Job ID = 1293208 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,836,323 reads read : 38,836,323 reads written : 38,836,323 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: 00:10:17 38836323 reads; of these: 38836323 (100.00%) were unpaired; of these: 3704903 (9.54%) aligned 0 times 28345538 (72.99%) aligned exactly 1 time 6785882 (17.47%) aligned >1 times 90.46% overall alignment rate Time searching: 00:10:17 Overall time: 00:10:17 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 16 files... [bam_rmdupse_core] 8782783 / 35131420 = 0.2500 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 22:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.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 22:48:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:48:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.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 22:48:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:48:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.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 22:48:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:48:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:48:46: 1000000 INFO @ Sun, 02 Jun 2019 22:48:46: 1000000 INFO @ Sun, 02 Jun 2019 22:48:46: 1000000 INFO @ Sun, 02 Jun 2019 22:48:53: 2000000 INFO @ Sun, 02 Jun 2019 22:48:54: 2000000 INFO @ Sun, 02 Jun 2019 22:48:55: 2000000 INFO @ Sun, 02 Jun 2019 22:49:01: 3000000 INFO @ Sun, 02 Jun 2019 22:49:03: 3000000 INFO @ Sun, 02 Jun 2019 22:49:03: 3000000 INFO @ Sun, 02 Jun 2019 22:49:10: 4000000 INFO @ Sun, 02 Jun 2019 22:49:13: 4000000 INFO @ Sun, 02 Jun 2019 22:49:13: 4000000 INFO @ Sun, 02 Jun 2019 22:49:20: 5000000 INFO @ Sun, 02 Jun 2019 22:49:21: 5000000 INFO @ Sun, 02 Jun 2019 22:49:22: 5000000 INFO @ Sun, 02 Jun 2019 22:49:28: 6000000 INFO @ Sun, 02 Jun 2019 22:49:30: 6000000 INFO @ Sun, 02 Jun 2019 22:49:30: 6000000 INFO @ Sun, 02 Jun 2019 22:49:36: 7000000 INFO @ Sun, 02 Jun 2019 22:49:38: 7000000 INFO @ Sun, 02 Jun 2019 22:49:39: 7000000 INFO @ Sun, 02 Jun 2019 22:49:44: 8000000 INFO @ Sun, 02 Jun 2019 22:49:46: 8000000 INFO @ Sun, 02 Jun 2019 22:49:47: 8000000 INFO @ Sun, 02 Jun 2019 22:49:52: 9000000 INFO @ Sun, 02 Jun 2019 22:49:55: 9000000 INFO @ Sun, 02 Jun 2019 22:49:56: 9000000 INFO @ Sun, 02 Jun 2019 22:50:00: 10000000 INFO @ Sun, 02 Jun 2019 22:50:03: 10000000 INFO @ Sun, 02 Jun 2019 22:50:04: 10000000 INFO @ Sun, 02 Jun 2019 22:50:07: 11000000 INFO @ Sun, 02 Jun 2019 22:50:11: 11000000 INFO @ Sun, 02 Jun 2019 22:50:12: 11000000 INFO @ Sun, 02 Jun 2019 22:50:15: 12000000 INFO @ Sun, 02 Jun 2019 22:50:20: 12000000 INFO @ Sun, 02 Jun 2019 22:50:22: 12000000 INFO @ Sun, 02 Jun 2019 22:50:26: 13000000 INFO @ Sun, 02 Jun 2019 22:50:29: 13000000 INFO @ Sun, 02 Jun 2019 22:50:30: 13000000 INFO @ Sun, 02 Jun 2019 22:50:33: 14000000 INFO @ Sun, 02 Jun 2019 22:50:37: 14000000 INFO @ Sun, 02 Jun 2019 22:50:38: 14000000 INFO @ Sun, 02 Jun 2019 22:50:41: 15000000 INFO @ Sun, 02 Jun 2019 22:50:45: 15000000 INFO @ Sun, 02 Jun 2019 22:50:47: 15000000 INFO @ Sun, 02 Jun 2019 22:50:49: 16000000 INFO @ Sun, 02 Jun 2019 22:50:53: 16000000 INFO @ Sun, 02 Jun 2019 22:50:55: 16000000 INFO @ Sun, 02 Jun 2019 22:50:57: 17000000 INFO @ Sun, 02 Jun 2019 22:51:01: 17000000 INFO @ Sun, 02 Jun 2019 22:51:03: 17000000 INFO @ Sun, 02 Jun 2019 22:51:05: 18000000 INFO @ Sun, 02 Jun 2019 22:51:09: 18000000 INFO @ Sun, 02 Jun 2019 22:51:11: 18000000 INFO @ Sun, 02 Jun 2019 22:51:12: 19000000 INFO @ Sun, 02 Jun 2019 22:51:17: 19000000 INFO @ Sun, 02 Jun 2019 22:51:20: 20000000 INFO @ Sun, 02 Jun 2019 22:51:20: 19000000 INFO @ Sun, 02 Jun 2019 22:51:26: 20000000 INFO @ Sun, 02 Jun 2019 22:51:29: 20000000 INFO @ Sun, 02 Jun 2019 22:51:29: 21000000 INFO @ Sun, 02 Jun 2019 22:51:34: 21000000 INFO @ Sun, 02 Jun 2019 22:51:37: 21000000 INFO @ Sun, 02 Jun 2019 22:51:38: 22000000 INFO @ Sun, 02 Jun 2019 22:51:42: 22000000 INFO @ Sun, 02 Jun 2019 22:51:45: 23000000 INFO @ Sun, 02 Jun 2019 22:51:45: 22000000 INFO @ Sun, 02 Jun 2019 22:51:50: 23000000 INFO @ Sun, 02 Jun 2019 22:51:53: 24000000 INFO @ Sun, 02 Jun 2019 22:51:53: 23000000 INFO @ Sun, 02 Jun 2019 22:51:58: 24000000 INFO @ Sun, 02 Jun 2019 22:52:01: 25000000 INFO @ Sun, 02 Jun 2019 22:52:02: 24000000 INFO @ Sun, 02 Jun 2019 22:52:06: 25000000 INFO @ Sun, 02 Jun 2019 22:52:08: 26000000 INFO @ Sun, 02 Jun 2019 22:52:10: 25000000 INFO @ Sun, 02 Jun 2019 22:52:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:52:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:52:11: #1 total tags in treatment: 26348637 INFO @ Sun, 02 Jun 2019 22:52:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:11: #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 