Job ID = 2590231 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,438,687 reads read : 30,438,687 reads written : 30,438,687 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: 00:10:53 30438687 reads; of these: 30438687 (100.00%) were unpaired; of these: 491424 (1.61%) aligned 0 times 25159373 (82.66%) aligned exactly 1 time 4787890 (15.73%) aligned >1 times 98.39% overall alignment rate Time searching: 00:10:53 Overall time: 00:10:53 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 16 files... [bam_rmdupse_core] 3350430 / 29947263 = 0.1119 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 20:56:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.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 20:56:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:56:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:56:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.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 20:56:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:56:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:56:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.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 20:56:29: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:56:29: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:56:37: 1000000 INFO @ Mon, 12 Aug 2019 20:56:40: 1000000 INFO @ Mon, 12 Aug 2019 20:56:41: 1000000 INFO @ Mon, 12 Aug 2019 20:56:45: 2000000 INFO @ Mon, 12 Aug 2019 20:56:52: 2000000 INFO @ Mon, 12 Aug 2019 20:56:53: 3000000 INFO @ Mon, 12 Aug 2019 20:56:53: 2000000 INFO @ Mon, 12 Aug 2019 20:57:02: 4000000 INFO @ Mon, 12 Aug 2019 20:57:04: 3000000 INFO @ Mon, 12 Aug 2019 20:57:05: 3000000 INFO @ Mon, 12 Aug 2019 20:57:11: 5000000 INFO @ Mon, 12 Aug 2019 20:57:15: 4000000 INFO @ Mon, 12 Aug 2019 20:57:16: 4000000 INFO @ Mon, 12 Aug 2019 20:57:20: 6000000 INFO @ Mon, 12 Aug 2019 20:57:27: 5000000 INFO @ Mon, 12 Aug 2019 20:57:28: 5000000 INFO @ Mon, 12 Aug 2019 20:57:29: 7000000 INFO @ Mon, 12 Aug 2019 20:57:38: 6000000 INFO @ Mon, 12 Aug 2019 20:57:39: 8000000 INFO @ Mon, 12 Aug 2019 20:57:40: 6000000 INFO @ Mon, 12 Aug 2019 20:57:48: 9000000 INFO @ Mon, 12 Aug 2019 20:57:50: 7000000 INFO @ Mon, 12 Aug 2019 20:57:51: 7000000 INFO @ Mon, 12 Aug 2019 20:57:57: 10000000 INFO @ Mon, 12 Aug 2019 20:58:02: 8000000 INFO @ Mon, 12 Aug 2019 20:58:03: 8000000 INFO @ Mon, 12 Aug 2019 20:58:06: 11000000 INFO @ Mon, 12 Aug 2019 20:58:13: 9000000 INFO @ Mon, 12 Aug 2019 20:58:14: 9000000 INFO @ Mon, 12 Aug 2019 20:58:15: 12000000 INFO @ Mon, 12 Aug 2019 20:58:24: 10000000 INFO @ Mon, 12 Aug 2019 20:58:25: 13000000 INFO @ Mon, 12 Aug 2019 20:58:25: 10000000 INFO @ Mon, 12 Aug 2019 20:58:34: 14000000 INFO @ Mon, 12 Aug 2019 20:58:35: 11000000 INFO @ Mon, 12 Aug 2019 20:58:36: 11000000 INFO @ Mon, 12 Aug 2019 20:58:43: 15000000 INFO @ Mon, 12 Aug 2019 20:58:46: 12000000 INFO @ Mon, 12 Aug 2019 20:58:47: 12000000 INFO @ Mon, 12 Aug 2019 20:58:51: 16000000 INFO @ Mon, 12 Aug 2019 20:58:57: 13000000 INFO @ Mon, 12 Aug 2019 20:58:57: 13000000 INFO @ Mon, 12 Aug 2019 20:59:00: 17000000 INFO @ Mon, 12 Aug 2019 20:59:08: 14000000 INFO @ Mon, 12 Aug 2019 20:59:08: 14000000 INFO @ Mon, 12 Aug 2019 20:59:09: 18000000 INFO @ Mon, 12 Aug 2019 20:59:18: 19000000 INFO @ Mon, 12 Aug 2019 20:59:19: 15000000 INFO @ Mon, 12 Aug 2019 20:59:19: 15000000 INFO @ Mon, 12 Aug 2019 20:59:27: 20000000 INFO @ Mon, 12 Aug 2019 20:59:30: 16000000 INFO @ Mon, 12 Aug 2019 20:59:31: 16000000 INFO @ Mon, 12 Aug 2019 20:59:35: 21000000 INFO @ Mon, 12 Aug 2019 20:59:41: 17000000 INFO @ Mon, 12 Aug 2019 20:59:42: 17000000 INFO @ Mon, 12 Aug 2019 20:59:44: 22000000 INFO @ Mon, 12 Aug 2019 20:59:52: 18000000 INFO @ Mon, 12 Aug 2019 20:59:53: 18000000 INFO @ Mon, 12 Aug 2019 20:59:53: 23000000 INFO @ Mon, 12 Aug 2019 21:00:02: 24000000 INFO @ Mon, 12 Aug 2019 21:00:03: 19000000 INFO @ Mon, 12 Aug 2019 21:00:04: 19000000 INFO @ Mon, 12 Aug 2019 21:00:12: 25000000 INFO @ Mon, 12 Aug 2019 21:00:14: 20000000 INFO @ Mon, 12 Aug 2019 21:00:14: 20000000 INFO @ Mon, 12 Aug 2019 21:00:21: 26000000 INFO @ Mon, 12 Aug 2019 21:00:25: 21000000 INFO @ Mon, 12 Aug 2019 21:00:25: 21000000 INFO @ Mon, 12 Aug 2019 21:00:26: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:00:26: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:00:26: #1 total tags in treatment: 26596833 INFO @ Mon, 12 Aug 2019 21:00:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:00:26: #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 21:00:27: #1 tags after filtering in treatment: 26596833 INFO @ Mon, 12 Aug 2019 21:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:00:27: #1 finished! INFO @ Mon, 12 Aug 2019 21:00:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:00:29: #2 number of paired peaks: 109 WARNING @ Mon, 12 Aug 2019 21:00:29: 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, 12 Aug 2019 21:00:29: start model_add_line... INFO @ Mon, 12 Aug 2019 