Job ID = 1292545 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,788,149 reads read : 30,788,149 reads written : 30,788,149 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: 00:06:04 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171806 (0.56%) aligned 0 times 25273629 (82.09%) aligned exactly 1 time 5342714 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 4711815 / 30616343 = 0.1539 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 19:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.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 19:49:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:49:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.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 19:49:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:49:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.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 19:49:46: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:49:46: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:49:55: 1000000 INFO @ Sun, 02 Jun 2019 19:49:55: 1000000 INFO @ Sun, 02 Jun 2019 19:49:56: 1000000 INFO @ Sun, 02 Jun 2019 19:50:03: 2000000 INFO @ Sun, 02 Jun 2019 19:50:04: 2000000 INFO @ Sun, 02 Jun 2019 19:50:05: 2000000 INFO @ Sun, 02 Jun 2019 19:50:10: 3000000 INFO @ Sun, 02 Jun 2019 19:50:12: 3000000 INFO @ Sun, 02 Jun 2019 19:50:14: 3000000 INFO @ Sun, 02 Jun 2019 19:50:19: 4000000 INFO @ Sun, 02 Jun 2019 19:50:20: 4000000 INFO @ Sun, 02 Jun 2019 19:50:23: 4000000 INFO @ Sun, 02 Jun 2019 19:50:27: 5000000 INFO @ Sun, 02 Jun 2019 19:50:29: 5000000 INFO @ Sun, 02 Jun 2019 19:50:32: 5000000 INFO @ Sun, 02 Jun 2019 19:50:35: 6000000 INFO @ Sun, 02 Jun 2019 19:50:38: 6000000 INFO @ Sun, 02 Jun 2019 19:50:40: 6000000 INFO @ Sun, 02 Jun 2019 19:50:42: 7000000 INFO @ Sun, 02 Jun 2019 19:50:46: 7000000 INFO @ Sun, 02 Jun 2019 19:50:49: 7000000 INFO @ Sun, 02 Jun 2019 19:50:50: 8000000 INFO @ Sun, 02 Jun 2019 19:50:55: 8000000 INFO @ Sun, 02 Jun 2019 19:50:58: 9000000 INFO @ Sun, 02 Jun 2019 19:50:59: 8000000 INFO @ Sun, 02 Jun 2019 19:51:03: 9000000 INFO @ Sun, 02 Jun 2019 19:51:05: 10000000 INFO @ Sun, 02 Jun 2019 19:51:08: 9000000 INFO @ Sun, 02 Jun 2019 19:51:11: 10000000 INFO @ Sun, 02 Jun 2019 19:51:13: 11000000 INFO @ Sun, 02 Jun 2019 19:51:16: 10000000 INFO @ Sun, 02 Jun 2019 19:51:20: 11000000 INFO @ Sun, 02 Jun 2019 19:51:21: 12000000 INFO @ Sun, 02 Jun 2019 19:51:25: 11000000 INFO @ Sun, 02 Jun 2019 19:51:28: 13000000 INFO @ Sun, 02 Jun 2019 19:51:29: 12000000 INFO @ Sun, 02 Jun 2019 19:51:34: 12000000 INFO @ Sun, 02 Jun 2019 19:51:36: 14000000 INFO @ Sun, 02 Jun 2019 19:51:37: 13000000 INFO @ Sun, 02 Jun 2019 19:51:43: 13000000 INFO @ Sun, 02 Jun 2019 19:51:43: 15000000 INFO @ Sun, 02 Jun 2019 19:51:45: 14000000 INFO @ Sun, 02 Jun 2019 19:51:52: 14000000 INFO @ Sun, 02 Jun 2019 19:51:52: 16000000 INFO @ Sun, 02 Jun 2019 19:51:54: 15000000 INFO @ Sun, 02 Jun 2019 19:52:00: 17000000 INFO @ Sun, 02 Jun 2019 19:52:00: 15000000 INFO @ Sun, 02 Jun 2019 19:52:02: 16000000 INFO @ Sun, 02 Jun 2019 19:52:08: 18000000 INFO @ Sun, 02 Jun 2019 19:52:09: 16000000 INFO @ Sun, 02 Jun 2019 19:52:11: 17000000 INFO @ Sun, 02 Jun 2019 19:52:15: 19000000 INFO @ Sun, 02 Jun 2019 19:52:19: 17000000 INFO @ Sun, 02 Jun 2019 19:52:19: 18000000 INFO @ Sun, 02 Jun 2019 19:52:23: 20000000 INFO @ Sun, 02 Jun 2019 19:52:28: 18000000 INFO @ Sun, 02 Jun 2019 19:52:28: 19000000 INFO @ Sun, 02 Jun 2019 19:52:30: 21000000 INFO @ Sun, 02 Jun 2019 19:52:36: 20000000 INFO @ Sun, 02 Jun 2019 19:52:36: 19000000 INFO @ Sun, 02 Jun 2019 19:52:38: 22000000 INFO @ Sun, 02 Jun 2019 19:52:45: 21000000 INFO @ Sun, 02 Jun 2019 19:52:45: 20000000 INFO @ Sun, 02 Jun 2019 19:52:45: 23000000 INFO @ Sun, 02 Jun 2019 19:52:53: 22000000 INFO @ Sun, 02 Jun 2019 19:52:53: 24000000 INFO @ Sun, 02 Jun 2019 19:52:54: 21000000 INFO @ Sun, 02 Jun 2019 19:53:01: 25000000 INFO @ Sun, 02 Jun 2019 19:53:02: 23000000 INFO @ Sun, 02 Jun 2019 19:53:03: 22000000 INFO @ Sun, 02 Jun 2019 19:53:08: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:53:08: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:53:08: #1 total tags in treatment: 25904528 INFO @ Sun, 02 Jun 2019 19:53:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:53:08: #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 19:53:08: #1 tags after filtering in treatment: 25904528 INFO @ Sun, 02 Jun 2019 19:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:53:08: #1 finished! INFO @ Sun, 02 Jun 2019 19:53:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:53:10: 24000000 INFO @ Sun, 02 Jun 2019 19:53:10: #2 number of paired peaks: 144 WARNING @ Sun, 02 Jun 2019 19:53:10: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 02 Jun 2019 