22:52:12: #1 tags after filtering in treatment: 26348637 INFO @ Sun, 02 Jun 2019 22:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:14: #2 number of paired peaks: 160 WARNING @ Sun, 02 Jun 2019 22:52:14: 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 22:52:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:14: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:52:14: #2 alternative fragment length(s) may be 0,14,40,329,349,532,553,589,597 bps INFO @ Sun, 02 Jun 2019 22:52:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.05_model.r WARNING @ Sun, 02 Jun 2019 22:52:14: #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 22:52:14: #2 You may need to consider one of the other alternative d(s): 0,14,40,329,349,532,553,589,597 WARNING @ Sun, 02 Jun 2019 22:52:14: #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 22:52:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:52:14: 26000000 INFO @ Sun, 02 Jun 2019 22:52:17: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:52:17: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:52:17: #1 total tags in treatment: 26348637 INFO @ Sun, 02 Jun 2019 22:52:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:17: #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 22:52:18: #1 tags after filtering in treatment: 26348637 INFO @ Sun, 02 Jun 2019 22:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:18: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:18: 26000000 INFO @ Sun, 02 Jun 2019 22:52:20: #2 number of paired peaks: 160 WARNING @ Sun, 02 Jun 2019 22:52:20: 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 22:52:20: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:20: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:20: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:20: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:20: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:52:20: #2 alternative fragment length(s) may be 0,14,40,329,349,532,553,589,597 bps INFO @ Sun, 02 Jun 2019 22:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.20_model.r WARNING @ Sun, 02 Jun 2019 22:52:20: #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 22:52:20: #2 You may need to consider one of the other alternative d(s): 0,14,40,329,349,532,553,589,597 WARNING @ Sun, 02 Jun 2019 22:52:20: #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 22:52:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:52:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:52:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:52:21: #1 total tags in treatment: 26348637 INFO @ Sun, 02 Jun 2019 22:52:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:21: #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 22:52:21: #1 tags after filtering in treatment: 26348637 INFO @ Sun, 02 Jun 2019 22:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:21: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:23: #2 number of paired peaks: 160 WARNING @ Sun, 02 Jun 2019 22:52:23: 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 22:52:23: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:24: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:24: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:24: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:24: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 22:52:24: #2 alternative fragment length(s) may be 0,14,40,329,349,532,553,589,597 bps INFO @ Sun, 02 Jun 2019 22:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402759/SRX5402759.10_model.r WARNING @ Sun, 02 Jun 2019 22:52:24: #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 22:52:24: #2 You may need to consider one of the other alternative d(s): 0,14,40,329,349,532,553,589,597 WARNING @ Sun, 02 Jun 2019 22:52:24: #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 22:52:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:24: #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 SRX5402759.05.bed: No such file or directory mv: cannot stat ‘SRX5402759.05.bed’: No such file or directory /var/spool/uge/at085/job_scripts/1293208: line 321: 28184 Terminated MACS $i /var/spool/uge/at085/job_scripts/1293208: line 321: 28185 Terminated MACS $i /var/spool/uge/at085/job_scripts/1293208: line 321: 28186 Terminated MACS $i mv: cannot stat ‘SRX5402759.05.bb’: No such file or directory ls: cannot access SRX5402759.10.bed: No such file or directory mv: cannot stat ‘SRX5402759.10.bed’: No such file or directory mv: cannot stat ‘SRX5402759.10.bb’: No such file or directory ls: cannot access SRX5402759.20.bed: No such file or directory mv: cannot stat ‘SRX5402759.20.bed’: No such file or directory mv: cannot stat ‘SRX5402759.20.bb’: No such file or directory