Job ID = 2010564 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 7,446,944 reads read : 14,893,888 reads written : 14,893,888 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: 00:06:32 7446944 reads; of these: 7446944 (100.00%) were paired; of these: 2312236 (31.05%) aligned concordantly 0 times 3766358 (50.58%) aligned concordantly exactly 1 time 1368350 (18.37%) aligned concordantly >1 times ---- 2312236 pairs aligned concordantly 0 times; of these: 129212 (5.59%) aligned discordantly 1 time ---- 2183024 pairs aligned 0 times concordantly or discordantly; of these: 4366048 mates make up the pairs; of these: 4130649 (94.61%) aligned 0 times 107895 (2.47%) aligned exactly 1 time 127504 (2.92%) aligned >1 times 72.27% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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] 453992 / 5254566 = 0.0864 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, 05 Jul 2019 23:22:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.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, 05 Jul 2019 23:22:01: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:22:01: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:22:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.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, 05 Jul 2019 23:22:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:22:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.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, 05 Jul 2019 23:22:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:22:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:22:09: 1000000 INFO @ Fri, 05 Jul 2019 23:22:10: 1000000 INFO @ Fri, 05 Jul 2019 23:22:14: 1000000 INFO @ Fri, 05 Jul 2019 23:22:16: 2000000 INFO @ Fri, 05 Jul 2019 23:22:19: 2000000 INFO @ Fri, 05 Jul 2019 23:22:24: 3000000 INFO @ Fri, 05 Jul 2019 23:22:24: 2000000 INFO @ Fri, 05 Jul 2019 23:22:28: 3000000 INFO @ Fri, 05 Jul 2019 23:22:32: 4000000 INFO @ Fri, 05 Jul 2019 23:22:35: 3000000 INFO @ Fri, 05 Jul 2019 23:22:36: 4000000 INFO @ Fri, 05 Jul 2019 23:22:41: 5000000 INFO @ Fri, 05 Jul 2019 23:22:45: 5000000 INFO @ Fri, 05 Jul 2019 23:22:46: 4000000 INFO @ Fri, 05 Jul 2019 23:22:48: 6000000 INFO @ Fri, 05 Jul 2019 23:22:53: 6000000 INFO @ Fri, 05 Jul 2019 23:22:56: 7000000 INFO @ Fri, 05 Jul 2019 23:22:56: 5000000 INFO @ Fri, 05 Jul 2019 23:23:01: 7000000 INFO @ Fri, 05 Jul 2019 23:23:03: 8000000 INFO @ Fri, 05 Jul 2019 23:23:07: 6000000 INFO @ Fri, 05 Jul 2019 23:23:10: 8000000 INFO @ Fri, 05 Jul 2019 23:23:11: 9000000 INFO @ Fri, 05 Jul 2019 23:23:17: 7000000 INFO @ Fri, 05 Jul 2019 23:23:17: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:23:17: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:23:17: #1 total tags in treatment: 4687600 INFO @ Fri, 05 Jul 2019 23:23:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:23:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:23:17: #1 tags after filtering in treatment: 3017630 INFO @ Fri, 05 Jul 2019 23:23:17: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:23:17: #1 finished! INFO @ Fri, 05 Jul 2019 23:23:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:23:18: #2 number of paired peaks: 302 WARNING @ Fri, 05 Jul 2019 23:23:18: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Fri, 05 Jul 2019 23:23:18: start model_add_line... INFO @ Fri, 05 Jul 2019 23:23:18: start X-correlation... INFO @ Fri, 05 Jul 2019 23:23:18: end of X-cor INFO @ Fri, 05 Jul 2019 23:23:18: #2 finished! INFO @ Fri, 05 Jul 2019 23:23:18: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:23:18: #2 alternative fragment length(s) may be 0,30,53,75,96,126,146,168,181,184,203,224,299 bps INFO @ Fri, 05 Jul 2019 23:23:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.05_model.r WARNING @ Fri, 05 Jul 2019 23:23:18: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 23:23:18: #2 You may need to consider one of the other alternative d(s): 0,30,53,75,96,126,146,168,181,184,203,224,299 WARNING @ Fri, 05 Jul 2019 23:23:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:23:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:23:18: 