Job ID = 4303037 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,289,633 reads read : 3,289,633 reads written : 3,289,633 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1164518.sra.cache’: 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: 00:00:16 3289633 reads; of these: 3289633 (100.00%) were unpaired; of these: 2255797 (68.57%) aligned 0 times 854610 (25.98%) aligned exactly 1 time 179226 (5.45%) aligned >1 times 31.43% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:17 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_rmdupse_core] 214226 / 1033836 = 0.2072 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:32:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.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 @ Thu, 12 Dec 2019 00:32:50: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:32:50: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:32:54: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:32:54: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:32:54: #1 total tags in treatment: 819610 INFO @ Thu, 12 Dec 2019 00:32:54: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:32:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:32:54: #1 tags after filtering in treatment: 819610 INFO @ Thu, 12 Dec 2019 00:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:32:54: #1 finished! INFO @ Thu, 12 Dec 2019 00:32:54: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:32:54: #2 number of paired peaks: 507 WARNING @ Thu, 12 Dec 2019 00:32:54: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Thu, 12 Dec 2019 00:32:54: start model_add_line... INFO @ Thu, 12 Dec 2019 00:32:54: start X-correlation... INFO @ Thu, 12 Dec 2019 00:32:54: end of X-cor INFO @ Thu, 12 Dec 2019 00:32:54: #2 finished! INFO @ Thu, 12 Dec 2019 00:32:54: #2 predicted fragment length is 52 bps INFO @ Thu, 12 Dec 2019 00:32:54: #2 alternative fragment length(s) may be 35,52,97,123,440,545,567 bps INFO @ Thu, 12 Dec 2019 00:32:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.05_model.r WARNING @ Thu, 12 Dec 2019 00:32:54: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:32:54: #2 You may need to consider one of the other alternative d(s): 35,52,97,123,440,545,567 WARNING @ Thu, 12 Dec 2019 00:32:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:32:54: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:32:56: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:32:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:32:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:32:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.05_summits.bed INFO @ Thu, 12 Dec 2019 00:32:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (115 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.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 @ Thu, 12 Dec 2019 00:33:18: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:33:18: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:33:23: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:33:23: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:33:23: #1 total tags in treatment: 819610 INFO @ Thu, 12 Dec 2019 00:33:23: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:33:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:33:23: #1 tags after filtering in treatment: 819610 INFO @ Thu, 12 Dec 2019 00:33:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:33:23: #1 finished! INFO @ Thu, 12 Dec 2019 00:33:23: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:33:23: #2 number of paired peaks: 507 WARNING @ Thu, 12 Dec 2019 00:33:23: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Thu, 12 Dec 2019 00:33:23: start model_add_line... INFO @ Thu, 12 Dec 2019 00:33:23: start X-correlation... INFO @ Thu, 12 Dec 2019 00:33:23: end of X-cor INFO @ Thu, 12 Dec 2019 00:33:23: #2 finished! INFO @ Thu, 12 Dec 2019 00:33:23: #2 predicted fragment length is 52 bps INFO @ Thu, 12 Dec 2019 00:33:23: #2 alternative fragment length(s) may be 35,52,97,123,440,545,567 bps INFO @ Thu, 12 Dec 2019 00:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.10_model.r WARNING @ Thu, 12 Dec 2019 00:33:23: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:33:23: #2 You may need to consider one of the other alternative d(s): 35,52,97,123,440,545,567 WARNING @ Thu, 12 Dec 2019 00:33:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:33:23: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:33:24: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:33:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:33:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:33:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.10_summits.bed INFO @ Thu, 12 Dec 2019 00:33:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:33:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.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 @ Thu, 12 Dec 2019 00:33:48: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:33:48: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:33:52: #1 tag size is determined as 32 bps INFO @ Thu, 12 Dec 2019 00:33:52: #1 tag size = 32 INFO @ Thu, 12 Dec 2019 00:33:52: #1 total tags in treatment: 819610 INFO @ Thu, 12 Dec 2019 00:33:52: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:33:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:33:52: #1 tags after filtering in treatment: 819610 INFO @ Thu, 12 Dec 2019 00:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:33:52: #1 finished! INFO @ Thu, 12 Dec 2019 00:33:52: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:33:52: #2 number of paired peaks: 507 WARNING @ Thu, 12 Dec 2019 00:33:52: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Thu, 12 Dec 2019 00:33:52: start model_add_line... INFO @ Thu, 12 Dec 2019 00:33:52: start X-correlation... INFO @ Thu, 12 Dec 2019 00:33:52: end of X-cor INFO @ Thu, 12 Dec 2019 00:33:52: #2 finished! INFO @ Thu, 12 Dec 2019 00:33:52: #2 predicted fragment length is 52 bps INFO @ Thu, 12 Dec 2019 00:33:52: #2 alternative fragment length(s) may be 35,52,97,123,440,545,567 bps INFO @ Thu, 12 Dec 2019 00:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.20_model.r WARNING @ Thu, 12 Dec 2019 00:33:52: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:33:52: #2 You may need to consider one of the other alternative d(s): 35,52,97,123,440,545,567 WARNING @ Thu, 12 Dec 2019 00:33:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:33:52: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:33:54: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:33:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:33:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:33:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467094/SRX467094.20_summits.bed INFO @ Thu, 12 Dec 2019 00:33:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。