Job ID = 1293139 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,531,212 reads read : 34,531,212 reads written : 34,531,212 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: 00:06:53 34531212 reads; of these: 34531212 (100.00%) were unpaired; of these: 7698827 (22.30%) aligned 0 times 22823789 (66.10%) aligned exactly 1 time 4008596 (11.61%) aligned >1 times 77.70% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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] 4771435 / 26832385 = 0.1778 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 22:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.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 22:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.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 22:27:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:27:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:27:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:27:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.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 22:27:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:27:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:27:33: 1000000 INFO @ Sun, 02 Jun 2019 22:27:34: 1000000 INFO @ Sun, 02 Jun 2019 22:27:34: 1000000 INFO @ Sun, 02 Jun 2019 22:27:41: 2000000 INFO @ Sun, 02 Jun 2019 22:27:43: 2000000 INFO @ Sun, 02 Jun 2019 22:27:43: 2000000 INFO @ Sun, 02 Jun 2019 22:27:48: 3000000 INFO @ Sun, 02 Jun 2019 22:27:51: 3000000 INFO @ Sun, 02 Jun 2019 22:27:51: 3000000 INFO @ Sun, 02 Jun 2019 22:27:55: 4000000 INFO @ Sun, 02 Jun 2019 22:27:59: 4000000 INFO @ Sun, 02 Jun 2019 22:27:59: 4000000 INFO @ Sun, 02 Jun 2019 22:28:03: 5000000 INFO @ Sun, 02 Jun 2019 22:28:07: 5000000 INFO @ Sun, 02 Jun 2019 22:28:08: 5000000 INFO @ Sun, 02 Jun 2019 22:28:10: 6000000 INFO @ Sun, 02 Jun 2019 22:28:16: 6000000 INFO @ Sun, 02 Jun 2019 22:28:16: 6000000 INFO @ Sun, 02 Jun 2019 22:28:17: 7000000 INFO @ Sun, 02 Jun 2019 22:28:24: 7000000 INFO @ Sun, 02 Jun 2019 22:28:24: 7000000 INFO @ Sun, 02 Jun 2019 22:28:25: 8000000 INFO @ Sun, 02 Jun 2019 22:28:32: 8000000 INFO @ Sun, 02 Jun 2019 22:28:32: 9000000 INFO @ Sun, 02 Jun 2019 22:28:32: 8000000 INFO @ Sun, 02 Jun 2019 22:28:39: 10000000 INFO @ Sun, 02 Jun 2019 22:28:40: 9000000 INFO @ Sun, 02 Jun 2019 22:28:40: 9000000 INFO @ Sun, 02 Jun 2019 22:28:47: 11000000 INFO @ Sun, 02 Jun 2019 22:28:48: 10000000 INFO @ Sun, 02 Jun 2019 22:28:48: 10000000 INFO @ Sun, 02 Jun 2019 22:28:54: 12000000 INFO @ Sun, 02 Jun 2019 22:28:56: 11000000 INFO @ Sun, 02 Jun 2019 22:28:57: 11000000 INFO @ Sun, 02 Jun 2019 22:29:01: 13000000 INFO @ Sun, 02 Jun 2019 22:29:04: 12000000 INFO @ Sun, 02 Jun 2019 22:29:05: 12000000 INFO @ Sun, 02 Jun 2019 22:29:09: 14000000 INFO @ Sun, 02 Jun 2019 22:29:12: 13000000 INFO @ Sun, 02 Jun 2019 22:29:13: 13000000 INFO @ Sun, 02 Jun 2019 22:29:16: 15000000 INFO @ Sun, 02 Jun 2019 22:29:20: 14000000 INFO @ Sun, 02 Jun 2019 22:29:21: 14000000 INFO @ Sun, 02 Jun 2019 22:29:24: 16000000 INFO @ Sun, 02 Jun 2019 22:29:28: 15000000 INFO @ Sun, 02 Jun 2019 22:29:29: 15000000 INFO @ Sun, 02 Jun 2019 22:29:32: 17000000 INFO @ Sun, 02 Jun 2019 22:29:36: 16000000 INFO @ Sun, 02 Jun 2019 22:29:37: 16000000 INFO @ Sun, 02 Jun 2019 22:29:39: 18000000 INFO @ Sun, 02 Jun 2019 22:29:44: 17000000 INFO @ Sun, 02 Jun 2019 22:29:45: 17000000 INFO @ Sun, 02 Jun 2019 22:29:47: 19000000 INFO @ Sun, 02 Jun 2019 22:29:52: 18000000 INFO @ Sun, 02 Jun 2019 22:29:53: 18000000 INFO @ Sun, 02 Jun 2019 22:29:55: 20000000 INFO @ Sun, 02 Jun 2019 22:30:00: 19000000 INFO @ Sun, 02 Jun 2019 22:30:01: 19000000 INFO @ Sun, 02 Jun 2019 22:30:02: 21000000 INFO @ Sun, 02 Jun 2019 22:30:08: 20000000 INFO @ Sun, 02 Jun 2019 22:30:09: 20000000 INFO @ Sun, 02 Jun 2019 22:30:09: 22000000 INFO @ Sun, 02 Jun 2019 22:30:10: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:30:10: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:30:10: #1 total tags in treatment: 22060950 INFO @ Sun, 02 Jun 2019 22:30:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:30:10: #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 22:30:10: #1 tags after filtering in treatment: 22060950 INFO @ Sun, 02 Jun 2019 22:30:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:30:10: #1 finished! INFO @ Sun, 02 Jun 2019 22:30:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:30:12: #2 number of paired peaks: 160 WARNING @ Sun, 02 Jun 2019 22:30:12: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 02 Jun 2019 22:30:12: start model_add_line... INFO @ Sun, 02 Jun 2019 22:30:12: start X-correlation... INFO @ Sun, 02 Jun 2019 22:30:12: end of X-cor INFO @ Sun, 02 