Job ID = 1292041 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,905,418 reads read : 27,905,418 reads written : 27,905,418 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: 00:04:27 27905418 reads; of these: 27905418 (100.00%) were unpaired; of these: 684387 (2.45%) aligned 0 times 22383554 (80.21%) aligned exactly 1 time 4837477 (17.34%) aligned >1 times 97.55% overall alignment rate Time searching: 00:04:27 Overall time: 00:04:27 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] 5233384 / 27221031 = 0.1923 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 17:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.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 17:31:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.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 17:31:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.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 17:31:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:31:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:31:23: 1000000 INFO @ Sun, 02 Jun 2019 17:31:24: 1000000 INFO @ Sun, 02 Jun 2019 17:31:24: 1000000 INFO @ Sun, 02 Jun 2019 17:31:31: 2000000 INFO @ Sun, 02 Jun 2019 17:31:31: 2000000 INFO @ Sun, 02 Jun 2019 17:31:33: 2000000 INFO @ Sun, 02 Jun 2019 17:31:38: 3000000 INFO @ Sun, 02 Jun 2019 17:31:39: 3000000 INFO @ Sun, 02 Jun 2019 17:31:41: 3000000 INFO @ Sun, 02 Jun 2019 17:31:46: 4000000 INFO @ Sun, 02 Jun 2019 17:31:46: 4000000 INFO @ Sun, 02 Jun 2019 17:31:49: 4000000 INFO @ Sun, 02 Jun 2019 17:31:53: 5000000 INFO @ Sun, 02 Jun 2019 17:31:54: 5000000 INFO @ Sun, 02 Jun 2019 17:31:58: 5000000 INFO @ Sun, 02 Jun 2019 17:32:01: 6000000 INFO @ Sun, 02 Jun 2019 17:32:01: 6000000 INFO @ Sun, 02 Jun 2019 17:32:06: 6000000 INFO @ Sun, 02 Jun 2019 17:32:08: 7000000 INFO @ Sun, 02 Jun 2019 17:32:09: 7000000 INFO @ Sun, 02 Jun 2019 17:32:14: 7000000 INFO @ Sun, 02 Jun 2019 17:32:16: 8000000 INFO @ Sun, 02 Jun 2019 17:32:16: 8000000 INFO @ Sun, 02 Jun 2019 17:32:22: 8000000 INFO @ Sun, 02 Jun 2019 17:32:23: 9000000 INFO @ Sun, 02 Jun 2019 17:32:23: 9000000 INFO @ Sun, 02 Jun 2019 17:32:31: 9000000 INFO @ Sun, 02 Jun 2019 17:32:31: 10000000 INFO @ Sun, 02 Jun 2019 17:32:31: 10000000 INFO @ Sun, 02 Jun 2019 17:32:38: 11000000 INFO @ Sun, 02 Jun 2019 17:32:39: 10000000 INFO @ Sun, 02 Jun 2019 17:32:39: 11000000 INFO @ Sun, 02 Jun 2019 17:32:45: 12000000 INFO @ Sun, 02 Jun 2019 17:32:47: 12000000 INFO @ Sun, 02 Jun 2019 17:32:47: 11000000 INFO @ Sun, 02 Jun 2019 17:32:53: 13000000 INFO @ Sun, 02 Jun 2019 17:32:55: 13000000 INFO @ Sun, 02 Jun 2019 17:32:55: 12000000 INFO @ Sun, 02 Jun 2019 17:33:00: 14000000 INFO @ Sun, 02 Jun 2019 17:33:03: 14000000 INFO @ Sun, 02 Jun 2019 17:33:03: 13000000 INFO @ Sun, 02 Jun 2019 17:33:07: 15000000 INFO @ Sun, 02 Jun 2019 17:33:10: 15000000 INFO @ Sun, 02 Jun 2019 17:33:11: 14000000 INFO @ Sun, 02 Jun 2019 17:33:15: 16000000 INFO @ Sun, 02 Jun 2019 17:33:18: 16000000 INFO @ Sun, 02 Jun 2019 17:33:20: 15000000 INFO @ Sun, 02 Jun 2019 17:33:23: 17000000 INFO @ Sun, 02 Jun 2019 17:33:25: 17000000 INFO @ Sun, 02 Jun 2019 17:33:28: 16000000 INFO @ Sun, 02 Jun 2019 17:33:30: 18000000 INFO @ Sun, 02 Jun 2019 17:33:33: 18000000 INFO @ Sun, 02 Jun 2019 17:33:37: 17000000 INFO @ Sun, 02 Jun 2019 17:33:38: 19000000 INFO @ Sun, 02 Jun 2019 17:33:40: 19000000 INFO @ Sun, 02 Jun 2019 17:33:45: 20000000 INFO @ Sun, 02 Jun 2019 17:33:45: 18000000 INFO @ Sun, 02 Jun 2019 17:33:48: 20000000 INFO @ Sun, 02 Jun 2019 17:33:53: 21000000 INFO @ Sun, 02 Jun 2019 17:33:54: 19000000 INFO @ Sun, 02 Jun 2019 17:33:55: 21000000 INFO @ Sun, 02 Jun 2019 17:34:00: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 17:34:00: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 17:34:00: #1 total tags in treatment: 21987647 INFO @ Sun, 02 Jun 2019 17:34:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:34:00: #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 17:34:01: #1 tags after filtering in treatment: 21987647 INFO @ Sun, 02 Jun 2019 17:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:34:01: #1 finished! INFO @ Sun, 02 Jun 2019 17:34:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:34:02: 20000000 INFO @ Sun, 02 Jun 2019 17:34:02: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 17:34:02: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 17:34:02: #1 total tags in treatment: 21987647 INFO @ Sun, 02 Jun 2019 17:34:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:34:02: #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 