Job ID = 1291690 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,318,925 reads read : 28,318,925 reads written : 28,318,925 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: 00:06:42 28318925 reads; of these: 28318925 (100.00%) were unpaired; of these: 1304296 (4.61%) aligned 0 times 22923853 (80.95%) aligned exactly 1 time 4090776 (14.45%) aligned >1 times 95.39% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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_sort_core] merging from 12 files... [bam_rmdupse_core] 3439033 / 27014629 = 0.1273 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 16:31:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.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 16:31:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:31:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:31:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.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 16:31:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:31:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:31:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.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 16:31:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:31:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:32:00: 1000000 INFO @ Sun, 02 Jun 2019 16:32:00: 1000000 INFO @ Sun, 02 Jun 2019 16:32:02: 1000000 INFO @ Sun, 02 Jun 2019 16:32:07: 2000000 INFO @ Sun, 02 Jun 2019 16:32:07: 2000000 INFO @ Sun, 02 Jun 2019 16:32:10: 2000000 INFO @ Sun, 02 Jun 2019 16:32:14: 3000000 INFO @ Sun, 02 Jun 2019 16:32:14: 3000000 INFO @ Sun, 02 Jun 2019 16:32:18: 3000000 INFO @ Sun, 02 Jun 2019 16:32:21: 4000000 INFO @ Sun, 02 Jun 2019 16:32:21: 4000000 INFO @ Sun, 02 Jun 2019 16:32:26: 4000000 INFO @ Sun, 02 Jun 2019 16:32:28: 5000000 INFO @ Sun, 02 Jun 2019 16:32:28: 5000000 INFO @ Sun, 02 Jun 2019 16:32:34: 5000000 INFO @ Sun, 02 Jun 2019 16:32:34: 6000000 INFO @ Sun, 02 Jun 2019 16:32:34: 6000000 INFO @ Sun, 02 Jun 2019 16:32:41: 7000000 INFO @ Sun, 02 Jun 2019 16:32:41: 7000000 INFO @ Sun, 02 Jun 2019 16:32:43: 6000000 INFO @ Sun, 02 Jun 2019 16:32:48: 8000000 INFO @ Sun, 02 Jun 2019 16:32:48: 8000000 INFO @ Sun, 02 Jun 2019 16:32:51: 7000000 INFO @ Sun, 02 Jun 2019 16:32:55: 9000000 INFO @ Sun, 02 Jun 2019 16:32:55: 9000000 INFO @ Sun, 02 Jun 2019 16:32:59: 8000000 INFO @ Sun, 02 Jun 2019 16:33:01: 10000000 INFO @ Sun, 02 Jun 2019 16:33:01: 10000000 INFO @ Sun, 02 Jun 2019 16:33:07: 9000000 INFO @ Sun, 02 Jun 2019 16:33:08: 11000000 INFO @ Sun, 02 Jun 2019 16:33:08: 11000000 INFO @ Sun, 02 Jun 2019 16:33:14: 10000000 INFO @ Sun, 02 Jun 2019 16:33:15: 12000000 INFO @ Sun, 02 Jun 2019 16:33:15: 12000000 INFO @ Sun, 02 Jun 2019 16:33:22: 11000000 INFO @ Sun, 02 Jun 2019 16:33:22: 13000000 INFO @ Sun, 02 Jun 2019 16:33:22: 13000000 INFO @ Sun, 02 Jun 2019 16:33:29: 14000000 INFO @ Sun, 02 Jun 2019 16:33:29: 14000000 INFO @ Sun, 02 Jun 2019 16:33:29: 12000000 INFO @ Sun, 02 Jun 2019 16:33:36: 15000000 INFO @ Sun, 02 Jun 2019 16:33:36: 15000000 INFO @ Sun, 02 Jun 2019 16:33:37: 13000000 INFO @ Sun, 02 Jun 2019 16:33:43: 16000000 INFO @ Sun, 02 Jun 2019 16:33:43: 16000000 INFO @ Sun, 02 Jun 2019 16:33:44: 14000000 INFO @ Sun, 02 Jun 2019 16:33:50: 17000000 INFO @ Sun, 02 Jun 2019 16:33:50: 17000000 INFO @ Sun, 02 Jun 2019 16:33:52: 15000000 INFO @ Sun, 02 Jun 2019 16:33:57: 18000000 INFO @ Sun, 02 Jun 2019 16:33:57: 18000000 INFO @ Sun, 02 Jun 2019 16:34:00: 16000000 INFO @ Sun, 02 Jun 2019 16:34:04: 19000000 INFO @ Sun, 02 Jun 2019 16:34:04: 19000000 INFO @ Sun, 02 Jun 2019 16:34:07: 17000000 INFO @ Sun, 02 Jun 2019 16:34:11: 20000000 INFO @ Sun, 02 Jun 2019 16:34:11: 20000000 INFO @ Sun, 02 Jun 2019 16:34:15: 18000000 INFO @ Sun, 02 Jun 2019 16:34:18: 21000000 INFO @ Sun, 02 Jun 2019 16:34:18: 21000000 INFO @ Sun, 02 Jun 2019 16:34:23: 19000000 INFO @ Sun, 02 Jun 2019 16:34:25: 22000000 INFO @ Sun, 02 Jun 2019 16:34:25: 22000000 INFO @ Sun, 02 Jun 2019 16:34:30: 20000000 INFO @ Sun, 02 Jun 2019 16:34:31: 23000000 INFO @ Sun, 02 Jun 2019 16:34:32: 23000000 INFO @ Sun, 02 Jun 2019 16:34:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:34:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:34:36: #1 total tags in treatment: 23575596 INFO @ Sun, 02 Jun 2019 16:34:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:34:36: #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 16:34:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:34:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:34:36: #1 total tags in treatment: 23575596 INFO @ Sun, 02 Jun 2019 16:34:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:34:36: #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 16:34:36: #1 tags after filtering in treatment: 