Job ID = 2590218 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,890,199 reads read : 55,780,398 reads written : 27,890,199 reads 0-length : 27,890,199 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: 00:06:35 27890199 reads; of these: 27890199 (100.00%) were unpaired; of these: 820033 (2.94%) aligned 0 times 22568068 (80.92%) aligned exactly 1 time 4502098 (16.14%) aligned >1 times 97.06% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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] 5423805 / 27070166 = 0.2004 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 @ Mon, 12 Aug 2019 20:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.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 @ Mon, 12 Aug 2019 20:27:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:27:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.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 @ Mon, 12 Aug 2019 20:27:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:27:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:27:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.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 @ Mon, 12 Aug 2019 20:27:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:27:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:28:02: 1000000 INFO @ Mon, 12 Aug 2019 20:28:05: 1000000 INFO @ Mon, 12 Aug 2019 20:28:06: 1000000 INFO @ Mon, 12 Aug 2019 20:28:10: 2000000 INFO @ Mon, 12 Aug 2019 20:28:14: 2000000 INFO @ Mon, 12 Aug 2019 20:28:14: 2000000 INFO @ Mon, 12 Aug 2019 20:28:17: 3000000 INFO @ Mon, 12 Aug 2019 20:28:21: 3000000 INFO @ Mon, 12 Aug 2019 20:28:22: 3000000 INFO @ Mon, 12 Aug 2019 20:28:25: 4000000 INFO @ Mon, 12 Aug 2019 20:28:29: 4000000 INFO @ Mon, 12 Aug 2019 20:28:31: 4000000 INFO @ Mon, 12 Aug 2019 20:28:32: 5000000 INFO @ Mon, 12 Aug 2019 20:28:36: 5000000 INFO @ Mon, 12 Aug 2019 20:28:39: 5000000 INFO @ Mon, 12 Aug 2019 20:28:40: 6000000 INFO @ Mon, 12 Aug 2019 20:28:44: 6000000 INFO @ Mon, 12 Aug 2019 20:28:47: 7000000 INFO @ Mon, 12 Aug 2019 20:28:47: 6000000 INFO @ Mon, 12 Aug 2019 20:28:51: 7000000 INFO @ Mon, 12 Aug 2019 20:28:55: 8000000 INFO @ Mon, 12 Aug 2019 20:28:56: 7000000 INFO @ Mon, 12 Aug 2019 20:28:59: 8000000 INFO @ Mon, 12 Aug 2019 20:29:02: 9000000 INFO @ Mon, 12 Aug 2019 20:29:04: 8000000 INFO @ Mon, 12 Aug 2019 20:29:07: 9000000 INFO @ Mon, 12 Aug 2019 20:29:10: 10000000 INFO @ Mon, 12 Aug 2019 20:29:12: 9000000 INFO @ Mon, 12 Aug 2019 20:29:14: 10000000 INFO @ Mon, 12 Aug 2019 20:29:16: 11000000 INFO @ Mon, 12 Aug 2019 20:29:20: 11000000 INFO @ Mon, 12 Aug 2019 20:29:21: 10000000 INFO @ Mon, 12 Aug 2019 20:29:23: 12000000 INFO @ Mon, 12 Aug 2019 20:29:28: 12000000 INFO @ Mon, 12 Aug 2019 20:29:29: 11000000 INFO @ Mon, 12 Aug 2019 20:29:30: 13000000 INFO @ Mon, 12 Aug 2019 20:29:35: 13000000 INFO @ Mon, 12 Aug 2019 20:29:36: 14000000 INFO @ Mon, 12 Aug 2019 20:29:38: 12000000 INFO @ Mon, 12 Aug 2019 20:29:42: 14000000 INFO @ Mon, 12 Aug 2019 20:29:43: 15000000 INFO @ Mon, 12 Aug 2019 20:29:46: 13000000 INFO @ Mon, 12 Aug 2019 20:29:49: 15000000 INFO @ Mon, 12 Aug 2019 20:29:50: 16000000 INFO @ Mon, 12 Aug 2019 20:29:54: 14000000 INFO @ Mon, 12 Aug 2019 20:29:56: 16000000 INFO @ Mon, 12 Aug 2019 20:29:57: 17000000 INFO @ Mon, 12 Aug 2019 20:30:03: 15000000 INFO @ Mon, 12 Aug 2019 20:30:03: 18000000 INFO @ Mon, 12 Aug 2019 20:30:04: 17000000 INFO @ Mon, 12 Aug 2019 20:30:10: 19000000 INFO @ Mon, 12 Aug 2019 20:30:11: 18000000 INFO @ Mon, 12 Aug 2019 20:30:11: 16000000 INFO @ Mon, 12 Aug 2019 20:30:16: 20000000 INFO @ Mon, 12 Aug 2019 20:30:18: 19000000 INFO @ Mon, 12 Aug 2019 20:30:20: 17000000 INFO @ Mon, 12 Aug 2019 20:30:23: 21000000 INFO @ Mon, 12 Aug 2019 20:30:25: 20000000 INFO @ Mon, 12 Aug 2019 20:30:27: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:30:27: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:30:27: #1 total tags in treatment: 21646361 INFO @ Mon, 12 Aug 2019 20:30:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:30:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:30:28: #1 tags after filtering in treatment: 21646361 INFO @ Mon, 12 Aug 2019 20:30:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:30:28: #1 finished! INFO @ Mon, 12 Aug 2019 20:30:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:30:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:30:28: 18000000 INFO @ Mon, 12 Aug 2019 20:30:30: #2 number of paired peaks: 221 WARNING @ Mon, 12 Aug 2019 20:30:30: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Mon, 12 Aug 2019 20:30:30: start model_add_line... INFO @ Mon, 12 Aug 2019 20:30:30: start