 INFO @ Sat, 24 Aug 2019 22:14:20: 10000000 INFO @ Sat, 24 Aug 2019 22:14:25: 15000000 INFO @ Sat, 24 Aug 2019 22:14:25: 7000000 INFO @ Sat, 24 Aug 2019 22:14:28: 11000000 INFO @ Sat, 24 Aug 2019 22:14:33: 16000000 INFO @ Sat, 24 Aug 2019 22:14:34: 8000000 INFO @ Sat, 24 Aug 2019 22:14:37: 12000000 INFO @ Sat, 24 Aug 2019 22:14:41: 17000000 INFO @ Sat, 24 Aug 2019 22:14:43: 9000000 INFO @ Sat, 24 Aug 2019 22:14:45: 13000000 INFO @ Sat, 24 Aug 2019 22:14:49: 18000000 INFO @ Sat, 24 Aug 2019 22:14:52: 10000000 INFO @ Sat, 24 Aug 2019 22:14:54: 14000000 INFO @ Sat, 24 Aug 2019 22:14:57: 19000000 INFO @ Sat, 24 Aug 2019 22:15:01: 11000000 INFO @ Sat, 24 Aug 2019 22:15:03: 15000000 INFO @ Sat, 24 Aug 2019 22:15:05: 20000000 INFO @ Sat, 24 Aug 2019 22:15:06: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:15:06: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:15:06: #1 total tags in treatment: 5202298 INFO @ Sat, 24 Aug 2019 22:15:06: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:06: #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 22:15:06: #1 tags after filtering in treatment: 4203260 INFO @ Sat, 24 Aug 2019 22:15:06: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:15:06: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:06: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:07: #2 number of paired peaks: 140 WARNING @ Sat, 24 Aug 2019 22:15:07: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sat, 24 Aug 2019 22:15:07: start model_add_line... INFO @ Sat, 24 Aug 2019 22:15:07: start X-correlation... INFO @ Sat, 24 Aug 2019 22:15:07: end of X-cor INFO @ Sat, 24 Aug 2019 22:15:07: #2 finished! INFO @ Sat, 24 Aug 2019 22:15:07: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:15:07: #2 alternative fragment length(s) may be 0,34,81,87,112,125,151,164,189,204,227,267,289,305,327,356,390,418,455,482,502,507,539,563,585 bps INFO @ Sat, 24 Aug 2019 22:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.05_model.r WARNING @ Sat, 24 Aug 2019 22:15:07: #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 22:15:07: #2 You may need to consider one of the other alternative d(s): 0,34,81,87,112,125,151,164,189,204,227,267,289,305,327,356,390,418,455,482,502,507,539,563,585 WARNING @ Sat, 24 Aug 2019 22:15:07: #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 22:15:07: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:15:10: 12000000 INFO @ Sat, 24 Aug 2019 22:15:11: 16000000 INFO @ Sat, 24 Aug 2019 22:15:19: 13000000 INFO @ Sat, 24 Aug 2019 22:15:20: 17000000 INFO @ Sat, 24 Aug 2019 22:15:27: 14000000 INFO @ Sat, 24 Aug 2019 22:15:29: 18000000 INFO @ Sat, 24 Aug 2019 22:15:36: 15000000 INFO @ Sat, 24 Aug 2019 22:15:37: 19000000 INFO @ Sat, 24 Aug 2019 22:15:44: 16000000 INFO @ Sat, 24 Aug 2019 22:15:46: 20000000 INFO @ Sat, 24 Aug 2019 22:15:47: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:15:47: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:15:47: #1 total tags in treatment: 5202298 INFO @ Sat, 24 Aug 2019 22:15:47: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:15:47: #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 22:15:47: #1 tags after filtering in treatment: 4203260 INFO @ Sat, 24 Aug 2019 22:15:47: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:15:47: #1 finished! INFO @ Sat, 24 Aug 2019 22:15:47: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:15:47: #2 number of paired peaks: 140 WARNING @ Sat, 24 Aug 2019 22:15:47: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sat, 24 Aug 2019 22:15:47: start model_add_line... INFO @ Sat, 24 Aug 2019 22:15:47: start