23575596 INFO @ Sun, 02 Jun 2019 16:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:34:36: #1 finished! INFO @ Sun, 02 Jun 2019 16:34:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:34:36: #1 tags after filtering in treatment: 23575596 INFO @ Sun, 02 Jun 2019 16:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:34:36: #1 finished! INFO @ Sun, 02 Jun 2019 16:34:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:34:38: 21000000 INFO @ Sun, 02 Jun 2019 16:34:38: #2 number of paired peaks: 183 WARNING @ Sun, 02 Jun 2019 16:34:38: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sun, 02 Jun 2019 16:34:38: start model_add_line... INFO @ Sun, 02 Jun 2019 16:34:38: #2 number of paired peaks: 183 WARNING @ Sun, 02 Jun 2019 16:34:38: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sun, 02 Jun 2019 16:34:38: start model_add_line... INFO @ Sun, 02 Jun 2019 16:34:38: start X-correlation... INFO @ Sun, 02 Jun 2019 16:34:38: end of X-cor INFO @ Sun, 02 Jun 2019 16:34:38: #2 finished! INFO @ Sun, 02 Jun 2019 16:34:38: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:34:38: #2 alternative fragment length(s) may be 0,18,43,107,582,597 bps INFO @ Sun, 02 Jun 2019 16:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.20_model.r WARNING @ Sun, 02 Jun 2019 16:34:38: #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 16:34:38: #2 You may need to consider one of the other alternative d(s): 0,18,43,107,582,597 WARNING @ Sun, 02 Jun 2019 16:34:38: #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 16:34:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:34:38: start X-correlation... INFO @ Sun, 02 Jun 2019 16:34:38: end of X-cor INFO @ Sun, 02 Jun 2019 16:34:38: #2 finished! INFO @ Sun, 02 Jun 2019 16:34:38: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:34:38: #2 alternative fragment length(s) may be 0,18,43,107,582,597 bps INFO @ Sun, 02 Jun 2019 16:34:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.05_model.r WARNING @ Sun, 02 Jun 2019 16:34:38: #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 16:34:38: #2 You may need to consider one of the other alternative d(s): 0,18,43,107,582,597 WARNING @ Sun, 02 Jun 2019 16:34:38: #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 16:34:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:34:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:34:45: 22000000 INFO @ Sun, 02 Jun 2019 16:34:53: 23000000 INFO @ Sun, 02 Jun 2019 16:34:57: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:34:57: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:34:57: #1 total tags in treatment: 23575596 INFO @ Sun, 02 Jun 2019 16:34:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:34:57: #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 16:34:58: #1 tags after filtering in treatment: 23575596 INFO @ Sun, 02 Jun 2019 16:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:34:58: #1 finished! INFO @ Sun, 02 Jun 2019 16:34:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:35:00: #2 number of paired peaks: 183 WARNING @ Sun, 02 Jun 2019 16:35:00: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sun, 02 Jun 2019 16:35:00: start model_add_line... INFO @ Sun, 02 Jun 2019 16:35:00: start X-correlation... INFO @ Sun, 02 Jun 2019 16:35:00: end of X-cor INFO @ Sun, 02 Jun 2019 16:35:00: #2 finished! INFO @ Sun, 02 Jun 2019 16:35:00: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:35:00: #2 alternative fragment length(s) may be 0,18,43,107,582,597 bps INFO @ Sun, 02 Jun 2019 16:35:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216761/SRX216761.10_model.r WARNING @ Sun, 02 Jun 2019 16:35:00: #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 16:35:00: #2 You may need to consider one of the other alternative d(s): 0,18,43,107,582,597 WARNING @ Sun, 02 Jun 2019 16:35:00: #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 16:35:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:35:00: #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 SRX216761.05.bed: No such file or directory mv: cannot stat ‘SRX216761.05.bed’: No such file or directory /var/spool/uge/at087/job_scripts/1291690: line 321: 54447 Terminated MACS $i /var/spool/uge/at087/job_scripts/1291690: line 321: 54448 Terminated MACS $i /var/spool/uge/at087/job_scripts/1291690: line 321: 54449 Terminated MACS $i mv: cannot stat ‘SRX216761.05.bb’: No such file or directory ls: cannot access SRX216761.10.bed: No such file or directory mv: cannot stat ‘SRX216761.10.bed’: No such file or directory mv: cannot stat ‘SRX216761.10.bb’: No such file or directory ls: cannot access SRX216761.20.bed: No such file or directory mv: cannot stat ‘SRX216761.20.bed’: No such file or directory mv: cannot stat ‘SRX216761.20.bb’: No such file or directory