Job ID = 1291524 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,375,428 reads read : 12,375,428 reads written : 12,375,428 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:09 12375428 reads; of these: 12375428 (100.00%) were unpaired; of these: 502067 (4.06%) aligned 0 times 9581047 (77.42%) aligned exactly 1 time 2292314 (18.52%) aligned >1 times 95.94% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 2622588 / 11873361 = 0.2209 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 @ Sun, 02 Jun 2019 15:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 15:59:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 15:59:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 15:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 15:59:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 15:59:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 15:59:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.bam'] # control file = None # effective genome size = 9.00e+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 @ Sun, 02 Jun 2019 15:59:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 15:59:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 15:59:42: 1000000 INFO @ Sun, 02 Jun 2019 15:59:42: 1000000 INFO @ Sun, 02 Jun 2019 15:59:43: 1000000 INFO @ Sun, 02 Jun 2019 15:59:50: 2000000 INFO @ Sun, 02 Jun 2019 15:59:50: 2000000 INFO @ Sun, 02 Jun 2019 15:59:51: 2000000 INFO @ Sun, 02 Jun 2019 15:59:57: 3000000 INFO @ Sun, 02 Jun 2019 15:59:57: 3000000 INFO @ Sun, 02 Jun 2019 15:59:58: 3000000 INFO @ Sun, 02 Jun 2019 16:00:04: 4000000 INFO @ Sun, 02 Jun 2019 16:00:04: 4000000 INFO @ Sun, 02 Jun 2019 16:00:05: 4000000 INFO @ Sun, 02 Jun 2019 16:00:11: 5000000 INFO @ Sun, 02 Jun 2019 16:00:11: 5000000 INFO @ Sun, 02 Jun 2019 16:00:12: 5000000 INFO @ Sun, 02 Jun 2019 16:00:18: 6000000 INFO @ Sun, 02 Jun 2019 16:00:18: 6000000 INFO @ Sun, 02 Jun 2019 16:00:19: 6000000 INFO @ Sun, 02 Jun 2019 16:00:25: 7000000 INFO @ Sun, 02 Jun 2019 16:00:25: 7000000 INFO @ Sun, 02 Jun 2019 16:00:27: 7000000 INFO @ Sun, 02 Jun 2019 16:00:32: 8000000 INFO @ Sun, 02 Jun 2019 16:00:33: 8000000 INFO @ Sun, 02 Jun 2019 16:00:34: 8000000 INFO @ Sun, 02 Jun 2019 16:00:39: 9000000 INFO @ Sun, 02 Jun 2019 16:00:40: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:00:40: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:00:40: #1 total tags in treatment: 9250773 INFO @ Sun, 02 Jun 2019 16:00:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:00:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:00:41: #1 tags after filtering in treatment: 9250773 INFO @ Sun, 02 Jun 2019 16:00:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:00:41: #1 finished! INFO @ Sun, 02 Jun 2019 16:00:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:00:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:00:41: 9000000 INFO @ Sun, 02 Jun 2019 16:00:41: #2 number of paired peaks: 133 WARNING @ Sun, 02 Jun 2019 16:00:41: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sun, 02 Jun 2019 16:00:41: start model_add_line... INFO @ Sun, 02 Jun 2019 16:00:41: start X-correlation... INFO @ Sun, 02 Jun 2019 16:00:41: end of X-cor INFO @ Sun, 02 Jun 2019 16:00:41: #2 finished! INFO @ Sun, 02 Jun 2019 16:00:41: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:00:41: #2 alternative fragment length(s) may be 0,15,38,93,135,192,213,253,280,295,342,356,374,405,425,451,456,528,566,592 bps INFO @ Sun, 02 Jun 2019 16:00:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.05_model.r WARNING @ Sun, 02 Jun 2019 16:00:41: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:00:41: #2 You may need to consider one of the other alternative d(s): 0,15,38,93,135,192,213,253,280,295,342,356,374,405,425,451,456,528,566,592 WARNING @ Sun, 02 Jun 2019 16:00:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:00:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:00:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:00:42: 9000000 INFO @ Sun, 02 Jun 2019 