Job ID = 1291518 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,706,298 reads read : 29,706,298 reads written : 29,706,298 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: 00:05:14 29706298 reads; of these: 29706298 (100.00%) were unpaired; of these: 7084743 (23.85%) aligned 0 times 18663284 (62.83%) aligned exactly 1 time 3958271 (13.32%) aligned >1 times 76.15% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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 8 files... [bam_rmdupse_core] 2635294 / 22621555 = 0.1165 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 16:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.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 16:14:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:14:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.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 16:14:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:14:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.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 16:14:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:14:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:14:42: 1000000 INFO @ Sun, 02 Jun 2019 16:14:42: 1000000 INFO @ Sun, 02 Jun 2019 16:14:43: 1000000 INFO @ Sun, 02 Jun 2019 16:14:49: 2000000 INFO @ Sun, 02 Jun 2019 16:14:49: 2000000 INFO @ Sun, 02 Jun 2019 16:14:51: 2000000 INFO @ Sun, 02 Jun 2019 16:14:56: 3000000 INFO @ Sun, 02 Jun 2019 16:14:57: 3000000 INFO @ Sun, 02 Jun 2019 16:15:00: 3000000 INFO @ Sun, 02 Jun 2019 16:15:04: 4000000 INFO @ Sun, 02 Jun 2019 16:15:04: 4000000 INFO @ Sun, 02 Jun 2019 16:15:08: 4000000 INFO @ Sun, 02 Jun 2019 16:15:11: 5000000 INFO @ Sun, 02 Jun 2019 16:15:11: 5000000 INFO @ Sun, 02 Jun 2019 16:15:16: 5000000 INFO @ Sun, 02 Jun 2019 16:15:18: 6000000 INFO @ Sun, 02 Jun 2019 16:15:18: 6000000 INFO @ Sun, 02 Jun 2019 16:15:25: 6000000 INFO @ Sun, 02 Jun 2019 16:15:25: 7000000 INFO @ Sun, 02 Jun 2019 16:15:25: 7000000 INFO @ Sun, 02 Jun 2019 16:15:32: 8000000 INFO @ Sun, 02 Jun 2019 16:15:32: 8000000 INFO @ Sun, 02 Jun 2019 16:15:33: 7000000 INFO @ Sun, 02 Jun 2019 16:15:39: 9000000 INFO @ Sun, 02 Jun 2019 16:15:39: 9000000 INFO @ Sun, 02 Jun 2019 16:15:41: 8000000 INFO @ Sun, 02 Jun 2019 16:15:46: 10000000 INFO @ Sun, 02 Jun 2019 16:15:46: 10000000 INFO @ Sun, 02 Jun 2019 16:15:49: 9000000 INFO @ Sun, 02 Jun 2019 16:15:53: 11000000 INFO @ Sun, 02 Jun 2019 16:15:54: 11000000 INFO @ Sun, 02 Jun 2019 16:15:57: 10000000 INFO @ Sun, 02 Jun 2019 16:16:00: 12000000 INFO @ Sun, 02 Jun 2019 16:16:01: 12000000 INFO @ Sun, 02 Jun 2019 16:16:05: 11000000 INFO @ Sun, 02 Jun 2019 16:16:07: 13000000 INFO @ Sun, 02 Jun 2019 16:16:08: 13000000 INFO @ Sun, 02 Jun 2019 16:16:13: 12000000 INFO @ Sun, 02 Jun 2019 16:16:14: 14000000 INFO @ Sun, 02 Jun 2019 16:16:15: 14000000 INFO @ Sun, 02 Jun 2019 16:16:21: 15000000 INFO @ Sun, 02 Jun 2019 16:16:21: 13000000 INFO @ Sun, 02 Jun 2019 16:16:22: 15000000 INFO @ Sun, 02 Jun 2019 16:16:28: 16000000 INFO @ Sun, 02 Jun 2019 16:16:29: 16000000 INFO @ Sun, 02 Jun 2019 16:16:29: 14000000 INFO @ Sun, 02 Jun 2019 16:16:35: 17000000 INFO @ Sun, 02 Jun 2019 16:16:37: 17000000 INFO @ Sun, 02 Jun 2019 16:16:37: 15000000 INFO @ Sun, 02 Jun 2019 16:16:42: 18000000 INFO @ Sun, 02 Jun 2019 16:16:44: 18000000 INFO @ Sun, 02 Jun 2019 16:16:45: 16000000 INFO @ Sun, 02 Jun 2019 16:16:49: 19000000 INFO @ Sun, 02 Jun 2019 16:16:51: 19000000 INFO @ Sun, 02 Jun 2019 16:16:53: 17000000 INFO @ Sun, 02 Jun 2019 16:16:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:56: #1 total tags in treatment: 19986261 INFO @ Sun, 02 Jun 2019 16:16:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:56: #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 16:16:56: #1 tags after filtering in treatment: 19986261 INFO @ Sun, 02 Jun 2019 16:16:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:56: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:58: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:16:58: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:16:58: #1 total tags in treatment: 19986261 INFO @ Sun, 02 Jun 2019 16:16:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:16:58: #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 16:16:58: #2 number of paired peaks: 177 WARNING @ Sun, 02 Jun 2019 16:16:58: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 02 Jun 2019 16:16:58: start model_add_line... INFO @ Sun, 