Job ID = 1292533 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: 00:06:19 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171784 (0.56%) aligned 0 times 25273650 (82.09%) aligned exactly 1 time 5342715 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 4711417 / 30616365 = 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 19:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.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 19:48:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:48:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.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 19:48:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:48:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.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 19:48:35: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:48:35: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:48:43: 1000000 INFO @ Sun, 02 Jun 2019 19:48:46: 1000000 INFO @ Sun, 02 Jun 2019 19:48:46: 1000000 INFO @ Sun, 02 Jun 2019 19:48:51: 2000000 INFO @ Sun, 02 Jun 2019 19:48:55: 2000000 INFO @ Sun, 02 Jun 2019 19:48:55: 2000000 INFO @ Sun, 02 Jun 2019 19:48:58: 3000000 INFO @ Sun, 02 Jun 2019 19:49:05: 3000000 INFO @ Sun, 02 Jun 2019 19:49:05: 3000000 INFO @ Sun, 02 Jun 2019 19:49:06: 4000000 INFO @ Sun, 02 Jun 2019 19:49:14: 5000000 INFO @ Sun, 02 Jun 2019 19:49:14: 4000000 INFO @ Sun, 02 Jun 2019 19:49:15: 4000000 INFO @ Sun, 02 Jun 2019 19:49:21: 6000000 INFO @ Sun, 02 Jun 2019 19:49:24: 5000000 INFO @ Sun, 02 Jun 2019 19:49:24: 5000000 INFO @ Sun, 02 Jun 2019 19:49:28: 7000000 INFO @ Sun, 02 Jun 2019 19:49:34: 6000000 INFO @ Sun, 02 Jun 2019 19:49:34: 6000000 INFO @ Sun, 02 Jun 2019 19:49:36: 8000000 INFO @ Sun, 02 Jun 2019 19:49:43: 9000000 INFO @ Sun, 02 Jun 2019 19:49:44: 7000000 INFO @ Sun, 02 Jun 2019 19:49:44: 7000000 INFO @ Sun, 02 Jun 2019 19:49:50: 10000000 INFO @ Sun, 02 Jun 2019 19:49:53: 8000000 INFO @ Sun, 02 Jun 2019 19:49:53: 8000000 INFO @ Sun, 02 Jun 2019 19:49:58: 11000000 INFO @ Sun, 02 Jun 2019 19:50:03: 9000000 INFO @ Sun, 02 Jun 2019 19:50:03: 9000000 INFO @ Sun, 02 Jun 2019 19:50:05: 12000000 INFO @ Sun, 02 Jun 2019 19:50:13: 13000000 INFO @ Sun, 02 Jun 2019 19:50:13: 10000000 INFO @ Sun, 02 Jun 2019 19:50:13: 10000000 INFO @ Sun, 02 Jun 2019 19:50:20: 14000000 INFO @ Sun, 02 Jun 2019 19:50:23: 11000000 INFO @ Sun, 02 Jun 2019 19:50:23: 11000000 INFO @ Sun, 02 Jun 2019 19:50:28: 15000000 INFO @ Sun, 02 Jun 2019 19:50:33: 12000000 INFO @ Sun, 02 Jun 2019 19:50:33: 12000000 INFO @ Sun, 02 Jun 2019 19:50:35: 16000000 INFO @ Sun, 02 Jun 2019 19:50:42: 13000000 INFO @ Sun, 02 Jun 2019 19:50:43: 13000000 INFO @ Sun, 02 Jun 2019 19:50:43: 17000000 INFO @ Sun, 02 Jun 2019 19:50:50: 18000000 INFO @ Sun, 02 Jun 2019 19:50:52: 14000000 INFO @ Sun, 02 Jun 2019 19:50:52: 14000000 INFO @ Sun, 02 Jun 2019 19:50:57: 19000000 INFO @ Sun, 02 Jun 2019 19:51:02: 15000000 INFO @ Sun, 02 Jun 2019 19:51:02: 15000000 INFO @ Sun, 02 Jun 2019 19:51:04: 20000000 INFO @ Sun, 02 Jun 2019 19:51:12: 21000000 INFO @ Sun, 02 Jun 2019 19:51:12: 16000000 INFO @ Sun, 02 Jun 2019 19:51:12: 16000000 INFO @ Sun, 02 Jun 2019 19:51:19: 22000000 INFO @ Sun, 02 Jun 2019 19:51:22: 17000000 INFO @ Sun, 02 Jun 2019 19:51:22: 17000000 INFO @ Sun, 02 Jun 2019 19:51:26: 23000000 INFO @ Sun, 02 Jun 2019 19:51:31: 18000000 INFO @ Sun, 02 Jun 2019 19:51:32: 18000000 INFO @ Sun, 02 Jun 2019 19:51:34: 24000000 INFO @ Sun, 02 Jun 2019 19:51:41: 19000000 INFO @ Sun, 02 Jun 2019 19:51:41: 19000000 INFO @ Sun, 02 Jun 2019 19:51:41: 25000000 INFO @ Sun, 02 Jun 2019 19:51:48: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:51:48: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:51:48: #1 total tags in treatment: 25904948 INFO @ Sun, 02 Jun 2019 19:51:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:51:48: #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 19:51:49: #1 tags after filtering in treatment: 25904948 INFO @ Sun, 02 Jun 2019 19:51:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:51:49: #1 finished! INFO @ Sun, 02 Jun 2019 19:51:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:51:51: 20000000 INFO @ Sun, 02 Jun 2019 19:51:51: 20000000 INFO @ Sun, 02 Jun 2019 19:51:51: #2 number of paired peaks: 140 WARNING @ Sun, 02 Jun 2019 19:51:51: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 02 Jun 2019 19:51:51: start model_add_line... INFO @ Sun, 02 Jun 2019 19:51:51: start X-correlation... INFO @ Sun, 02 Jun 2019 19:51:51: end of X-cor INFO @ Sun, 02 Jun 2019 19:51:51: #2 finished! INFO @ Sun, 02 Jun 2019 19:51:51: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:51:51: #2 alternative fragment length(s) may be 