Job ID = 1293211 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,798,811 reads read : 29,798,811 reads written : 29,798,811 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: 00:07:18 29798811 reads; of these: 29798811 (100.00%) were unpaired; of these: 5695976 (19.11%) aligned 0 times 19767430 (66.34%) aligned exactly 1 time 4335405 (14.55%) aligned >1 times 80.89% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 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 12 files... [bam_rmdupse_core] 5256950 / 24102835 = 0.2181 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 22:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.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 22:39:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:39:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.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 22:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.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 22:39:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:39:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:39:31: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:39:31: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:39:38: 1000000 INFO @ Sun, 02 Jun 2019 22:39:40: 1000000 INFO @ Sun, 02 Jun 2019 22:39:40: 1000000 INFO @ Sun, 02 Jun 2019 22:39:45: 2000000 INFO @ Sun, 02 Jun 2019 22:39:49: 2000000 INFO @ Sun, 02 Jun 2019 22:39:49: 2000000 INFO @ Sun, 02 Jun 2019 22:39:52: 3000000 INFO @ Sun, 02 Jun 2019 22:39:58: 3000000 INFO @ Sun, 02 Jun 2019 22:39:58: 4000000 INFO @ Sun, 02 Jun 2019 22:39:58: 3000000 INFO @ Sun, 02 Jun 2019 22:40:05: 5000000 INFO @ Sun, 02 Jun 2019 22:40:07: 4000000 INFO @ Sun, 02 Jun 2019 22:40:07: 4000000 INFO @ Sun, 02 Jun 2019 22:40:12: 6000000 INFO @ Sun, 02 Jun 2019 22:40:16: 5000000 INFO @ Sun, 02 Jun 2019 22:40:16: 5000000 INFO @ Sun, 02 Jun 2019 22:40:18: 7000000 INFO @ Sun, 02 Jun 2019 22:40:24: 6000000 INFO @ Sun, 02 Jun 2019 22:40:24: 6000000 INFO @ Sun, 02 Jun 2019 22:40:25: 8000000 INFO @ Sun, 02 Jun 2019 22:40:32: 9000000 INFO @ Sun, 02 Jun 2019 22:40:33: 7000000 INFO @ Sun, 02 Jun 2019 22:40:33: 7000000 INFO @ Sun, 02 Jun 2019 22:40:38: 10000000 INFO @ Sun, 02 Jun 2019 22:40:42: 8000000 INFO @ Sun, 02 Jun 2019 22:40:42: 8000000 INFO @ Sun, 02 Jun 2019 22:40:45: 11000000 INFO @ Sun, 02 Jun 2019 22:40:51: 9000000 INFO @ Sun, 02 Jun 2019 22:40:51: 9000000 INFO @ Sun, 02 Jun 2019 22:40:52: 12000000 INFO @ Sun, 02 Jun 2019 22:40:59: 13000000 INFO @ Sun, 02 Jun 2019 22:41:00: 10000000 INFO @ Sun, 02 Jun 2019 22:41:00: 10000000 INFO @ Sun, 02 Jun 2019 22:41:06: 14000000 INFO @ Sun, 02 Jun 2019 22:41:08: 11000000 INFO @ Sun, 02 Jun 2019 22:41:09: 11000000 INFO @ Sun, 02 Jun 2019 22:41:14: 15000000 INFO @ Sun, 02 Jun 2019 22:41:17: 12000000 INFO @ Sun, 02 Jun 2019 22:41:17: 12000000 INFO @ Sun, 02 Jun 2019 22:41:20: 16000000 INFO @ Sun, 02 Jun 2019 22:41:25: 13000000 INFO @ Sun, 02 Jun 2019 22:41:26: 13000000 INFO @ Sun, 02 Jun 2019 22:41:27: 17000000 INFO @ Sun, 02 Jun 2019 22:41:34: 14000000 INFO @ Sun, 02 Jun 2019 22:41:34: 18000000 INFO @ Sun, 02 Jun 2019 22:41:34: 14000000 INFO @ Sun, 02 Jun 2019 22:41:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:41:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:41:40: #1 total tags in treatment: 18845885 INFO @ Sun, 02 Jun 2019 22:41:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:41:40: #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 22:41:40: #1 tags after filtering in treatment: 18845885 INFO @ Sun, 02 Jun 2019 22:41:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:41:40: #1 finished! INFO @ Sun, 02 Jun 2019 22:41:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:41:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:41:42: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 22:41:42: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 22:41:42: start model_add_line... INFO @ Sun, 02 Jun 2019 22:41:42: 15000000 INFO @ Sun, 02 Jun 2019 22:41:42: start X-correlation... INFO @ Sun, 02 Jun 2019 22:41:42: end of X-cor INFO @ Sun, 02 Jun 2019 22:41:42: #2 finished! INFO @ Sun, 02 Jun 2019 22:41:42: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:41:42: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sun, 02 Jun 2019 22:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.20_model.r WARNING @ Sun, 02 Jun 2019 22:41:42: #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 22:41:42: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sun, 02 Jun 2019 22:41:42: #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 22:41:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:41:43: 15000000 INFO @ Sun, 02 Jun 2019 22:41:50: 16000000 INFO @ Sun, 02 Jun 2019 22:41:51: 16000000 INFO @ Sun, 02 Jun 2019 22:41:58: 17000000 INFO @ Sun, 02 Jun 2019 22:42:00: 17000000 INFO @ Sun, 02 Jun 2019 22:42:06: 18000000 INFO @ Sun, 02 Jun 2019 22:42:08: 18000000 INFO @ Sun, 02 Jun 2019 22:42:14: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:14: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:14: #1 total tags in treatment: 18845885 INFO @ Sun, 02 Jun 2019 22:42:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:14: #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 22:42:14: #1 tags after filtering in treatment: 18845885 INFO @ Sun, 02 Jun 2019 22:42:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:14: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:15: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 22:42:15: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 22:42:15: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:16: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:42:16: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:42:16: #1 total tags in treatment: 18845885 INFO @ Sun, 02 Jun 2019 22:42:16: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:42:16: #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 22:42:16: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:16: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:16: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:16: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:42:16: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sun, 02 Jun 2019 22:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.05_model.r WARNING @ Sun, 02 Jun 2019 22:42:16: #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 22:42:16: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sun, 02 Jun 2019 22:42:16: #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 22:42:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:16: #1 tags after filtering in treatment: 18845885 INFO @ Sun, 02 Jun 2019 22:42:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:42:16: #1 finished! INFO @ Sun, 02 Jun 2019 22:42:16: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:42:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:42:18: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 22:42:18: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 22:42:18: start model_add_line... INFO @ Sun, 02 Jun 2019 22:42:18: start X-correlation... INFO @ Sun, 02 Jun 2019 22:42:18: end of X-cor INFO @ Sun, 02 Jun 2019 22:42:18: #2 finished! INFO @ Sun, 02 Jun 2019 22:42:18: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:42:18: #2 alternative fragment length(s) may be 1,39 bps INFO @ Sun, 02 Jun 2019 22:42:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.10_model.r WARNING @ Sun, 02 Jun 2019 22:42:18: #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 22:42:18: #2 You may need to consider one of the other alternative d(s): 1,39 WARNING @ Sun, 02 Jun 2019 22:42:18: #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 22:42:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:42:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:42:24: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.20_summits.bed INFO @ Sun, 02 Jun 2019 22:42:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:42:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.05_summits.bed INFO @ Sun, 02 Jun 2019 22:43:16: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402761/SRX5402761.10_summits.bed INFO @ Sun, 02 Jun 2019 22:43:18: Done! pass1 - making usageList (0 chroms): 2 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。