16:00:43: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:00:43: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:00:43: #1 total tags in treatment: 9250773 INFO @ Sun, 02 Jun 2019 16:00:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:00:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:00:43: #1 tags after filtering in treatment: 9250773 INFO @ Sun, 02 Jun 2019 16:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:00:43: #1 finished! INFO @ Sun, 02 Jun 2019 16:00:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:00:44: #2 number of paired peaks: 133 WARNING @ Sun, 02 Jun 2019 16:00:44: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sun, 02 Jun 2019 16:00:44: start model_add_line... INFO @ Sun, 02 Jun 2019 16:00:44: start X-correlation... INFO @ Sun, 02 Jun 2019 16:00:44: end of X-cor INFO @ Sun, 02 Jun 2019 16:00:44: #2 finished! INFO @ Sun, 02 Jun 2019 16:00:44: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:00:44: #2 alternative fragment length(s) may be 0,15,38,93,135,192,213,253,280,295,342,356,374,405,425,451,456,528,566,592 bps INFO @ Sun, 02 Jun 2019 16:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.20_model.r WARNING @ Sun, 02 Jun 2019 16:00:44: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:00:44: #2 You may need to consider one of the other alternative d(s): 0,15,38,93,135,192,213,253,280,295,342,356,374,405,425,451,456,528,566,592 WARNING @ Sun, 02 Jun 2019 16:00:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:00:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:00:44: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:00:44: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:00:44: #1 total tags in treatment: 9250773 INFO @ Sun, 02 Jun 2019 16:00:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:00:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:00:44: #1 tags after filtering in treatment: 9250773 INFO @ Sun, 02 Jun 2019 16:00:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:00:44: #1 finished! INFO @ Sun, 02 Jun 2019 16:00:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:00:45: #2 number of paired peaks: 133 WARNING @ Sun, 02 Jun 2019 16:00:45: Fewer paired peaks (133) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 133 pairs to build model! INFO @ Sun, 02 Jun 2019 16:00:45: start model_add_line... INFO @ Sun, 02 Jun 2019 16:00:45: start X-correlation... INFO @ Sun, 02 Jun 2019 16:00:45: end of X-cor INFO @ Sun, 02 Jun 2019 16:00:45: #2 finished! INFO @ Sun, 02 Jun 2019 16:00:45: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:00:45: #2 alternative fragment length(s) may be 0,15,38,93,135,192,213,253,280,295,342,356,374,405,425,451,456,528,566,592 bps INFO @ Sun, 02 Jun 2019 16:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113602/SRX113602.10_model.r WARNING @ Sun, 02 Jun 2019 16:00:45: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:00:45: #2 You may need to consider one of the other alternative d(s): 0,15,38,93,135,192,213,253,280,295,342,356,374,405,425,451,456,528,566,592 WARNING @ Sun, 02 Jun 2019 16:00:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 16:00:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:00:45: #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 SRX113602.05.bed: No such file or directory mv: cannot stat ‘SRX113602.05.bed’: No such file or directory /var/spool/uge/at116/job_scripts/1291524: line 321: 46228 Terminated MACS $i /var/spool/uge/at116/job_scripts/1291524: line 321: 46229 Terminated MACS $i /var/spool/uge/at116/job_scripts/1291524: line 321: 46230 Terminated MACS $i mv: cannot stat ‘SRX113602.05.bb’: No such file or directory ls: cannot access SRX113602.10.bed: No such file or directory mv: cannot stat ‘SRX113602.10.bed’: No such file or directory mv: cannot stat ‘SRX113602.10.bb’: No such file or directory ls: cannot access SRX113602.20.bed: No such file or directory mv: cannot stat ‘SRX113602.20.bed’: No such file or directory mv: cannot stat ‘SRX113602.20.bb’: No such file or directory