Job ID = 1292599 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: 171814 (0.56%) aligned 0 times 25273652 (82.09%) aligned exactly 1 time 5342683 (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] 4711375 / 30616335 = 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 20:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.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 20:02:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:02:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.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 20:02:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:02:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.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 20:02:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:02:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:02:34: 1000000 INFO @ Sun, 02 Jun 2019 20:02:35: 1000000 INFO @ Sun, 02 Jun 2019 20:02:36: 1000000 INFO @ Sun, 02 Jun 2019 20:02:40: 2000000 INFO @ Sun, 02 Jun 2019 20:02:42: 2000000 INFO @ Sun, 02 Jun 2019 20:02:44: 2000000 INFO @ Sun, 02 Jun 2019 20:02:47: 3000000 INFO @ Sun, 02 Jun 2019 20:02:49: 3000000 INFO @ Sun, 02 Jun 2019 20:02:53: 3000000 INFO @ Sun, 02 Jun 2019 20:02:54: 4000000 INFO @ Sun, 02 Jun 2019 20:02:57: 4000000 INFO @ Sun, 02 Jun 2019 20:03:01: 5000000 INFO @ Sun, 02 Jun 2019 20:03:01: 4000000 INFO @ Sun, 02 Jun 2019 20:03:04: 5000000 INFO @ Sun, 02 Jun 2019 20:03:08: 6000000 INFO @ Sun, 02 Jun 2019 20:03:10: 5000000 INFO @ Sun, 02 Jun 2019 20:03:12: 6000000 INFO @ Sun, 02 Jun 2019 20:03:14: 7000000 INFO @ Sun, 02 Jun 2019 20:03:18: 6000000 INFO @ Sun, 02 Jun 2019 20:03:19: 7000000 INFO @ Sun, 02 Jun 2019 20:03:21: 8000000 INFO @ Sun, 02 Jun 2019 20:03:27: 8000000 INFO @ Sun, 02 Jun 2019 20:03:27: 7000000 INFO @ Sun, 02 Jun 2019 20:03:28: 9000000 INFO @ Sun, 02 Jun 2019 20:03:34: 9000000 INFO @ Sun, 02 Jun 2019 20:03:34: 10000000 INFO @ Sun, 02 Jun 2019 20:03:35: 8000000 INFO @ Sun, 02 Jun 2019 20:03:41: 11000000 INFO @ Sun, 02 Jun 2019 20:03:42: 10000000 INFO @ Sun, 02 Jun 2019 20:03:44: 9000000 INFO @ Sun, 02 Jun 2019 20:03:48: 12000000 INFO @ Sun, 02 Jun 2019 20:03:49: 11000000 INFO @ Sun, 02 Jun 2019 20:03:53: 10000000 INFO @ Sun, 02 Jun 2019 20:03:55: 13000000 INFO @ Sun, 02 Jun 2019 20:03:57: 12000000 INFO @ Sun, 02 Jun 2019 20:04:02: 14000000 INFO @ Sun, 02 Jun 2019 20:04:02: 11000000 INFO @ Sun, 02 Jun 2019 20:04:04: 13000000 INFO @ Sun, 02 Jun 2019 20:04:08: 15000000 INFO @ Sun, 02 Jun 2019 20:04:10: 12000000 INFO @ Sun, 02 Jun 2019 20:04:12: 14000000 INFO @ Sun, 02 Jun 2019 20:04:15: 16000000 INFO @ Sun, 02 Jun 2019 20:04:19: 13000000 INFO @ Sun, 02 Jun 2019 20:04:19: 15000000 INFO @ Sun, 02 Jun 2019 20:04:22: 17000000 INFO @ Sun, 02 Jun 2019 20:04:27: 16000000 INFO @ Sun, 02 Jun 2019 20:04:27: 14000000 INFO @ Sun, 02 Jun 2019 20:04:29: 18000000 INFO @ Sun, 02 Jun 2019 20:04:34: 17000000 INFO @ Sun, 02 Jun 2019 20:04:35: 19000000 INFO @ Sun, 02 Jun 2019 20:04:36: 15000000 INFO @ Sun, 02 Jun 2019 20:04:42: 18000000 INFO @ Sun, 02 Jun 2019 20:04:42: 20000000 INFO @ Sun, 02 Jun 2019 20:04:45: 16000000 INFO @ Sun, 02 Jun 2019 20:04:49: 21000000 INFO @ Sun, 02 Jun 2019 20:04:49: 19000000 INFO @ Sun, 02 Jun 2019 20:04:53: 17000000 INFO @ Sun, 02 Jun 2019 20:04:55: 22000000 INFO @ Sun, 02 Jun 2019 20:04:56: 20000000 INFO @ Sun, 02 Jun 2019 20:05:02: 18000000 INFO @ Sun, 02 Jun 2019 20:05:02: 23000000 INFO @ Sun, 02 Jun 2019 20:05:04: 21000000 INFO @ Sun, 02 Jun 2019 20:05:08: 24000000 INFO @ Sun, 02 Jun 2019 20:05:10: 19000000 INFO @ Sun, 02 Jun 2019 20:05:11: 22000000 INFO @ Sun, 02 Jun 2019 20:05:15: 25000000 INFO @ Sun, 02 Jun 2019 20:05:18: 20000000 INFO @ Sun, 02 Jun 2019 20:05:18: 23000000 INFO @ Sun, 02 Jun 2019 20:05:21: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 20:05:21: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 20:05:21: #1 total tags in treatment: 25904960 INFO @ Sun, 02 Jun 2019 20:05:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:05:21: #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 20:05:22: #1 tags after filtering in treatment: 25904960 INFO @ Sun, 02 Jun 2019 20:05:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:05:22: #1 finished! INFO @ Sun, 02 Jun 2019 20:05:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:05:24: #2 number of paired peaks: 140 WARNING @ Sun, 02 Jun 2019 20:05:24: 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 20:05:24: start model_add_line... INFO @ Sun, 02 Jun 2019 20:05:24: start X-correlation... INFO @ Sun, 02 Jun 2019 20:05:24: end of X-cor INFO @ Sun, 02 Jun 2019 20:05:24: #2 finished! INFO @ Sun, 02 Jun 2019 20:05:24: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 20:05:24: #2 alternative fragment length(s) may be 