19:53:10: start model_add_line... INFO @ Sun, 02 Jun 2019 19:53:11: start X-correlation... INFO @ Sun, 02 Jun 2019 19:53:11: end of X-cor INFO @ Sun, 02 Jun 2019 19:53:11: #2 finished! INFO @ Sun, 02 Jun 2019 19:53:11: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:53:11: #2 alternative fragment length(s) may be 0,34,128,412,421,551,579 bps INFO @ Sun, 02 Jun 2019 19:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.20_model.r WARNING @ Sun, 02 Jun 2019 19:53:11: #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 19:53:11: #2 You may need to consider one of the other alternative d(s): 0,34,128,412,421,551,579 WARNING @ Sun, 02 Jun 2019 19:53:11: #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 19:53:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:53:12: 23000000 INFO @ Sun, 02 Jun 2019 19:53:18: 25000000 INFO @ Sun, 02 Jun 2019 19:53:20: 24000000 INFO @ Sun, 02 Jun 2019 19:53:26: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:53:26: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:53:26: #1 total tags in treatment: 25904528 INFO @ Sun, 02 Jun 2019 19:53:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:53:26: #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 19:53:27: #1 tags after filtering in treatment: 25904528 INFO @ Sun, 02 Jun 2019 19:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:53:27: #1 finished! INFO @ Sun, 02 Jun 2019 19:53:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:53:29: 25000000 INFO @ Sun, 02 Jun 2019 19:53:29: #2 number of paired peaks: 144 WARNING @ Sun, 02 Jun 2019 19:53:29: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 02 Jun 2019 19:53:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:53:29: start X-correlation... INFO @ Sun, 02 Jun 2019 19:53:29: end of X-cor INFO @ Sun, 02 Jun 2019 19:53:29: #2 finished! INFO @ Sun, 02 Jun 2019 19:53:29: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:53:29: #2 alternative fragment length(s) may be 0,34,128,412,421,551,579 bps INFO @ Sun, 02 Jun 2019 19:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.10_model.r WARNING @ Sun, 02 Jun 2019 19:53:29: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:53:29: #2 You may need to consider one of the other alternative d(s): 0,34,128,412,421,551,579 WARNING @ Sun, 02 Jun 2019 19:53:29: #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 19:53:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:53:37: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:53:37: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:53:37: #1 total tags in treatment: 25904528 INFO @ Sun, 02 Jun 2019 19:53:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:53:37: #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 19:53:37: #1 tags after filtering in treatment: 25904528 INFO @ Sun, 02 Jun 2019 19:53:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:53:37: #1 finished! INFO @ Sun, 02 Jun 2019 19:53:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:53:39: #2 number of paired peaks: 144 WARNING @ Sun, 02 Jun 2019 19:53:39: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sun, 02 Jun 2019 19:53:39: start model_add_line... INFO @ Sun, 02 Jun 2019 19:53:39: start X-correlation... INFO @ Sun, 02 Jun 2019 19:53:40: end of X-cor INFO @ Sun, 02 Jun 2019 19:53:40: #2 finished! INFO @ Sun, 02 Jun 2019 19:53:40: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:53:40: #2 alternative fragment length(s) may be 0,34,128,412,421,551,579 bps INFO @ Sun, 02 Jun 2019 19:53:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466559/SRX466559.05_model.r WARNING @ Sun, 02 Jun 2019 19:53:40: #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 19:53:40: #2 You may need to consider one of the other alternative d(s): 0,34,128,412,421,551,579 WARNING @ Sun, 02 Jun 2019 19:53:40: #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 19:53:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:53:40: #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 SRX466559.05.bed: No such file or directory mv: cannot stat ‘SRX466559.05.bed’: No such file or directory /var/spool/uge/at093/job_scripts/1292545: line 321: 18269 Terminated MACS $i /var/spool/uge/at093/job_scripts/1292545: line 321: 18270 Terminated MACS $i /var/spool/uge/at093/job_scripts/1292545: line 321: 18271 Terminated MACS $i mv: cannot stat ‘SRX466559.05.bb’: No such file or directory ls: cannot access SRX466559.10.bed: No such file or directory mv: cannot stat ‘SRX466559.10.bed’: No such file or directory mv: cannot stat ‘SRX466559.10.bb’: No such file or directory ls: cannot access SRX466559.20.bed: No such file or directory mv: cannot stat ‘SRX466559.20.bed’: No such file or directory mv: cannot stat ‘SRX466559.20.bb’: No such file or directory