9000000 INFO @ Fri, 05 Jul 2019 23:23:26: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:23:26: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:23:26: #1 total tags in treatment: 4687600 INFO @ Fri, 05 Jul 2019 23:23:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:23:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:23:26: #1 tags after filtering in treatment: 3017630 INFO @ Fri, 05 Jul 2019 23:23:26: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:23:26: #1 finished! INFO @ Fri, 05 Jul 2019 23:23:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:23:26: #2 number of paired peaks: 302 WARNING @ Fri, 05 Jul 2019 23:23:26: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Fri, 05 Jul 2019 23:23:26: start model_add_line... INFO @ Fri, 05 Jul 2019 23:23:26: start X-correlation... INFO @ Fri, 05 Jul 2019 23:23:26: end of X-cor INFO @ Fri, 05 Jul 2019 23:23:26: #2 finished! INFO @ Fri, 05 Jul 2019 23:23:26: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:23:26: #2 alternative fragment length(s) may be 0,30,53,75,96,126,146,168,181,184,203,224,299 bps INFO @ Fri, 05 Jul 2019 23:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.10_model.r WARNING @ Fri, 05 Jul 2019 23:23:26: #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, 05 Jul 2019 23:23:26: #2 You may need to consider one of the other alternative d(s): 0,30,53,75,96,126,146,168,181,184,203,224,299 WARNING @ Fri, 05 Jul 2019 23:23:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:23:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:23:27: 8000000 INFO @ Fri, 05 Jul 2019 23:23:37: 9000000 INFO @ Fri, 05 Jul 2019 23:23:45: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:23:45: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:23:45: #1 total tags in treatment: 4687600 INFO @ Fri, 05 Jul 2019 23:23:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:23:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 23:23:45: #1 tags after filtering in treatment: 3017630 INFO @ Fri, 05 Jul 2019 23:23:45: #1 Redundant rate of treatment: 0.36 INFO @ Fri, 05 Jul 2019 23:23:45: #1 finished! INFO @ Fri, 05 Jul 2019 23:23:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:23:46: #2 number of paired peaks: 302 WARNING @ Fri, 05 Jul 2019 23:23:46: Fewer paired peaks (302) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 302 pairs to build model! INFO @ Fri, 05 Jul 2019 23:23:46: start model_add_line... INFO @ Fri, 05 Jul 2019 23:23:46: start X-correlation... INFO @ Fri, 05 Jul 2019 23:23:46: end of X-cor INFO @ Fri, 05 Jul 2019 23:23:46: #2 finished! INFO @ Fri, 05 Jul 2019 23:23:46: #2 predicted fragment length is 0 bps INFO @ Fri, 05 Jul 2019 23:23:46: #2 alternative fragment length(s) may be 0,30,53,75,96,126,146,168,181,184,203,224,299 bps INFO @ Fri, 05 Jul 2019 23:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381265/SRX381265.20_model.r WARNING @ Fri, 05 Jul 2019 23:23:46: #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, 05 Jul 2019 23:23:46: #2 You may need to consider one of the other alternative d(s): 0,30,53,75,96,126,146,168,181,184,203,224,299 WARNING @ Fri, 05 Jul 2019 23:23:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 23:23:46: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:23:46: #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 SRX381265.05.bed: No such file or directory mv: cannot stat ‘SRX381265.05.bed’: No such file or directory /var/spool/uge/at040/job_scripts/2010564: line 335: 44623 Terminated MACS $i /var/spool/uge/at040/job_scripts/2010564: line 335: 44638 Terminated MACS $i /var/spool/uge/at040/job_scripts/2010564: line 335: 44814 Terminated MACS $i mv: cannot stat ‘SRX381265.05.bb’: No such file or directory ls: cannot access SRX381265.10.bed: No such file or directory mv: cannot stat ‘SRX381265.10.bed’: No such file or directory mv: cannot stat ‘SRX381265.10.bb’: No such file or directory ls: cannot access SRX381265.20.bed: No such file or directory mv: cannot stat ‘SRX381265.20.bed’: No such file or directory mv: cannot stat ‘SRX381265.20.bb’: No such file or directory