X-correlation... INFO @ Mon, 12 Aug 2019 20:30:30: end of X-cor INFO @ Mon, 12 Aug 2019 20:30:30: #2 finished! INFO @ Mon, 12 Aug 2019 20:30:30: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:30:30: #2 alternative fragment length(s) may be 0,17,20,42,526 bps INFO @ Mon, 12 Aug 2019 20:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.05_model.r WARNING @ Mon, 12 Aug 2019 20:30:30: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:30:30: #2 You may need to consider one of the other alternative d(s): 0,17,20,42,526 WARNING @ Mon, 12 Aug 2019 20:30:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:30:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:30:32: 21000000 INFO @ Mon, 12 Aug 2019 20:30:37: 19000000 INFO @ Mon, 12 Aug 2019 20:30:37: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:30:37: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:30:37: #1 total tags in treatment: 21646361 INFO @ Mon, 12 Aug 2019 20:30:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:30:37: #1 tags after filtering in treatment: 21646361 INFO @ Mon, 12 Aug 2019 20:30:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:30:37: #1 finished! INFO @ Mon, 12 Aug 2019 20:30:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:30:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:30:39: #2 number of paired peaks: 221 WARNING @ Mon, 12 Aug 2019 20:30:39: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Mon, 12 Aug 2019 20:30:39: start model_add_line... INFO @ Mon, 12 Aug 2019 20:30:40: start X-correlation... INFO @ Mon, 12 Aug 2019 20:30:40: end of X-cor INFO @ Mon, 12 Aug 2019 20:30:40: #2 finished! INFO @ Mon, 12 Aug 2019 20:30:40: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:30:40: #2 alternative fragment length(s) may be 0,17,20,42,526 bps INFO @ Mon, 12 Aug 2019 20:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.20_model.r WARNING @ Mon, 12 Aug 2019 20:30:40: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:30:40: #2 You may need to consider one of the other alternative d(s): 0,17,20,42,526 WARNING @ Mon, 12 Aug 2019 20:30:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:30:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:30:45: 20000000 INFO @ Mon, 12 Aug 2019 20:30:52: 21000000 INFO @ Mon, 12 Aug 2019 20:30:57: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:30:57: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:30:57: #1 total tags in treatment: 21646361 INFO @ Mon, 12 Aug 2019 20:30:57: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:30:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:30:57: #1 tags after filtering in treatment: 21646361 INFO @ Mon, 12 Aug 2019 20:30:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:30:57: #1 finished! INFO @ Mon, 12 Aug 2019 20:30:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:30:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:30:59: #2 number of paired peaks: 221 WARNING @ Mon, 12 Aug 2019 20:30:59: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Mon, 12 Aug 2019 20:30:59: start model_add_line... INFO @ Mon, 12 Aug 2019 20:30:59: start X-correlation... INFO @ Mon, 12 Aug 2019 20:31:00: end of X-cor INFO @ Mon, 12 Aug 2019 20:31:00: #2 finished! INFO @ Mon, 12 Aug 2019 20:31:00: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:31:00: #2 alternative fragment length(s) may be 0,17,20,42,526 bps INFO @ Mon, 12 Aug 2019 20:31:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709759/SRX5709759.10_model.r WARNING @ Mon, 12 Aug 2019 20:31:00: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:31:00: #2 You may need to consider one of the other alternative d(s): 0,17,20,42,526 WARNING @ Mon, 12 Aug 2019 20:31:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:31:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:31:00: #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 SRX5709759.05.bed: No such file or directory mv: cannot stat ‘SRX5709759.05.bed’: No such file or directory /var/spool/uge/at101/job_scripts/2590218: line 335: 62219 Terminated MACS $i /var/spool/uge/at101/job_scripts/2590218: line 335: 62235 Terminated MACS $i /var/spool/uge/at101/job_scripts/2590218: line 335: 62248 Terminated MACS $i mv: cannot stat ‘SRX5709759.05.bb’: No such file or directory ls: cannot access SRX5709759.10.bed: No such file or directory mv: cannot stat ‘SRX5709759.10.bed’: No such file or directory mv: cannot stat ‘SRX5709759.10.bb’: No such file or directory ls: cannot access SRX5709759.20.bed: No such file or directory mv: cannot stat ‘SRX5709759.20.bed’: No such file or directory mv: cannot stat ‘SRX5709759.20.bb’: No such file or directory