Job ID = 2590219 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,155,426 reads read : 60,310,852 reads written : 30,155,426 reads 0-length : 30,155,426 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: 00:07:07 30155426 reads; of these: 30155426 (100.00%) were unpaired; of these: 906272 (3.01%) aligned 0 times 24402380 (80.92%) aligned exactly 1 time 4846774 (16.07%) aligned >1 times 96.99% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 6011376 / 29249154 = 0.2055 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 20:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.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 20:29:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:29:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.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 20:29:19: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:29:19: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.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 20:29:20: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:29:20: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:29:28: 1000000 INFO @ Mon, 12 Aug 2019 20:29:29: 1000000 INFO @ Mon, 12 Aug 2019 20:29:29: 1000000 INFO @ Mon, 12 Aug 2019 20:29:36: 2000000 INFO @ Mon, 12 Aug 2019 20:29:37: 2000000 INFO @ Mon, 12 Aug 2019 20:29:38: 2000000 INFO @ Mon, 12 Aug 2019 20:29:44: 3000000 INFO @ Mon, 12 Aug 2019 20:29:45: 3000000 INFO @ Mon, 12 Aug 2019 20:29:48: 3000000 INFO @ Mon, 12 Aug 2019 20:29:53: 4000000 INFO @ Mon, 12 Aug 2019 20:29:53: 4000000 INFO @ Mon, 12 Aug 2019 20:29:57: 4000000 INFO @ Mon, 12 Aug 2019 20:30:01: 5000000 INFO @ Mon, 12 Aug 2019 20:30:01: 5000000 INFO @ Mon, 12 Aug 2019 20:30:07: 5000000 INFO @ Mon, 12 Aug 2019 20:30:09: 6000000 INFO @ Mon, 12 Aug 2019 20:30:09: 6000000 INFO @ Mon, 12 Aug 2019 20:30:16: 6000000 INFO @ Mon, 12 Aug 2019 20:30:18: 7000000 INFO @ Mon, 12 Aug 2019 20:30:18: 7000000 INFO @ Mon, 12 Aug 2019 20:30:26: 7000000 INFO @ Mon, 12 Aug 2019 20:30:26: 8000000 INFO @ Mon, 12 Aug 2019 20:30:26: 8000000 INFO @ Mon, 12 Aug 2019 20:30:34: 9000000 INFO @ Mon, 12 Aug 2019 20:30:34: 9000000 INFO @ Mon, 12 Aug 2019 20:30:35: 8000000 INFO @ Mon, 12 Aug 2019 20:30:43: 10000000 INFO @ Mon, 12 Aug 2019 20:30:43: 10000000 INFO @ Mon, 12 Aug 2019 20:30:45: 9000000 INFO @ Mon, 12 Aug 2019 20:30:51: 11000000 INFO @ Mon, 12 Aug 2019 20:30:51: 11000000 INFO @ Mon, 12 Aug 2019 20:30:54: 10000000 INFO @ Mon, 12 Aug 2019 20:30:59: 12000000 INFO @ Mon, 12 Aug 2019 20:30:59: 12000000 INFO @ Mon, 12 Aug 2019 20:31:04: 11000000 INFO @ Mon, 12 Aug 2019 20:31:07: 13000000 INFO @ Mon, 12 Aug 2019 20:31:08: 13000000 INFO @ Mon, 12 Aug 2019 20:31:13: 12000000 INFO @ Mon, 12 Aug 2019 20:31:15: 14000000 INFO @ Mon, 12 Aug 2019 20:31:16: 14000000 INFO @ Mon, 12 Aug 2019 20:31:23: 13000000 INFO @ Mon, 12 Aug 2019 20:31:24: 15000000 INFO @ Mon, 12 Aug 2019 20:31:25: 15000000 INFO @ Mon, 12 Aug 2019 20:31:32: 16000000 INFO @ Mon, 12 Aug 2019 20:31:33: 14000000 INFO @ Mon, 12 Aug 2019 20:31:33: 16000000 INFO @ Mon, 12 Aug 2019 20:31:40: 17000000 INFO @ Mon, 12 Aug 2019 20:31:42: 17000000 INFO @ Mon, 12 Aug 2019 20:31:43: 15000000 INFO @ Mon, 12 Aug 2019 20:31:49: 18000000 INFO @ Mon, 12 Aug 2019 20:31:51: 18000000 INFO @ Mon, 12 Aug 2019 20:31:53: 16000000 INFO @ Mon, 12 Aug 2019 20:31:58: 19000000 INFO @ Mon, 12 Aug 2019 20:31:59: 19000000 INFO @ Mon, 12 Aug 2019 20:32:03: 17000000 INFO @ Mon, 12 Aug 2019 20:32:06: 20000000 INFO @ Mon, 12 Aug 2019 20:32:08: 20000000 INFO @ Mon, 12 Aug 2019 20:32:14: 18000000 INFO @ Mon, 12 Aug 2019 20:32:14: 21000000 INFO @ Mon, 12 Aug 2019 20:32:16: 21000000 INFO @ Mon, 12 Aug 2019 20:32:22: 22000000 INFO @ Mon, 12 Aug 2019 20:32:24: 19000000 INFO @ Mon, 12 Aug 2019 20:32:25: 22000000 INFO @ Mon, 12 Aug 2019 20:32:30: 23000000 INFO @ Mon, 12 Aug 2019 20:32:32: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:32: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:32: #1 total tags in treatment: 23237778 INFO @ Mon, 12 Aug 2019 20:32:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:32: #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 20:32:33: #1 tags after filtering in treatment: 23237778 INFO @ Mon, 12 Aug 2019 20:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:33: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:34: 23000000 INFO @ Mon, 12 Aug 2019 20:32:35: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 20:32:35: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:35: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:35: 20000000 INFO @ Mon, 12 Aug 2019 