X-correlation... INFO @ Sat, 24 Aug 2019 22:15:47: end of X-cor INFO @ Sat, 24 Aug 2019 22:15:47: #2 finished! INFO @ Sat, 24 Aug 2019 22:15:47: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:15:47: #2 alternative fragment length(s) may be 0,34,81,87,112,125,151,164,189,204,227,267,289,305,327,356,390,418,455,482,502,507,539,563,585 bps INFO @ Sat, 24 Aug 2019 22:15:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.10_model.r WARNING @ Sat, 24 Aug 2019 22:15:47: #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 22:15:47: #2 You may need to consider one of the other alternative d(s): 0,34,81,87,112,125,151,164,189,204,227,267,289,305,327,356,390,418,455,482,502,507,539,563,585 WARNING @ Sat, 24 Aug 2019 22:15:47: #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 22:15:47: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:15:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:15:53: 17000000 INFO @ Sat, 24 Aug 2019 22:16:01: 18000000 INFO @ Sat, 24 Aug 2019 22:16:09: 19000000 INFO @ Sat, 24 Aug 2019 22:16:18: 20000000 INFO @ Sat, 24 Aug 2019 22:16:19: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 22:16:19: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 22:16:19: #1 total tags in treatment: 5202298 INFO @ Sat, 24 Aug 2019 22:16:19: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:16:19: #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 22:16:19: #1 tags after filtering in treatment: 4203260 INFO @ Sat, 24 Aug 2019 22:16:19: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 24 Aug 2019 22:16:19: #1 finished! INFO @ Sat, 24 Aug 2019 22:16:19: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:16:19: #2 number of paired peaks: 140 WARNING @ Sat, 24 Aug 2019 22:16:19: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sat, 24 Aug 2019 22:16:19: start model_add_line... INFO @ Sat, 24 Aug 2019 22:16:19: start X-correlation... INFO @ Sat, 24 Aug 2019 22:16:19: end of X-cor INFO @ Sat, 24 Aug 2019 22:16:19: #2 finished! INFO @ Sat, 24 Aug 2019 22:16:19: #2 predicted fragment length is 0 bps INFO @ Sat, 24 Aug 2019 22:16:19: #2 alternative fragment length(s) may be 0,34,81,87,112,125,151,164,189,204,227,267,289,305,327,356,390,418,455,482,502,507,539,563,585 bps INFO @ Sat, 24 Aug 2019 22:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5546561/SRX5546561.20_model.r WARNING @ Sat, 24 Aug 2019 22:16:19: #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 22:16:19: #2 You may need to consider one of the other alternative d(s): 0,34,81,87,112,125,151,164,189,204,227,267,289,305,327,356,390,418,455,482,502,507,539,563,585 WARNING @ Sat, 24 Aug 2019 22:16:19: #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 22:16:19: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:16:19: #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。 /var/spool/uge/at108/job_scripts/2641123: line 336: 7792 Terminated MACS $i /var/spool/uge/at108/job_scripts/2641123: line 336: 10429 Terminated MACS $i /var/spool/uge/at108/job_scripts/2641123: line 336: 13552 Terminated MACS $i ls: cannot access SRX5546561.05.bed: No such file or directory mv: cannot stat ‘SRX5546561.05.bed’: No such file or directory mv: cannot stat ‘SRX5546561.05.bb’: No such file or directory ls: cannot access SRX5546561.10.bed: No such file or directory mv: cannot stat ‘SRX5546561.10.bed’: No such file or directory mv: cannot stat ‘SRX5546561.10.bb’: No such file or directory ls: cannot access SRX5546561.20.bed: No such file or directory mv: cannot stat ‘SRX5546561.20.bed’: No such file or directory mv: cannot stat ‘SRX5546561.20.bb’: No such file or directory