0,20,33,92,440,464,497,552 bps INFO @ Sun, 02 Jun 2019 19:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.05_model.r WARNING @ Sun, 02 Jun 2019 19:51:51: #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 19:51:51: #2 You may need to consider one of the other alternative d(s): 0,20,33,92,440,464,497,552 WARNING @ Sun, 02 Jun 2019 19:51:51: #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 19:51:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:52:00: 21000000 INFO @ Sun, 02 Jun 2019 19:52:00: 21000000 INFO @ Sun, 02 Jun 2019 19:52:09: 22000000 INFO @ Sun, 02 Jun 2019 19:52:09: 22000000 INFO @ Sun, 02 Jun 2019 19:52:18: 23000000 INFO @ Sun, 02 Jun 2019 19:52:18: 23000000 INFO @ Sun, 02 Jun 2019 19:52:28: 24000000 INFO @ Sun, 02 Jun 2019 19:52:28: 24000000 INFO @ Sun, 02 Jun 2019 19:52:36: 25000000 INFO @ Sun, 02 Jun 2019 19:52:36: 25000000 INFO @ Sun, 02 Jun 2019 19:52:45: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:52:45: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:52:45: #1 total tags in treatment: 25904948 INFO @ Sun, 02 Jun 2019 19:52:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:52:45: #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 19:52:45: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:52:45: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:52:45: #1 total tags in treatment: 25904948 INFO @ Sun, 02 Jun 2019 19:52:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:52:45: #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 19:52:45: #1 tags after filtering in treatment: 25904948 INFO @ Sun, 02 Jun 2019 19:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:52:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:52:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:52:45: #1 tags after filtering in treatment: 25904948 INFO @ Sun, 02 Jun 2019 19:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:52:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:52:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:52:47: #2 number of paired peaks: 140 WARNING @ Sun, 02 Jun 2019 19:52:47: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 02 Jun 2019 19:52:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:52:47: #2 number of paired peaks: 140 WARNING @ Sun, 02 Jun 2019 19:52:47: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Sun, 02 Jun 2019 19:52:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:52:48: start X-correlation... INFO @ Sun, 02 Jun 2019 19:52:48: end of X-cor INFO @ Sun, 02 Jun 2019 19:52:48: #2 finished! INFO @ Sun, 02 Jun 2019 19:52:48: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:52:48: #2 alternative fragment length(s) may be 0,20,33,92,440,464,497,552 bps INFO @ Sun, 02 Jun 2019 19:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.10_model.r WARNING @ Sun, 02 Jun 2019 19:52:48: #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 19:52:48: #2 You may need to consider one of the other alternative d(s): 0,20,33,92,440,464,497,552 WARNING @ Sun, 02 Jun 2019 19:52:48: #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 19:52:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:52:48: start X-correlation... INFO @ Sun, 02 Jun 2019 19:52:48: end of X-cor INFO @ Sun, 02 Jun 2019 19:52:48: #2 finished! INFO @ Sun, 02 Jun 2019 19:52:48: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 19:52:48: #2 alternative fragment length(s) may be 0,20,33,92,440,464,497,552 bps INFO @ Sun, 02 Jun 2019 19:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466547/SRX466547.20_model.r WARNING @ Sun, 02 Jun 2019 19:52:48: #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 19:52:48: #2 You may need to consider one of the other alternative d(s): 0,20,33,92,440,464,497,552 WARNING @ Sun, 02 Jun 2019 19:52:48: #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 19:52:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:52:48: #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 SRX466547.05.bed: No such file or directory mv: cannot stat ‘SRX466547.05.bed’: No such file or directory /var/spool/uge/at126/job_scripts/1292533: line 321: 49888 Terminated MACS $i /var/spool/uge/at126/job_scripts/1292533: line 321: 49889 Terminated MACS $i /var/spool/uge/at126/job_scripts/1292533: line 321: 49890 Terminated MACS $i mv: cannot stat ‘SRX466547.05.bb’: No such file or directory ls: cannot access SRX466547.10.bed: No such file or directory mv: cannot stat ‘SRX466547.10.bed’: No such file or directory mv: cannot stat ‘SRX466547.10.bb’: No such file or directory ls: cannot access SRX466547.20.bed: No such file or directory mv: cannot stat ‘SRX466547.20.bed’: No such file or directory mv: cannot stat ‘SRX466547.20.bb’: No such file or directory