17:34:03: #2 number of paired peaks: 149 WARNING @ Sun, 02 Jun 2019 17:34:03: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sun, 02 Jun 2019 17:34:03: start model_add_line... INFO @ Sun, 02 Jun 2019 17:34:03: start X-correlation... INFO @ Sun, 02 Jun 2019 17:34:03: end of X-cor INFO @ Sun, 02 Jun 2019 17:34:03: #2 finished! INFO @ Sun, 02 Jun 2019 17:34:03: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 17:34:03: #2 alternative fragment length(s) may be 0,26,326,533,560 bps INFO @ Sun, 02 Jun 2019 17:34:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.20_model.r WARNING @ Sun, 02 Jun 2019 17:34:03: #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 17:34:03: #2 You may need to consider one of the other alternative d(s): 0,26,326,533,560 WARNING @ Sun, 02 Jun 2019 17:34:03: #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 17:34:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:34:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:34:03: #1 tags after filtering in treatment: 21987647 INFO @ Sun, 02 Jun 2019 17:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:34:03: #1 finished! INFO @ Sun, 02 Jun 2019 17:34:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:34:05: #2 number of paired peaks: 149 WARNING @ Sun, 02 Jun 2019 17:34:05: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sun, 02 Jun 2019 17:34:05: start model_add_line... INFO @ Sun, 02 Jun 2019 17:34:05: start X-correlation... INFO @ Sun, 02 Jun 2019 17:34:05: end of X-cor INFO @ Sun, 02 Jun 2019 17:34:05: #2 finished! INFO @ Sun, 02 Jun 2019 17:34:05: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 17:34:05: #2 alternative fragment length(s) may be 0,26,326,533,560 bps INFO @ Sun, 02 Jun 2019 17:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.05_model.r WARNING @ Sun, 02 Jun 2019 17:34:05: #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 17:34:05: #2 You may need to consider one of the other alternative d(s): 0,26,326,533,560 WARNING @ Sun, 02 Jun 2019 17:34:05: #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 17:34:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:34:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:34:10: 21000000 INFO @ Sun, 02 Jun 2019 17:34:18: #1 tag size is determined as 28 bps INFO @ Sun, 02 Jun 2019 17:34:18: #1 tag size = 28 INFO @ Sun, 02 Jun 2019 17:34:18: #1 total tags in treatment: 21987647 INFO @ Sun, 02 Jun 2019 17:34:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:34:18: #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 17:34:19: #1 tags after filtering in treatment: 21987647 INFO @ Sun, 02 Jun 2019 17:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:34:19: #1 finished! INFO @ Sun, 02 Jun 2019 17:34:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:34:21: #2 number of paired peaks: 149 WARNING @ Sun, 02 Jun 2019 17:34:21: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sun, 02 Jun 2019 17:34:21: start model_add_line... INFO @ Sun, 02 Jun 2019 17:34:21: start X-correlation... INFO @ Sun, 02 Jun 2019 17:34:21: end of X-cor INFO @ Sun, 02 Jun 2019 17:34:21: #2 finished! INFO @ Sun, 02 Jun 2019 17:34:21: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 17:34:21: #2 alternative fragment length(s) may be 0,26,326,533,560 bps INFO @ Sun, 02 Jun 2019 17:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX323687/SRX323687.10_model.r WARNING @ Sun, 02 Jun 2019 17:34:21: #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 17:34:21: #2 You may need to consider one of the other alternative d(s): 0,26,326,533,560 WARNING @ Sun, 02 Jun 2019 17:34:21: #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 17:34:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:34:21: #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 SRX323687.05.bed: No such file or directory mv: cannot stat ‘SRX323687.05.bed’: No such file or directory /var/spool/uge/at085/job_scripts/1292041: line 321: 50134 Terminated MACS $i /var/spool/uge/at085/job_scripts/1292041: line 321: 50135 Terminated MACS $i /var/spool/uge/at085/job_scripts/1292041: line 321: 50136 Terminated MACS $i mv: cannot stat ‘SRX323687.05.bb’: No such file or directory ls: cannot access SRX323687.10.bed: No such file or directory mv: cannot stat ‘SRX323687.10.bed’: No such file or directory mv: cannot stat ‘SRX323687.10.bb’: No such file or directory ls: cannot access SRX323687.20.bed: No such file or directory mv: cannot stat ‘SRX323687.20.bed’: No such file or directory mv: cannot stat ‘SRX323687.20.bb’: No such file or directory