21:00:29: start X-correlation... INFO @ Mon, 12 Aug 2019 21:00:29: end of X-cor INFO @ Mon, 12 Aug 2019 21:00:29: #2 finished! INFO @ Mon, 12 Aug 2019 21:00:29: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 21:00:29: #2 alternative fragment length(s) may be 0,69,186,407,548 bps INFO @ Mon, 12 Aug 2019 21:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.10_model.r WARNING @ Mon, 12 Aug 2019 21:00:29: #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 21:00:29: #2 You may need to consider one of the other alternative d(s): 0,69,186,407,548 WARNING @ Mon, 12 Aug 2019 21:00:29: #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 21:00:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:00:36: 22000000 INFO @ Mon, 12 Aug 2019 21:00:37: 22000000 INFO @ Mon, 12 Aug 2019 21:00:47: 23000000 INFO @ Mon, 12 Aug 2019 21:00:48: 23000000 INFO @ Mon, 12 Aug 2019 21:00:58: 24000000 INFO @ Mon, 12 Aug 2019 21:00:59: 24000000 INFO @ Mon, 12 Aug 2019 21:01:09: 25000000 INFO @ Mon, 12 Aug 2019 21:01:10: 25000000 INFO @ Mon, 12 Aug 2019 21:01:21: 26000000 INFO @ Mon, 12 Aug 2019 21:01:21: 26000000 INFO @ Mon, 12 Aug 2019 21:01:28: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:01:28: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:01:28: #1 total tags in treatment: 26596833 INFO @ Mon, 12 Aug 2019 21:01:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:28: #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 21:01:28: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 21:01:28: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 21:01:28: #1 total tags in treatment: 26596833 INFO @ Mon, 12 Aug 2019 21:01:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:01:28: #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 21:01:28: #1 tags after filtering in treatment: 26596833 INFO @ Mon, 12 Aug 2019 21:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:28: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:29: #1 tags after filtering in treatment: 26596833 INFO @ Mon, 12 Aug 2019 21:01:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:01:29: #1 finished! INFO @ Mon, 12 Aug 2019 21:01:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:01:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:01:30: #2 number of paired peaks: 109 WARNING @ Mon, 12 Aug 2019 21:01:30: 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, 12 Aug 2019 21:01:30: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:31: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:31: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:31: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:31: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 21:01:31: #2 alternative fragment length(s) may be 0,69,186,407,548 bps INFO @ Mon, 12 Aug 2019 21:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.20_model.r WARNING @ Mon, 12 Aug 2019 21:01:31: #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 21:01:31: #2 You may need to consider one of the other alternative d(s): 0,69,186,407,548 WARNING @ Mon, 12 Aug 2019 21:01:31: #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 21:01:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:01:31: #2 number of paired peaks: 109 WARNING @ Mon, 12 Aug 2019 21:01:31: 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, 12 Aug 2019 21:01:31: start model_add_line... INFO @ Mon, 12 Aug 2019 21:01:31: start X-correlation... INFO @ Mon, 12 Aug 2019 21:01:31: end of X-cor INFO @ Mon, 12 Aug 2019 21:01:31: #2 finished! INFO @ Mon, 12 Aug 2019 21:01:31: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 21:01:31: #2 alternative fragment length(s) may be 0,69,186,407,548 bps INFO @ Mon, 12 Aug 2019 21:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985665/SRX5985665.05_model.r WARNING @ Mon, 12 Aug 2019 21:01:31: #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 21:01:31: #2 You may need to consider one of the other alternative d(s): 0,69,186,407,548 WARNING @ Mon, 12 Aug 2019 21:01:31: #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 21:01:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:01:31: #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 SRX5985665.05.bed: No such file or directory mv: cannot stat ‘SRX5985665.05.bed’: No such file or directory /var/spool/uge/at074/job_scripts/2590231: line 335: 23663 Terminated MACS $i /var/spool/uge/at074/job_scripts/2590231: line 335: 23678 Terminated MACS $i /var/spool/uge/at074/job_scripts/2590231: line 335: 23692 Terminated MACS $i mv: cannot stat ‘SRX5985665.05.bb’: No such file or directory ls: cannot access SRX5985665.10.bed: No such file or directory mv: cannot stat ‘SRX5985665.10.bed’: No such file or directory mv: cannot stat ‘SRX5985665.10.bb’: No such file or directory ls: cannot access SRX5985665.20.bed: No such file or directory mv: cannot stat ‘SRX5985665.20.bed’: No such file or directory mv: cannot stat ‘SRX5985665.20.bb’: No such file or directory