Job ID = 2589368 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,268,796 reads read : 31,268,796 reads written : 31,268,796 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: 00:08:16 31268796 reads; of these: 31268796 (100.00%) were unpaired; of these: 359581 (1.15%) aligned 0 times 25999080 (83.15%) aligned exactly 1 time 4910135 (15.70%) aligned >1 times 98.85% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 4887335 / 30909215 = 0.1581 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 18:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.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 18:05:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:05:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.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 18:06:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:06:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:06:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.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 18:06:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:06:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:06:09: 1000000 INFO @ Mon, 12 Aug 2019 18:06:12: 1000000 INFO @ Mon, 12 Aug 2019 18:06:13: 1000000 INFO @ Mon, 12 Aug 2019 18:06:19: 2000000 INFO @ Mon, 12 Aug 2019 18:06:23: 2000000 INFO @ Mon, 12 Aug 2019 18:06:24: 2000000 INFO @ Mon, 12 Aug 2019 18:06:29: 3000000 INFO @ Mon, 12 Aug 2019 18:06:33: 3000000 INFO @ Mon, 12 Aug 2019 18:06:34: 3000000 INFO @ Mon, 12 Aug 2019 18:06:38: 4000000 INFO @ Mon, 12 Aug 2019 18:06:43: 4000000 INFO @ Mon, 12 Aug 2019 18:06:44: 4000000 INFO @ Mon, 12 Aug 2019 18:06:47: 5000000 INFO @ Mon, 12 Aug 2019 18:06:53: 5000000 INFO @ Mon, 12 Aug 2019 18:06:54: 5000000 INFO @ Mon, 12 Aug 2019 18:06:57: 6000000 INFO @ Mon, 12 Aug 2019 18:07:03: 6000000 INFO @ Mon, 12 Aug 2019 18:07:05: 6000000 INFO @ Mon, 12 Aug 2019 18:07:06: 7000000 INFO @ Mon, 12 Aug 2019 18:07:14: 7000000 INFO @ Mon, 12 Aug 2019 18:07:15: 7000000 INFO @ Mon, 12 Aug 2019 18:07:15: 8000000 INFO @ Mon, 12 Aug 2019 18:07:23: 8000000 INFO @ Mon, 12 Aug 2019 18:07:24: 9000000 INFO @ Mon, 12 Aug 2019 18:07:25: 8000000 INFO @ Mon, 12 Aug 2019 18:07:33: 10000000 INFO @ Mon, 12 Aug 2019 18:07:33: 9000000 INFO @ Mon, 12 Aug 2019 18:07:35: 9000000 INFO @ Mon, 12 Aug 2019 18:07:42: 11000000 INFO @ Mon, 12 Aug 2019 18:07:43: 10000000 INFO @ Mon, 12 Aug 2019 18:07:44: 10000000 INFO @ Mon, 12 Aug 2019 18:07:52: 12000000 INFO @ Mon, 12 Aug 2019 18:07:53: 11000000 INFO @ Mon, 12 Aug 2019 18:07:55: 11000000 INFO @ Mon, 12 Aug 2019 18:08:01: 13000000 INFO @ Mon, 12 Aug 2019 18:08:02: 12000000 INFO @ Mon, 12 Aug 2019 18:08:05: 12000000 INFO @ Mon, 12 Aug 2019 18:08:11: 14000000 INFO @ Mon, 12 Aug 2019 18:08:12: 13000000 INFO @ Mon, 12 Aug 2019 18:08:16: 13000000 INFO @ Mon, 12 Aug 2019 18:08:21: 15000000 INFO @ Mon, 12 Aug 2019 18:08:21: 14000000 INFO @ Mon, 12 Aug 2019 18:08:26: 14000000 INFO @ Mon, 12 Aug 2019 18:08:30: 16000000 INFO @ Mon, 12 Aug 2019 18:08:31: 15000000 INFO @ Mon, 12 Aug 2019 18:08:36: 15000000 INFO @ Mon, 12 Aug 2019 18:08:40: 17000000 INFO @ Mon, 12 Aug 2019 18:08:41: 16000000 INFO @ Mon, 12 Aug 2019 18:08:46: 16000000 INFO @ Mon, 12 Aug 2019 18:08:49: 18000000 INFO @ Mon, 12 Aug 2019 18:08:50: 17000000 INFO @ Mon, 12 Aug 2019 18:08:56: 17000000 INFO @ Mon, 12 Aug 2019 18:08:58: 19000000 INFO @ Mon, 12 Aug 2019 18:09:01: 18000000 INFO @ Mon, 12 Aug 2019 18:09:06: 18000000 INFO @ Mon, 12 Aug 2019 18:09:08: 20000000 INFO @ Mon, 12 Aug 2019 18:09:11: 19000000 INFO @ Mon, 12 Aug 2019 18:09:16: 19000000 INFO @ Mon, 12 Aug 2019 18:09:18: 21000000 INFO @ Mon, 12 Aug 2019 18:09:21: 20000000 INFO @ Mon, 12 Aug 2019 18:09:25: 20000000 INFO @ Mon, 12 Aug 2019 18:09:28: 22000000 INFO @ Mon, 12 Aug 2019 18:09:31: 21000000 INFO @ Mon, 12 Aug 2019 18:09:35: 21000000 INFO @ Mon, 12 Aug 2019 18:09:38: 23000000 INFO @ Mon, 12 Aug 2019 18:09:42: 22000000 INFO @ Mon, 12 Aug 2019 18:09:44: 22000000 INFO @ Mon, 12 Aug 2019 18:09:47: 24000000 INFO @ Mon, 12 Aug 2019 18:09:52: 23000000 INFO @ Mon, 12 Aug 2019 18:09:55: 23000000 INFO @ Mon, 12 Aug 2019 18:09:57: 25000000 INFO @ Mon, 12 Aug 2019 18:10:02: 24000000 INFO @ Mon, 12 Aug 2019 18:10:05: 24000000 INFO @ Mon, 12 Aug 2019 18:10:07: 26000000 INFO @ Mon, 12 Aug 2019 18:10:07: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:10:07: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:10:07: #1 total tags in treatment: 26021880 INFO @ Mon, 12 Aug 2019 18:10:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:10:07: #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 18:10:08: #1 tags after filtering in treatment: 26021880 INFO @ Mon, 12 Aug 2019 18:10:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:10:08: #1 finished! INFO @ Mon, 12 Aug 2019 18:10:08: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:10:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:10:10: #2 number of paired peaks: 115 WARNING @ Mon, 