Job ID = 1292605 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: 00:05:53 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171800 (0.56%) aligned 0 times 25273576 (82.09%) aligned exactly 1 time 5342773 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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 8 files... [bam_rmdupse_core] 4711122 / 30616349 = 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 20:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.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 20:04:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:04:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.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 20:04:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:04:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.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 20:04:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:04:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:04:15: 1000000 INFO @ Sun, 02 Jun 2019 20:04:16: 1000000 INFO @ Sun, 02 Jun 2019 20:04:17: 1000000 INFO @ Sun, 02 Jun 2019 20:04:22: 2000000 INFO @ Sun, 02 Jun 2019 20:04:23: 2000000 INFO @ Sun, 02 Jun 2019 20:04:25: 2000000 INFO @ Sun, 02 Jun 2019 20:04:28: 3000000 INFO @ Sun, 02 Jun 2019 20:04:30: 3000000 INFO @ Sun, 02 Jun 2019 20:04:34: 3000000 INFO @ Sun, 02 Jun 2019 20:04:35: 4000000 INFO @ Sun, 02 Jun 2019 20:04:37: 4000000 INFO @ Sun, 02 Jun 2019 20:04:41: 5000000 INFO @ Sun, 02 Jun 2019 20:04:42: 4000000 INFO @ Sun, 02 Jun 2019 20:04:45: 5000000 INFO @ Sun, 02 Jun 2019 20:04:48: 6000000 INFO @ Sun, 02 Jun 2019 20:04:50: 5000000 INFO @ Sun, 02 Jun 2019 20:04:52: 6000000 INFO @ Sun, 02 Jun 2019 20:04:55: 7000000 INFO @ Sun, 02 Jun 2019 20:04:58: 6000000 INFO @ Sun, 02 Jun 2019 20:04:59: 7000000 INFO @ Sun, 02 Jun 2019 20:05:01: 8000000 INFO @ Sun, 02 Jun 2019 20:05:06: 8000000 INFO @ Sun, 02 Jun 2019 20:05:07: 7000000 INFO @ Sun, 02 Jun 2019 20:05:08: 9000000 INFO @ Sun, 02 Jun 2019 20:05:13: 9000000 INFO @ Sun, 02 Jun 2019 20:05:14: 10000000 INFO @ Sun, 02 Jun 2019 20:05:15: 8000000 INFO @ Sun, 02 Jun 2019 20:05:20: 10000000 INFO @ Sun, 02 Jun 2019 20:05:21: 11000000 INFO @ Sun, 02 Jun 2019 20:05:23: 9000000 INFO @ Sun, 02 Jun 2019 20:05:27: 12000000 INFO @ Sun, 02 Jun 2019 20:05:28: 11000000 INFO @ Sun, 02 Jun 2019 20:05:32: 10000000 INFO @ Sun, 02 Jun 2019 20:05:34: 13000000 INFO @ Sun, 02 Jun 2019 20:05:35: 12000000 INFO @ Sun, 02 Jun 2019 20:05:40: 11000000 INFO @ Sun, 02 Jun 2019 20:05:41: 14000000 INFO @ Sun, 02 Jun 2019 20:05:42: 13000000 INFO @ Sun, 02 Jun 2019 20:05:47: 15000000 INFO @ Sun, 02 Jun 2019 20:05:48: 12000000 INFO @ Sun, 02 Jun 2019 20:05:49: 14000000 INFO @ Sun, 02 Jun 2019 20:05:54: 16000000 INFO @ Sun, 02 Jun 2019 20:05:56: 15000000 INFO @ Sun, 02 Jun 2019 20:05:57: 13000000 INFO @ Sun, 02 Jun 2019 20:06:00: 17000000 INFO @ Sun, 02 Jun 2019 20:06:03: 16000000 INFO @ Sun, 02 Jun 2019 20:06:05: 14000000 INFO @ Sun, 02 Jun 2019 20:06:07: 18000000 INFO @ Sun, 02 Jun 2019 20:06:10: 17000000 INFO @ Sun, 02 Jun 2019 20:06:13: 19000000 INFO @ Sun, 02 Jun 2019 20:06:13: 15000000 INFO @ Sun, 02 Jun 2019 20:06:17: 18000000 INFO @ Sun, 02 Jun 2019 20:06:20: 20000000 INFO @ Sun, 02 Jun 2019 20:06:21: 16000000 INFO @ Sun, 02 Jun 2019 20:06:24: 19000000 INFO @ Sun, 02 Jun 2019 20:06:26: 21000000 INFO @ Sun, 02 Jun 2019 20:06:30: 17000000 INFO @ Sun, 02 Jun 2019 20:06:31: 20000000 INFO @ Sun, 02 Jun 2019 20:06:33: 22000000 INFO @ Sun, 02 Jun 2019 20:06:38: 18000000 INFO @ Sun, 02 Jun 2019 20:06:38: 21000000 INFO @ Sun, 02 Jun 2019 20:06:39: 23000000 INFO @ Sun, 02 Jun 2019 20:06:45: 22000000 INFO @ Sun, 02 Jun 2019 20:06:46: 24000000 INFO @ Sun, 02 Jun 2019 20:06:46: 19000000 INFO @ Sun, 02 Jun 2019 20:06:52: 25000000 INFO @ Sun, 02 Jun 2019 20:06:52: 23000000 INFO @ Sun, 02 Jun 2019 20:06:54: 20000000 INFO @ Sun, 02 Jun 2019 20:06:58: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 20:06:58: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 20:06:58: #1 total tags in treatment: 25905227 INFO @ Sun, 02 Jun 2019 20:06:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:06:58: #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 20:06:59: #1 tags after filtering in treatment: 25905227 INFO @ Sun, 02 Jun 2019 20:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:06:59: #1 finished! INFO @ Sun, 02 Jun 2019 20:06:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:07:00: 24000000 INFO @ Sun, 02 Jun 2019 20:07:01: #2 number of paired peaks: 142 WARNING @ Sun, 02 Jun 2019 20:07:01: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sun, 02 Jun 2019 20:07:01: start model_add_line... INFO @ Sun, 02 Jun 2019 20:07:01: start X-correlation... INFO @ Sun, 02 Jun 2019 20:07:01: end of X-cor INFO @ Sun, 02 Jun 2019 20:07:01: #2 finished! INFO @ Sun, 02 