20:32:35: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:35: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:35: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:35: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:32:35: #2 alternative fragment length(s) may be 0,45,529,542,557,574 bps INFO @ Mon, 12 Aug 2019 20:32:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.20_model.r WARNING @ Mon, 12 Aug 2019 20:32:35: #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 20:32:35: #2 You may need to consider one of the other alternative d(s): 0,45,529,542,557,574 WARNING @ Mon, 12 Aug 2019 20:32:35: #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 20:32:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:36: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:32:36: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:32:36: #1 total tags in treatment: 23237778 INFO @ Mon, 12 Aug 2019 20:32:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:32:36: #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 20:32:36: #1 tags after filtering in treatment: 23237778 INFO @ Mon, 12 Aug 2019 20:32:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:32:36: #1 finished! INFO @ Mon, 12 Aug 2019 20:32:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:32:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:32:38: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 20:32:38: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 20:32:38: start model_add_line... INFO @ Mon, 12 Aug 2019 20:32:38: start X-correlation... INFO @ Mon, 12 Aug 2019 20:32:38: end of X-cor INFO @ Mon, 12 Aug 2019 20:32:38: #2 finished! INFO @ Mon, 12 Aug 2019 20:32:38: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:32:38: #2 alternative fragment length(s) may be 0,45,529,542,557,574 bps INFO @ Mon, 12 Aug 2019 20:32:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.10_model.r WARNING @ Mon, 12 Aug 2019 20:32:38: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:32:38: #2 You may need to consider one of the other alternative d(s): 0,45,529,542,557,574 WARNING @ Mon, 12 Aug 2019 20:32:38: #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 20:32:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:32:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:32:45: 21000000 INFO @ Mon, 12 Aug 2019 20:32:55: 22000000 INFO @ Mon, 12 Aug 2019 20:33:06: 23000000 INFO @ Mon, 12 Aug 2019 20:33:08: #1 tag size is determined as 49 bps INFO @ Mon, 12 Aug 2019 20:33:08: #1 tag size = 49 INFO @ Mon, 12 Aug 2019 20:33:08: #1 total tags in treatment: 23237778 INFO @ Mon, 12 Aug 2019 20:33:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:33:08: #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 20:33:08: #1 tags after filtering in treatment: 23237778 INFO @ Mon, 12 Aug 2019 20:33:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:33:08: #1 finished! INFO @ Mon, 12 Aug 2019 20:33:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:33:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:33:10: #2 number of paired peaks: 192 WARNING @ Mon, 12 Aug 2019 20:33:10: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Mon, 12 Aug 2019 20:33:10: start model_add_line... INFO @ Mon, 12 Aug 2019 20:33:10: start X-correlation... INFO @ Mon, 12 Aug 2019 20:33:10: end of X-cor INFO @ Mon, 12 Aug 2019 20:33:10: #2 finished! INFO @ Mon, 12 Aug 2019 20:33:10: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 20:33:10: #2 alternative fragment length(s) may be 0,45,529,542,557,574 bps INFO @ Mon, 12 Aug 2019 20:33:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5709760/SRX5709760.05_model.r WARNING @ Mon, 12 Aug 2019 20:33:10: #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 20:33:10: #2 You may need to consider one of the other alternative d(s): 0,45,529,542,557,574 WARNING @ Mon, 12 Aug 2019 20:33:10: #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 20:33:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:33:10: #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 SRX5709760.05.bed: No such file or directory mv: cannot stat ‘SRX5709760.05.bed’: No such file or directory /var/spool/uge/at101/job_scripts/2590219: line 335: 62754 Terminated MACS $i /var/spool/uge/at101/job_scripts/2590219: line 335: 62769 Terminated MACS $i /var/spool/uge/at101/job_scripts/2590219: line 335: 62783 Terminated MACS $i mv: cannot stat ‘SRX5709760.05.bb’: No such file or directory ls: cannot access SRX5709760.10.bed: No such file or directory mv: cannot stat ‘SRX5709760.10.bed’: No such file or directory mv: cannot stat ‘SRX5709760.10.bb’: No such file or directory ls: cannot access SRX5709760.20.bed: No such file or directory mv: cannot stat ‘SRX5709760.20.bed’: No such file or directory mv: cannot stat ‘SRX5709760.20.bb’: No such file or directory