12 Aug 2019 18:10:10: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 12 Aug 2019 18:10:10: start model_add_line... INFO @ Mon, 12 Aug 2019 18:10:10: start X-correlation... INFO @ Mon, 12 Aug 2019 18:10:10: end of X-cor INFO @ Mon, 12 Aug 2019 18:10:10: #2 finished! INFO @ Mon, 12 Aug 2019 18:10:10: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 18:10:10: #2 alternative fragment length(s) may be 0,23,48,124,271,495,543,572 bps INFO @ Mon, 12 Aug 2019 18:10:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.05_model.r WARNING @ Mon, 12 Aug 2019 18:10:10: #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 18:10:10: #2 You may need to consider one of the other alternative d(s): 0,23,48,124,271,495,543,572 WARNING @ Mon, 12 Aug 2019 18:10:10: #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 18:10:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:10:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:10:12: 25000000 INFO @ Mon, 12 Aug 2019 18:10:15: 25000000 INFO @ Mon, 12 Aug 2019 18:10:21: 26000000 INFO @ Mon, 12 Aug 2019 18:10:22: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:10:22: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:10:22: #1 total tags in treatment: 26021880 INFO @ Mon, 12 Aug 2019 18:10:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:10:22: #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 18:10:22: #1 tags after filtering in treatment: 26021880 INFO @ Mon, 12 Aug 2019 18:10:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:10:22: #1 finished! INFO @ Mon, 12 Aug 2019 18:10:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:10:23: 26000000 INFO @ Mon, 12 Aug 2019 18:10:24: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 18:10:24: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 18:10:24: #1 total tags in treatment: 26021880 INFO @ Mon, 12 Aug 2019 18:10:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:10:24: #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 18:10:24: #1 tags after filtering in treatment: 26021880 INFO @ Mon, 12 Aug 2019 18:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:10:24: #1 finished! INFO @ Mon, 12 Aug 2019 18:10:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:10:25: #2 number of paired peaks: 115 WARNING @ Mon, 12 Aug 2019 18:10:25: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 12 Aug 2019 18:10:25: start model_add_line... INFO @ Mon, 12 Aug 2019 18:10:25: start X-correlation... INFO @ Mon, 12 Aug 2019 18:10:25: end of X-cor INFO @ Mon, 12 Aug 2019 18:10:25: #2 finished! INFO @ Mon, 12 Aug 2019 18:10:25: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 18:10:25: #2 alternative fragment length(s) may be 0,23,48,124,271,495,543,572 bps INFO @ Mon, 12 Aug 2019 18:10:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.10_model.r WARNING @ Mon, 12 Aug 2019 18:10:25: #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 18:10:25: #2 You may need to consider one of the other alternative d(s): 0,23,48,124,271,495,543,572 WARNING @ Mon, 12 Aug 2019 18:10:25: #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 18:10:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:10:26: #2 number of paired peaks: 115 WARNING @ Mon, 12 Aug 2019 18:10:26: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Mon, 12 Aug 2019 18:10:26: start model_add_line... INFO @ Mon, 12 Aug 2019 18:10:26: start X-correlation... INFO @ Mon, 12 Aug 2019 18:10:26: end of X-cor INFO @ Mon, 12 Aug 2019 18:10:26: #2 finished! INFO @ Mon, 12 Aug 2019 18:10:26: #2 predicted fragment length is 0 bps INFO @ Mon, 12 Aug 2019 18:10:26: #2 alternative fragment length(s) may be 0,23,48,124,271,495,543,572 bps INFO @ Mon, 12 Aug 2019 18:10:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1078720/SRX1078720.20_model.r WARNING @ Mon, 12 Aug 2019 18:10:26: #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 18:10:26: #2 You may need to consider one of the other alternative d(s): 0,23,48,124,271,495,543,572 WARNING @ Mon, 12 Aug 2019 18:10:26: #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 18:10:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:10:26: #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 SRX1078720.05.bed: No such file or directory mv: cannot stat ‘SRX1078720.05.bed’: No such file or directory /var/spool/uge/at095/job_scripts/2589368: line 335: 41744 Terminated MACS $i /var/spool/uge/at095/job_scripts/2589368: line 335: 41759 Terminated MACS $i /var/spool/uge/at095/job_scripts/2589368: line 335: 41774 Terminated MACS $i mv: cannot stat ‘SRX1078720.05.bb’: No such file or directory ls: cannot access SRX1078720.10.bed: No such file or directory mv: cannot stat ‘SRX1078720.10.bed’: No such file or directory mv: cannot stat ‘SRX1078720.10.bb’: No such file or directory ls: cannot access SRX1078720.20.bed: No such file or directory mv: cannot stat ‘SRX1078720.20.bed’: No such file or directory mv: cannot stat ‘SRX1078720.20.bb’: No such file or directory