Jun 2019 22:30:12: #2 finished! INFO @ Sun, 02 Jun 2019 22:30:12: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:30:12: #2 alternative fragment length(s) may be 0,45,47,534,562 bps INFO @ Sun, 02 Jun 2019 22:30:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.20_model.r WARNING @ Sun, 02 Jun 2019 22:30:12: #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 22:30:12: #2 You may need to consider one of the other alternative d(s): 0,45,47,534,562 WARNING @ Sun, 02 Jun 2019 22:30:12: #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 22:30:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:30:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:30:16: 21000000 INFO @ Sun, 02 Jun 2019 22:30:17: 21000000 INFO @ Sun, 02 Jun 2019 22:30:24: 22000000 INFO @ Sun, 02 Jun 2019 22:30:25: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:30:25: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:30:25: #1 total tags in treatment: 22060950 INFO @ Sun, 02 Jun 2019 22:30:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:30:25: #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 22:30:25: 22000000 INFO @ Sun, 02 Jun 2019 22:30:25: #1 tags after filtering in treatment: 22060950 INFO @ Sun, 02 Jun 2019 22:30:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:30:25: #1 finished! INFO @ Sun, 02 Jun 2019 22:30:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:30:25: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:30:25: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:30:25: #1 total tags in treatment: 22060950 INFO @ Sun, 02 Jun 2019 22:30:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:30:25: #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 22:30:26: #1 tags after filtering in treatment: 22060950 INFO @ Sun, 02 Jun 2019 22:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:30:26: #1 finished! INFO @ Sun, 02 Jun 2019 22:30:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:30:27: #2 number of paired peaks: 160 WARNING @ Sun, 02 Jun 2019 22:30:27: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 02 Jun 2019 22:30:27: start model_add_line... INFO @ Sun, 02 Jun 2019 22:30:27: start X-correlation... INFO @ Sun, 02 Jun 2019 22:30:27: end of X-cor INFO @ Sun, 02 Jun 2019 22:30:27: #2 finished! INFO @ Sun, 02 Jun 2019 22:30:27: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:30:27: #2 alternative fragment length(s) may be 0,45,47,534,562 bps INFO @ Sun, 02 Jun 2019 22:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.05_model.r WARNING @ Sun, 02 Jun 2019 22:30:27: #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 22:30:27: #2 You may need to consider one of the other alternative d(s): 0,45,47,534,562 WARNING @ Sun, 02 Jun 2019 22:30:27: #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 22:30:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:30:28: #2 number of paired peaks: 160 WARNING @ Sun, 02 Jun 2019 22:30:28: Fewer paired peaks (160) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 160 pairs to build model! INFO @ Sun, 02 Jun 2019 22:30:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:30:28: start X-correlation... INFO @ Sun, 02 Jun 2019 22:30:28: end of X-cor INFO @ Sun, 02 Jun 2019 22:30:28: #2 finished! INFO @ Sun, 02 Jun 2019 22:30:28: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:30:28: #2 alternative fragment length(s) may be 0,45,47,534,562 bps INFO @ Sun, 02 Jun 2019 22:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402711/SRX5402711.10_model.r WARNING @ Sun, 02 Jun 2019 22:30:28: #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 22:30:28: #2 You may need to consider one of the other alternative d(s): 0,45,47,534,562 WARNING @ Sun, 02 Jun 2019 22:30:28: #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 22:30:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:30:28: #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 SRX5402711.05.bed: No such file or directory mv: cannot stat ‘SRX5402711.05.bed’: No such file or directory /var/spool/uge/at109/job_scripts/1293139: line 321: 46189 Terminated MACS $i /var/spool/uge/at109/job_scripts/1293139: line 321: 46190 Terminated MACS $i /var/spool/uge/at109/job_scripts/1293139: line 321: 46191 Terminated MACS $i mv: cannot stat ‘SRX5402711.05.bb’: No such file or directory ls: cannot access SRX5402711.10.bed: No such file or directory mv: cannot stat ‘SRX5402711.10.bed’: No such file or directory mv: cannot stat ‘SRX5402711.10.bb’: No such file or directory ls: cannot access SRX5402711.20.bed: No such file or directory mv: cannot stat ‘SRX5402711.20.bed’: No such file or directory mv: cannot stat ‘SRX5402711.20.bb’: No such file or directory