Jun 2019 20:07:01: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 20:07:01: #2 alternative fragment length(s) may be 0,13,32,84,130,352,421,512,553,571 bps INFO @ Sun, 02 Jun 2019 20:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.10_model.r WARNING @ Sun, 02 Jun 2019 20:07:01: #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 20:07:01: #2 You may need to consider one of the other alternative d(s): 0,13,32,84,130,352,421,512,553,571 WARNING @ Sun, 02 Jun 2019 20:07:01: #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 20:07:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:07:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:07:02: 21000000 INFO @ Sun, 02 Jun 2019 20:07:07: 25000000 INFO @ Sun, 02 Jun 2019 20:07:10: 22000000 INFO @ Sun, 02 Jun 2019 20:07:13: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 20:07:13: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 20:07:13: #1 total tags in treatment: 25905227 INFO @ Sun, 02 Jun 2019 20:07:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:07:13: #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 20:07:14: #1 tags after filtering in treatment: 25905227 INFO @ Sun, 02 Jun 2019 20:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:07:14: #1 finished! INFO @ Sun, 02 Jun 2019 20:07:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:07:16: #2 number of paired peaks: 142 WARNING @ Sun, 02 Jun 2019 20:07:16: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sun, 02 Jun 2019 20:07:16: start model_add_line... INFO @ Sun, 02 Jun 2019 20:07:16: start X-correlation... INFO @ Sun, 02 Jun 2019 20:07:16: end of X-cor INFO @ Sun, 02 Jun 2019 20:07:16: #2 finished! INFO @ Sun, 02 Jun 2019 20:07:16: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 20:07:16: #2 alternative fragment length(s) may be 0,13,32,84,130,352,421,512,553,571 bps INFO @ Sun, 02 Jun 2019 20:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.05_model.r WARNING @ Sun, 02 Jun 2019 20:07:16: #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 20:07:16: #2 You may need to consider one of the other alternative d(s): 0,13,32,84,130,352,421,512,553,571 WARNING @ Sun, 02 Jun 2019 20:07:16: #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 20:07:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:07:18: 23000000 INFO @ Sun, 02 Jun 2019 20:07:26: 24000000 INFO @ Sun, 02 Jun 2019 20:07:34: 25000000 INFO @ Sun, 02 Jun 2019 20:07:41: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 20:07:41: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 20:07:41: #1 total tags in treatment: 25905227 INFO @ Sun, 02 Jun 2019 20:07:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:07:41: #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 20:07:42: #1 tags after filtering in treatment: 25905227 INFO @ Sun, 02 Jun 2019 20:07:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:07:42: #1 finished! INFO @ Sun, 02 Jun 2019 20:07:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:07:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:07:44: #2 number of paired peaks: 142 WARNING @ Sun, 02 Jun 2019 20:07:44: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Sun, 02 Jun 2019 20:07:44: start model_add_line... INFO @ Sun, 02 Jun 2019 20:07:44: start X-correlation... INFO @ Sun, 02 Jun 2019 20:07:44: end of X-cor INFO @ Sun, 02 Jun 2019 20:07:44: #2 finished! INFO @ Sun, 02 Jun 2019 20:07:44: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 20:07:44: #2 alternative fragment length(s) may be 0,13,32,84,130,352,421,512,553,571 bps INFO @ Sun, 02 Jun 2019 20:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494852/SRX494852.20_model.r WARNING @ Sun, 02 Jun 2019 20:07:44: #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 20:07:44: #2 You may need to consider one of the other alternative d(s): 0,13,32,84,130,352,421,512,553,571 WARNING @ Sun, 02 Jun 2019 20:07:44: #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 20:07:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:07:44: #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 SRX494852.05.bed: No such file or directory mv: cannot stat ‘SRX494852.05.bed’: No such file or directory /var/spool/uge/at085/job_scripts/1292605: line 321: 39641 Terminated MACS $i /var/spool/uge/at085/job_scripts/1292605: line 321: 39642 Terminated MACS $i /var/spool/uge/at085/job_scripts/1292605: line 321: 39643 Terminated MACS $i mv: cannot stat ‘SRX494852.05.bb’: No such file or directory ls: cannot access SRX494852.10.bed: No such file or directory mv: cannot stat ‘SRX494852.10.bed’: No such file or directory mv: cannot stat ‘SRX494852.10.bb’: No such file or directory ls: cannot access SRX494852.20.bed: No such file or directory mv: cannot stat ‘SRX494852.20.bed’: No such file or directory mv: cannot stat ‘SRX494852.20.bb’: No such file or directory