Job ID = 1294114 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,132,284 reads read : 37,132,284 reads written : 37,132,284 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: 00:14:44 37132284 reads; of these: 37132284 (100.00%) were unpaired; of these: 1001792 (2.70%) aligned 0 times 24319843 (65.50%) aligned exactly 1 time 11810649 (31.81%) aligned >1 times 97.30% overall alignment rate Time searching: 00:14:44 Overall time: 00:14:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9565103 / 36130492 = 0.2647 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, 03 Jun 2019 05:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 05:30:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:30:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 05:30:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:30:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:30:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 05:30:14: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:30:14: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:30:21: 1000000 INFO @ Mon, 03 Jun 2019 05:30:23: 1000000 INFO @ Mon, 03 Jun 2019 05:30:23: 1000000 INFO @ Mon, 03 Jun 2019 05:30:28: 2000000 INFO @ Mon, 03 Jun 2019 05:30:32: 2000000 INFO @ Mon, 03 Jun 2019 05:30:32: 2000000 INFO @ Mon, 03 Jun 2019 05:30:37: 3000000 INFO @ Mon, 03 Jun 2019 05:30:40: 3000000 INFO @ Mon, 03 Jun 2019 05:30:41: 3000000 INFO @ Mon, 03 Jun 2019 05:30:45: 4000000 INFO @ Mon, 03 Jun 2019 05:30:49: 4000000 INFO @ Mon, 03 Jun 2019 05:30:49: 4000000 INFO @ Mon, 03 Jun 2019 05:30:51: 5000000 INFO @ Mon, 03 Jun 2019 05:30:57: 5000000 INFO @ Mon, 03 Jun 2019 05:30:57: 5000000 INFO @ Mon, 03 Jun 2019 05:30:58: 6000000 INFO @ Mon, 03 Jun 2019 05:31:05: 6000000 INFO @ Mon, 03 Jun 2019 05:31:05: 7000000 INFO @ Mon, 03 Jun 2019 05:31:06: 6000000 INFO @ Mon, 03 Jun 2019 05:31:12: 8000000 INFO @ Mon, 03 Jun 2019 05:31:13: 7000000 INFO @ Mon, 03 Jun 2019 05:31:14: 7000000 INFO @ Mon, 03 Jun 2019 05:31:18: 9000000 INFO @ Mon, 03 Jun 2019 05:31:20: 8000000 INFO @ Mon, 03 Jun 2019 05:31:22: 8000000 INFO @ Mon, 03 Jun 2019 05:31:25: 10000000 INFO @ Mon, 03 Jun 2019 05:31:28: 9000000 INFO @ Mon, 03 Jun 2019 05:31:29: 9000000 INFO @ Mon, 03 Jun 2019 05:31:33: 11000000 INFO @ Mon, 03 Jun 2019 05:31:37: 10000000 INFO @ Mon, 03 Jun 2019 05:31:38: 10000000 INFO @ Mon, 03 Jun 2019 05:31:42: 12000000 INFO @ Mon, 03 Jun 2019 05:31:45: 11000000 INFO @ Mon, 03 Jun 2019 05:31:46: 11000000 INFO @ Mon, 03 Jun 2019 05:31:48: 13000000 INFO @ Mon, 03 Jun 2019 05:31:52: 12000000 INFO @ Mon, 03 Jun 2019 05:31:54: 12000000 INFO @ Mon, 03 Jun 2019 05:31:55: 14000000 INFO @ Mon, 03 Jun 2019 05:32:00: 13000000 INFO @ Mon, 03 Jun 2019 05:32:02: 13000000 INFO @ Mon, 03 Jun 2019 05:32:02: 15000000 INFO @ Mon, 03 Jun 2019 05:32:07: 14000000 INFO @ Mon, 03 Jun 2019 05:32:09: 16000000 INFO @ Mon, 03 Jun 2019 05:32:10: 14000000 INFO @ Mon, 03 Jun 2019 05:32:16: 17000000 INFO @ Mon, 03 Jun 2019 05:32:16: 15000000 INFO @ Mon, 03 Jun 2019 05:32:19: 15000000 INFO @ Mon, 03 Jun 2019 05:32:22: 18000000 INFO @ Mon, 03 Jun 2019 05:32:24: 16000000 INFO @ Mon, 03 Jun 2019 05:32:27: 16000000 INFO @ Mon, 03 Jun 2019 05:32:30: 19000000 INFO @ Mon, 03 Jun 2019 05:32:32: 17000000 INFO @ Mon, 03 Jun 2019 05:32:35: 17000000 INFO @ Mon, 03 Jun 2019 05:32:38: 20000000 INFO @ Mon, 03 Jun 2019 05:32:40: 18000000 INFO @ Mon, 03 Jun 2019 05:32:44: 18000000 INFO @ Mon, 03 Jun 2019 05:32:45: 21000000 INFO @ Mon, 03 Jun 2019 05:32:48: 19000000 INFO @ Mon, 03 Jun 2019 05:32:52: 22000000 INFO @ Mon, 03 Jun 2019 05:32:53: 19000000 INFO @ Mon, 03 Jun 2019 05:32:55: 20000000 INFO @ Mon, 03 Jun 2019 05:32:59: 23000000 INFO @ Mon, 03 Jun 2019 05:33:00: 20000000 INFO @ Mon, 03 Jun 2019 05:33:03: 21000000 INFO @ Mon, 03 Jun 2019 05:33:06: 24000000 INFO @ Mon, 03 Jun 2019 05:33:08: 21000000 INFO @ Mon, 03 Jun 2019 05:33:10: 22000000 INFO @ Mon, 03 Jun 2019 05:33:13: 25000000 INFO @ Mon, 03 Jun 2019 05:33:16: 22000000 INFO @ Mon, 03 Jun 2019 05:33:18: 23000000 INFO @ Mon, 03 Jun 2019 05:33:20: 26000000 INFO @ Mon, 03 Jun 2019 05:33:24: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:33:24: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:33:24: #1 total tags in treatment: 26565389 INFO @ Mon, 03 Jun 2019 05:33:24: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:33:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:33:25: 23000000 INFO @ Mon, 03 Jun 2019 05:33:25: #1 tags after filtering in treatment: 26565389 INFO @ Mon, 03 Jun 2019 05:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:33:25: #1 finished! INFO @ Mon, 03 Jun 2019 05:33:25: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:33:26: 24000000 INFO @ Mon, 03 Jun 2019 05:33:27: #2 number of paired peaks: 109 WARNING @ Mon, 03 Jun 2019 05:33:27: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Mon, 03 Jun 2019 05:33:27: start model_add_line... INFO @ Mon, 03 Jun 2019 05:33:27: start X-correlation... INFO @ Mon, 03 Jun 2019 05:33:27: end of X-cor INFO @ Mon, 03 Jun 2019 05:33:27: #2 finished! INFO @ Mon, 03 Jun 2019 05:33:27: #2 predicted fragment length is 0 bps INFO @ Mon, 03 Jun 2019 05:33:27: #2 alternative fragment length(s) may be 0,33,85,107,123,137,155,178,263,318,373,412,479,503,512,532,547,591 bps INFO @ Mon, 03 Jun 2019 05:33:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.05_model.r WARNING @ Mon, 03 Jun 2019 05:33:27: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 05:33:27: #2 You may need to consider one of the other alternative d(s): 0,33,85,107,123,137,155,178,263,318,373,412,479,503,512,532,547,591 WARNING @ Mon, 03 Jun 2019 05:33:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:33:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:33:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:33:33: 24000000 INFO @ Mon, 03 Jun 2019 05:33:34: 25000000 INFO @ Mon, 03 Jun 2019 05:33:43: 26000000 INFO @ Mon, 03 Jun 2019 05:33:43: 25000000 INFO @ Mon, 03 Jun 2019 05:33:47: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:33:47: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:33:47: #1 total tags in treatment: 26565389 INFO @ Mon, 03 Jun 2019 05:33:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:33:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:33:48: #1 tags after filtering in treatment: 26565389 INFO @ Mon, 03 Jun 2019 05:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:33:48: #1 finished! INFO @ Mon, 03 Jun 2019 05:33:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:33:50: #2 number of paired peaks: 109 WARNING @ Mon, 03 Jun 2019 05:33:50: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Mon, 03 Jun 2019 05:33:50: start