Job ID = 1293126 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,786,876 reads read : 25,786,876 reads written : 25,786,876 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:20 25786876 reads; of these: 25786876 (100.00%) were unpaired; of these: 7395317 (28.68%) aligned 0 times 13557744 (52.58%) aligned exactly 1 time 4833815 (18.75%) aligned >1 times 71.32% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 5612974 / 18391559 = 0.3052 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 22:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.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 22:13:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.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 22:13:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.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 22:13:40: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:13:40: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:13:48: 1000000 INFO @ Sun, 02 Jun 2019 22:13:49: 1000000 INFO @ Sun, 02 Jun 2019 22:13:49: 1000000 INFO @ Sun, 02 Jun 2019 22:13:55: 2000000 INFO @ Sun, 02 Jun 2019 22:13:57: 2000000 INFO @ Sun, 02 Jun 2019 22:13:58: 2000000 INFO @ Sun, 02 Jun 2019 22:14:03: 3000000 INFO @ Sun, 02 Jun 2019 22:14:04: 3000000 INFO @ Sun, 02 Jun 2019 22:14:06: 3000000 INFO @ Sun, 02 Jun 2019 22:14:10: 4000000 INFO @ Sun, 02 Jun 2019 22:14:11: 4000000 INFO @ Sun, 02 Jun 2019 22:14:14: 4000000 INFO @ Sun, 02 Jun 2019 22:14:17: 5000000 INFO @ Sun, 02 Jun 2019 22:14:19: 5000000 INFO @ Sun, 02 Jun 2019 22:14:22: 5000000 INFO @ Sun, 02 Jun 2019 22:14:24: 6000000 INFO @ Sun, 02 Jun 2019 22:14:26: 6000000 INFO @ Sun, 02 Jun 2019 22:14:30: 6000000 INFO @ Sun, 02 Jun 2019 22:14:32: 7000000 INFO @ Sun, 02 Jun 2019 22:14:33: 7000000 INFO @ Sun, 02 Jun 2019 22:14:38: 7000000 INFO @ Sun, 02 Jun 2019 22:14:39: 8000000 INFO @ Sun, 02 Jun 2019 22:14:40: 8000000 INFO @ Sun, 02 Jun 2019 22:14:46: 9000000 INFO @ Sun, 02 Jun 2019 22:14:46: 8000000 INFO @ Sun, 02 Jun 2019 22:14:48: 9000000 INFO @ Sun, 02 Jun 2019 22:14:53: 10000000 INFO @ Sun, 02 Jun 2019 22:14:54: 9000000 INFO @ Sun, 02 Jun 2019 22:14:55: 10000000 INFO @ Sun, 02 Jun 2019 22:15:01: 11000000 INFO @ Sun, 02 Jun 2019 22:15:02: 11000000 INFO @ Sun, 02 Jun 2019 22:15:02: 10000000 INFO @ Sun, 02 Jun 2019 22:15:08: 12000000 INFO @ Sun, 02 Jun 2019 22:15:10: 12000000 INFO @ Sun, 02 Jun 2019 22:15:10: 11000000 INFO @ Sun, 02 Jun 2019 22:15:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:15:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:15:14: #1 total tags in treatment: 12778585 INFO @ Sun, 02 Jun 2019 22:15:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:15:14: #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 22:15:14: #1 tags after filtering in treatment: 12778585 INFO @ Sun, 02 Jun 2019 22:15:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:15:14: #1 finished! INFO @ Sun, 02 Jun 2019 22:15:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:15:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:15:15: #2 number of paired peaks: 518 WARNING @ Sun, 02 Jun 2019 22:15:15: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Sun, 02 Jun 2019 22:15:15: start model_add_line... INFO @ Sun, 02 Jun 2019 22:15:15: start X-correlation... INFO @ Sun, 02 Jun 2019 22:15:15: end of X-cor INFO @ Sun, 02 Jun 2019 22:15:15: #2 finished! INFO @ Sun, 02 Jun 2019 22:15:15: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:15:15: #2 alternative fragment length(s) may be 1,18,35,548,598 bps INFO @ Sun, 02 Jun 2019 22:15:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.10_model.r WARNING @ Sun, 02 Jun 2019 22:15:15: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:15:15: #2 You may need to consider one of the other alternative d(s): 1,18,35,548,598 WARNING @ Sun, 02 Jun 2019 22:15:15: #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 22:15:15: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:15:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:15:16: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:15:16: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:15:16: #1 total tags in treatment: 12778585 INFO @ Sun, 02 Jun 2019 22:15:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:15:16: #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 22:15:16: #1 tags after filtering in treatment: 12778585 INFO @ Sun, 02 Jun 2019 22:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:15:16: #1 finished! INFO @ Sun, 02 Jun 2019 22:15:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:15:17: #2 number of paired peaks: 518 WARNING @ Sun, 02 Jun 2019 22:15:17: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Sun, 02 Jun 2019 22:15:17: start model_add_line... INFO @ Sun, 02 Jun 2019 22:15:17: start X-correlation... INFO @ Sun, 02 Jun 2019 22:15:17: end of X-cor INFO @ Sun, 02 Jun 2019 22:15:17: #2 finished! INFO @ Sun, 02 Jun 2019 22:15:17: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:15:17: #2 alternative fragment length(s) may be 1,18,35,548,598 bps INFO @ Sun, 02 Jun 2019 22:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.05_model.r WARNING @ Sun, 02 Jun 2019 22:15:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:15:17: #2 You may need to consider one of the other alternative d(s): 1,18,35,548,598 WARNING @ Sun, 02 Jun 2019 22:15:17: #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 22:15:17: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:15:19: 12000000 INFO @ Sun, 02 Jun 2019 22:15:25: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:15:25: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:15:25: #1 total tags in treatment: 12778585 INFO @ Sun, 02 Jun 2019 22:15:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:15:25: #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 22:15:25: #1 tags after filtering in treatment: 12778585 INFO @ Sun, 02 Jun 2019 22:15:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:15:25: #1 finished! INFO @ Sun, 02 Jun 2019 22:15:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:15:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:15:27: #2 number of paired peaks: 518 WARNING @ Sun, 02 Jun 2019 22:15:27: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Sun, 02 Jun 2019 22:15:27: start model_add_line... INFO @ Sun, 02 Jun 2019 22:15:27: start X-correlation... INFO @ Sun, 02 Jun 2019 22:15:27: end of X-cor INFO @ Sun, 02 Jun 2019 22:15:27: #2 finished! INFO @ Sun, 02 Jun 2019 22:15:27: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:15:27: #2 alternative fragment length(s) may be 1,18,35,548,598 bps INFO @ Sun, 02 Jun 2019 22:15:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.20_model.r WARNING @ Sun, 02 Jun 2019 22:15:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:15:27: #2 You may need to consider one of the other alternative d(s): 1,18,35,548,598 WARNING @ Sun, 02 Jun 2019 22:15:27: #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 22:15:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:15:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:15:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:15:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:15:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.10_summits.bed INFO @ Sun, 02 Jun 2019 22:16:00: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.05_summits.bed INFO @ Sun, 02 Jun 2019 22:16:02: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:16:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402701/SRX5402701.20_summits.bed INFO @ Sun, 02 Jun 2019 22:16:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。