02 Jun 2019 16:16:58: #1 tags after filtering in treatment: 19986261 INFO @ Sun, 02 Jun 2019 16:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:16:58: #1 finished! INFO @ Sun, 02 Jun 2019 16:16:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:16:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:16:58: start X-correlation... INFO @ Sun, 02 Jun 2019 16:16:58: end of X-cor INFO @ Sun, 02 Jun 2019 16:16:58: #2 finished! INFO @ Sun, 02 Jun 2019 16:16:58: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:16:58: #2 alternative fragment length(s) may be 0,33,424,446 bps INFO @ Sun, 02 Jun 2019 16:16:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.20_model.r WARNING @ Sun, 02 Jun 2019 16:16:58: #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 16:16:58: #2 You may need to consider one of the other alternative d(s): 0,33,424,446 WARNING @ Sun, 02 Jun 2019 16:16:58: #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 16:16:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:16:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:17:00: #2 number of paired peaks: 177 WARNING @ Sun, 02 Jun 2019 16:17:00: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 02 Jun 2019 16:17:00: start model_add_line... INFO @ Sun, 02 Jun 2019 16:17:00: start X-correlation... INFO @ Sun, 02 Jun 2019 16:17:00: end of X-cor INFO @ Sun, 02 Jun 2019 16:17:00: #2 finished! INFO @ Sun, 02 Jun 2019 16:17:00: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:17:00: #2 alternative fragment length(s) may be 0,33,424,446 bps INFO @ Sun, 02 Jun 2019 16:17:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.05_model.r WARNING @ Sun, 02 Jun 2019 16:17:00: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:17:00: #2 You may need to consider one of the other alternative d(s): 0,33,424,446 WARNING @ Sun, 02 Jun 2019 16:17:00: #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 16:17:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:17:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:17:01: 18000000 INFO @ Sun, 02 Jun 2019 16:17:09: 19000000 INFO @ Sun, 02 Jun 2019 16:17:17: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:17:17: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:17:17: #1 total tags in treatment: 19986261 INFO @ Sun, 02 Jun 2019 16:17:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:17:17: #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 16:17:18: #1 tags after filtering in treatment: 19986261 INFO @ Sun, 02 Jun 2019 16:17:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:17:18: #1 finished! INFO @ Sun, 02 Jun 2019 16:17:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:17:19: #2 number of paired peaks: 177 WARNING @ Sun, 02 Jun 2019 16:17:19: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Sun, 02 Jun 2019 16:17:19: start model_add_line... INFO @ Sun, 02 Jun 2019 16:17:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:17:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:17:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:17:20: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 16:17:20: #2 alternative fragment length(s) may be 0,33,424,446 bps INFO @ Sun, 02 Jun 2019 16:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX105311/SRX105311.10_model.r WARNING @ Sun, 02 Jun 2019 16:17:20: #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 16:17:20: #2 You may need to consider one of the other alternative d(s): 0,33,424,446 WARNING @ Sun, 02 Jun 2019 16:17:20: #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 16:17:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:17:20: #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 SRX105311.05.bed: No such file or directory mv: cannot stat ‘SRX105311.05.bed’: No such file or directory /var/spool/uge/at107/job_scripts/1291518: line 321: 12992 Terminated MACS $i /var/spool/uge/at107/job_scripts/1291518: line 321: 12993 Terminated MACS $i /var/spool/uge/at107/job_scripts/1291518: line 321: 12994 Terminated MACS $i mv: cannot stat ‘SRX105311.05.bb’: No such file or directory ls: cannot access SRX105311.10.bed: No such file or directory mv: cannot stat ‘SRX105311.10.bed’: No such file or directory mv: cannot stat ‘SRX105311.10.bb’: No such file or directory ls: cannot access SRX105311.20.bed: No such file or directory mv: cannot stat ‘SRX105311.20.bed’: No such file or directory mv: cannot stat ‘SRX105311.20.bb’: No such file or directory