model_add_line... INFO @ Mon, 03 Jun 2019 05:33:50: start X-correlation... INFO @ Mon, 03 Jun 2019 05:33:50: end of X-cor INFO @ Mon, 03 Jun 2019 05:33:50: #2 finished! INFO @ Mon, 03 Jun 2019 05:33:50: #2 predicted fragment length is 0 bps INFO @ Mon, 03 Jun 2019 05:33:50: #2 alternative fragment length(s) may be 0,33,85,107,123,137,155,178,263,318,373,412,479,503,512,532,547,591 bps INFO @ Mon, 03 Jun 2019 05:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.20_model.r WARNING @ Mon, 03 Jun 2019 05:33:50: #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, 03 Jun 2019 05:33:50: #2 You may need to consider one of the other alternative d(s): 0,33,85,107,123,137,155,178,263,318,373,412,479,503,512,532,547,591 WARNING @ Mon, 03 Jun 2019 05:33:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:33:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:33:52: 26000000 INFO @ Mon, 03 Jun 2019 05:33:57: #1 tag size is determined as 36 bps INFO @ Mon, 03 Jun 2019 05:33:57: #1 tag size = 36 INFO @ Mon, 03 Jun 2019 05:33:57: #1 total tags in treatment: 26565389 INFO @ Mon, 03 Jun 2019 05:33:57: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:33:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 05:33:57: #1 tags after filtering in treatment: 26565389 INFO @ Mon, 03 Jun 2019 05:33:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:33:57: #1 finished! INFO @ Mon, 03 Jun 2019 05:33:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:33:59: #2 number of paired peaks: 109 WARNING @ Mon, 03 Jun 2019 05:33:59: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Mon, 03 Jun 2019 05:33:59: start model_add_line... INFO @ Mon, 03 Jun 2019 05:33:59: start X-correlation... INFO @ Mon, 03 Jun 2019 05:34:00: end of X-cor INFO @ Mon, 03 Jun 2019 05:34:00: #2 finished! INFO @ Mon, 03 Jun 2019 05:34:00: #2 predicted fragment length is 0 bps INFO @ Mon, 03 Jun 2019 05:34:00: #2 alternative fragment length(s) may be 0,33,85,107,123,137,155,178,263,318,373,412,479,503,512,532,547,591 bps INFO @ Mon, 03 Jun 2019 05:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX187084/SRX187084.10_model.r WARNING @ Mon, 03 Jun 2019 05:34:00: #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, 03 Jun 2019 05:34:00: #2 You may need to consider one of the other alternative d(s): 0,33,85,107,123,137,155,178,263,318,373,412,479,503,512,532,547,591 WARNING @ Mon, 03 Jun 2019 05:34:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 05:34:00: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:34:00: #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 SRX187084.05.bed: No such file or directory mv: cannot stat ‘SRX187084.05.bed’: No such file or directory /var/spool/uge/at078/job_scripts/1294114: line 321: 33816 Terminated MACS $i /var/spool/uge/at078/job_scripts/1294114: line 321: 33817 Terminated MACS $i /var/spool/uge/at078/job_scripts/1294114: line 321: 33818 Terminated MACS $i mv: cannot stat ‘SRX187084.05.bb’: No such file or directory ls: cannot access SRX187084.10.bed: No such file or directory mv: cannot stat ‘SRX187084.10.bed’: No such file or directory mv: cannot stat ‘SRX187084.10.bb’: No such file or directory ls: cannot access SRX187084.20.bed: No such file or directory mv: cannot stat ‘SRX187084.20.bed’: No such file or directory mv: cannot stat ‘SRX187084.20.bb’: No such file or directory