Job ID = 1292308 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: 00:05:55 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171803 (0.56%) aligned 0 times 25273662 (82.09%) aligned exactly 1 time 5342684 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:55 Overall time: 00:05:55 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] 4711363 / 30616346 = 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 18:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.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 18:05:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:05:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.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 18:05:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:05:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:05:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.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 18:05:33: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:05:33: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:05:41: 1000000 INFO @ Sun, 02 Jun 2019 18:05:41: 1000000 INFO @ Sun, 02 Jun 2019 18:05:42: 1000000 INFO @ Sun, 02 Jun 2019 18:05:49: 2000000 INFO @ Sun, 02 Jun 2019 18:05:49: 2000000 INFO @ Sun, 02 Jun 2019 18:05:50: 2000000 INFO @ Sun, 02 Jun 2019 18:05:56: 3000000 INFO @ Sun, 02 Jun 2019 18:05:56: 3000000 INFO @ Sun, 02 Jun 2019 18:05:59: 3000000 INFO @ Sun, 02 Jun 2019 18:06:04: 4000000 INFO @ Sun, 02 Jun 2019 18:06:04: 4000000 INFO @ Sun, 02 Jun 2019 18:06:07: 4000000 INFO @ Sun, 02 Jun 2019 18:06:11: 5000000 INFO @ Sun, 02 Jun 2019 18:06:11: 5000000 INFO @ Sun, 02 Jun 2019 18:06:15: 5000000 INFO @ Sun, 02 Jun 2019 18:06:19: 6000000 INFO @ Sun, 02 Jun 2019 18:06:19: 6000000 INFO @ Sun, 02 Jun 2019 18:06:24: 6000000 INFO @ Sun, 02 Jun 2019 18:06:26: 7000000 INFO @ Sun, 02 Jun 2019 18:06:27: 7000000 INFO @ Sun, 02 Jun 2019 18:06:33: 7000000 INFO @ Sun, 02 Jun 2019 18:06:34: 8000000 INFO @ Sun, 02 Jun 2019 18:06:35: 8000000 INFO @ Sun, 02 Jun 2019 18:06:41: 8000000 INFO @ Sun, 02 Jun 2019 18:06:42: 9000000 INFO @ Sun, 02 Jun 2019 18:06:43: 9000000 INFO @ Sun, 02 Jun 2019 18:06:49: 10000000 INFO @ Sun, 02 Jun 2019 18:06:50: 9000000 INFO @ Sun, 02 Jun 2019 18:06:51: 10000000 INFO @ Sun, 02 Jun 2019 18:06:57: 11000000 INFO @ Sun, 02 Jun 2019 18:06:58: 10000000 INFO @ Sun, 02 Jun 2019 18:06:59: 11000000 INFO @ Sun, 02 Jun 2019 18:07:04: 12000000 INFO @ Sun, 02 Jun 2019 18:07:07: 11000000 INFO @ Sun, 02 Jun 2019 18:07:09: 12000000 INFO @ Sun, 02 Jun 2019 18:07:12: 13000000 INFO @ Sun, 02 Jun 2019 18:07:17: 12000000 INFO @ Sun, 02 Jun 2019 18:07:19: 13000000 INFO @ Sun, 02 Jun 2019 18:07:19: 14000000 INFO @ Sun, 02 Jun 2019 18:07:27: 13000000 INFO @ Sun, 02 Jun 2019 18:07:27: 15000000 INFO @ Sun, 02 Jun 2019 18:07:28: 14000000 INFO @ Sun, 02 Jun 2019 18:07:34: 16000000 INFO @ Sun, 02 Jun 2019 18:07:36: 14000000 INFO @ Sun, 02 Jun 2019 18:07:37: 15000000 INFO @ Sun, 02 Jun 2019 18:07:42: 17000000 INFO @ Sun, 02 Jun 2019 18:07:45: 15000000 INFO @ Sun, 02 Jun 2019 18:07:46: 16000000 INFO @ Sun, 02 Jun 2019 18:07:49: 18000000 INFO @ Sun, 02 Jun 2019 18:07:53: 16000000 INFO @ Sun, 02 Jun 2019 18:07:55: 17000000 INFO @ Sun, 02 Jun 2019 18:07:56: 19000000 INFO @ Sun, 02 Jun 2019 18:08:02: 17000000 INFO @ Sun, 02 Jun 2019 18:08:03: 18000000 INFO @ Sun, 02 Jun 2019 18:08:03: 20000000 INFO @ Sun, 02 Jun 2019 18:08:10: 18000000 INFO @ Sun, 02 Jun 2019 18:08:11: 21000000 INFO @ Sun, 02 Jun 2019 18:08:11: 19000000 INFO @ Sun, 02 Jun 2019 18:08:18: 22000000 INFO @ Sun, 02 Jun 2019 18:08:19: 19000000 INFO @ Sun, 02 Jun 2019 18:08:19: 20000000 INFO @ Sun, 02 Jun 2019 18:08:25: 23000000 INFO @ Sun, 02 Jun 2019 18:08:27: 21000000 INFO @ Sun, 02 Jun 2019 18:08:27: 20000000 INFO @ Sun, 02 Jun 2019 18:08:32: 24000000 INFO @ Sun, 02 Jun 2019 18:08:35: 22000000 INFO @ Sun, 02 Jun 2019 18:08:36: 21000000 INFO @ Sun, 02 Jun 2019 18:08:40: 25000000 INFO @ Sun, 02 Jun 2019 18:08:43: 23000000 INFO @ Sun, 02 Jun 2019 18:08:44: 22000000 INFO @ Sun, 02 Jun 2019 18:08:46: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:08:46: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:08:46: #1 total tags in treatment: 25904983 INFO @ Sun, 02 Jun 2019 18:08:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:08:46: #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 18:08:47: #1 tags after filtering in treatment: 25904983 INFO @ Sun, 02 Jun 2019 18:08:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:08:47: #1 finished! INFO @ Sun, 02 Jun 2019 18:08:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:08:49: #2 number of paired peaks: 148 WARNING @ Sun, 02 Jun 2019 18:08:49: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sun, 02 Jun 2019 18:08:49: start model_add_line... INFO @ Sun, 02 Jun 2019 18:08:49: start X-correlation... INFO @ Sun, 