0,13,15,30,98,150,308,340,361,483,488,516,549,564 bps INFO @ Sun, 02 Jun 2019 20:05:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.20_model.r WARNING @ Sun, 02 Jun 2019 20:05:24: #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 20:05:24: #2 You may need to consider one of the other alternative d(s): 0,13,15,30,98,150,308,340,361,483,488,516,549,564 WARNING @ Sun, 02 Jun 2019 20:05:24: #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 20:05:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:05:26: 24000000 INFO @ Sun, 02 Jun 2019 20:05:27: 21000000 INFO @ Sun, 02 Jun 2019 20:05:33: 25000000 INFO @ Sun, 02 Jun 2019 20:05:35: 22000000 INFO @ Sun, 02 Jun 2019 20:05:40: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 20:05:40: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 20:05:40: #1 total tags in treatment: 25904960 INFO @ Sun, 02 Jun 2019 20:05:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:05:40: #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 20:05:41: #1 tags after filtering in treatment: 25904960 INFO @ Sun, 02 Jun 2019 20:05:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:05:41: #1 finished! INFO @ Sun, 02 Jun 2019 20:05:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:05:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:05:43: #2 number of paired peaks: 140 WARNING @ Sun, 02 Jun 2019 20:05:43: 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 20:05:43: start model_add_line... INFO @ Sun, 02 Jun 2019 20:05:43: start X-correlation... INFO @ Sun, 02 Jun 2019 20:05:43: end of X-cor INFO @ Sun, 02 Jun 2019 20:05:43: #2 finished! INFO @ Sun, 02 Jun 2019 20:05:43: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 20:05:43: #2 alternative fragment length(s) may be 0,13,15,30,98,150,308,340,361,483,488,516,549,564 bps INFO @ Sun, 02 Jun 2019 20:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.05_model.r WARNING @ Sun, 02 Jun 2019 20:05:43: #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 20:05:43: #2 You may need to consider one of the other alternative d(s): 0,13,15,30,98,150,308,340,361,483,488,516,549,564 WARNING @ Sun, 02 Jun 2019 20:05:43: #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 20:05:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:05:43: 23000000 INFO @ Sun, 02 Jun 2019 20:05:52: 24000000 INFO @ Sun, 02 Jun 2019 20:06:00: 25000000 INFO @ Sun, 02 Jun 2019 20:06:07: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 20:06:07: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 20:06:07: #1 total tags in treatment: 25904960 INFO @ Sun, 02 Jun 2019 20:06:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:06:07: #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 20:06:08: #1 tags after filtering in treatment: 25904960 INFO @ Sun, 02 Jun 2019 20:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:06:08: #1 finished! INFO @ Sun, 02 Jun 2019 20:06:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:06:10: #2 number of paired peaks: 140 WARNING @ Sun, 02 Jun 2019 20:06:10: 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 20:06:10: start model_add_line... INFO @ Sun, 02 Jun 2019 20:06:10: start X-correlation... INFO @ Sun, 02 Jun 2019 20:06:10: end of X-cor INFO @ Sun, 02 Jun 2019 20:06:10: #2 finished! INFO @ Sun, 02 Jun 2019 20:06:10: #2 predicted fragment length is 0 bps INFO @ Sun, 02 Jun 2019 20:06:10: #2 alternative fragment length(s) may be 0,13,15,30,98,150,308,340,361,483,488,516,549,564 bps INFO @ Sun, 02 Jun 2019 20:06:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494848/SRX494848.10_model.r WARNING @ Sun, 02 Jun 2019 20:06:10: #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 20:06:10: #2 You may need to consider one of the other alternative d(s): 0,13,15,30,98,150,308,340,361,483,488,516,549,564 WARNING @ Sun, 02 Jun 2019 20:06:10: #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 20:06:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:06:10: #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 SRX494848.05.bed: No such file or directory mv: cannot stat ‘SRX494848.05.bed’: No such file or directory /var/spool/uge/at126/job_scripts/1292599: line 321: 52420 Terminated MACS $i /var/spool/uge/at126/job_scripts/1292599: line 321: 52421 Terminated MACS $i /var/spool/uge/at126/job_scripts/1292599: line 321: 52422 Terminated MACS $i mv: cannot stat ‘SRX494848.05.bb’: No such file or directory ls: cannot access SRX494848.10.bed: No such file or directory mv: cannot stat ‘SRX494848.10.bed’: No such file or directory mv: cannot stat ‘SRX494848.10.bb’: No such file or directory ls: cannot access SRX494848.20.bed: No such file or directory mv: cannot stat ‘SRX494848.20.bed’: No such file or directory mv: cannot stat ‘SRX494848.20.bb’: No such file or directory