02 Jun 2019 18:08:49: end of X-cor INFO @ Sun, 02 Jun 2019 18:08:49: #2 finished! INFO @ Sun, 02 Jun 2019 18:08:49: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 18:08:49: #2 alternative fragment length(s) may be 0,32,151,438,510 bps INFO @ Sun, 02 Jun 2019 18:08:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.05_model.r WARNING @ Sun, 02 Jun 2019 18:08:49: #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 18:08:49: #2 You may need to consider one of the other alternative d(s): 0,32,151,438,510 WARNING @ Sun, 02 Jun 2019 18:08:49: #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 18:08:49: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:08:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:08:52: 24000000 INFO @ Sun, 02 Jun 2019 18:08:53: 23000000 INFO @ Sun, 02 Jun 2019 18:09:00: 25000000 INFO @ Sun, 02 Jun 2019 18:09:01: 24000000 INFO @ Sun, 02 Jun 2019 18:09:07: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:09:07: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:09:07: #1 total tags in treatment: 25904983 INFO @ Sun, 02 Jun 2019 18:09:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:09:07: #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 18:09:07: #1 tags after filtering in treatment: 25904983 INFO @ Sun, 02 Jun 2019 18:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:09:07: #1 finished! INFO @ Sun, 02 Jun 2019 18:09:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:09:09: 25000000 INFO @ Sun, 02 Jun 2019 18:09:10: #2 number of paired peaks: 148 WARNING @ Sun, 02 Jun 2019 18:09:10: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sun, 02 Jun 2019 18:09:10: start model_add_line... INFO @ Sun, 02 Jun 2019 18:09:10: start X-correlation... INFO @ Sun, 02 Jun 2019 18:09:10: end of X-cor INFO @ Sun, 02 Jun 2019 18:09:10: #2 finished! INFO @ Sun, 02 Jun 2019 18:09:10: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 18:09:10: #2 alternative fragment length(s) may be 0,32,151,438,510 bps INFO @ Sun, 02 Jun 2019 18:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.20_model.r WARNING @ Sun, 02 Jun 2019 18:09:10: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:09:10: #2 You may need to consider one of the other alternative d(s): 0,32,151,438,510 WARNING @ Sun, 02 Jun 2019 18:09:10: #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 18:09:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:09:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:09:17: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 18:09:17: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 18:09:17: #1 total tags in treatment: 25904983 INFO @ Sun, 02 Jun 2019 18:09:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:09:17: #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 18:09:17: #1 tags after filtering in treatment: 25904983 INFO @ Sun, 02 Jun 2019 18:09:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:09:17: #1 finished! INFO @ Sun, 02 Jun 2019 18:09:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:09:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:09:19: #2 number of paired peaks: 148 WARNING @ Sun, 02 Jun 2019 18:09:19: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sun, 02 Jun 2019 18:09:19: start model_add_line... INFO @ Sun, 02 Jun 2019 18:09:20: start X-correlation... INFO @ Sun, 02 Jun 2019 18:09:20: end of X-cor INFO @ Sun, 02 Jun 2019 18:09:20: #2 finished! INFO @ Sun, 02 Jun 2019 18:09:20: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 18:09:20: #2 alternative fragment length(s) may be 0,32,151,438,510 bps INFO @ Sun, 02 Jun 2019 18:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331333/SRX331333.10_model.r WARNING @ Sun, 02 Jun 2019 18:09:20: #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 18:09:20: #2 You may need to consider one of the other alternative d(s): 0,32,151,438,510 WARNING @ Sun, 02 Jun 2019 18:09:20: #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 18:09:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:09:20: #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 SRX331333.05.bed: No such file or directory mv: cannot stat ‘SRX331333.05.bed’: No such file or directory /var/spool/uge/at108/job_scripts/1292308: line 321: 35647 Terminated MACS $i /var/spool/uge/at108/job_scripts/1292308: line 321: 35648 Terminated MACS $i /var/spool/uge/at108/job_scripts/1292308: line 321: 35649 Terminated MACS $i mv: cannot stat ‘SRX331333.05.bb’: No such file or directory ls: cannot access SRX331333.10.bed: No such file or directory mv: cannot stat ‘SRX331333.10.bed’: No such file or directory mv: cannot stat ‘SRX331333.10.bb’: No such file or directory ls: cannot access SRX331333.20.bed: No such file or directory mv: cannot stat ‘SRX331333.20.bed’: No such file or directory mv: cannot stat ‘SRX331333.20.bb’: No such file or directory