Job ID = 1293251 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,907,316 reads read : 9,814,632 reads written : 4,907,316 reads 0-length : 4,907,316 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: 00:02:12 4907316 reads; of these: 4907316 (100.00%) were unpaired; of these: 869724 (17.72%) aligned 0 times 3636988 (74.11%) aligned exactly 1 time 400604 (8.16%) aligned >1 times 82.28% overall alignment rate Time searching: 00:02:12 Overall time: 00:02:12 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] 2720418 / 4037592 = 0.6738 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 22:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.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 22:36:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.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 22:36:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.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 22:36:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:29: 1000000 INFO @ Sun, 02 Jun 2019 22:36:30: 1000000 INFO @ Sun, 02 Jun 2019 22:36:32: #1 tag size is determined as 101 bps INFO @ Sun, 02 Jun 2019 22:36:32: #1 tag size = 101 INFO @ Sun, 02 Jun 2019 22:36:32: #1 total tags in treatment: 1317174 INFO @ Sun, 02 Jun 2019 22:36:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:36:32: #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 22:36:32: #1 tags after filtering in treatment: 1317174 INFO @ Sun, 02 Jun 2019 22:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:36:32: #1 finished! INFO @ Sun, 02 Jun 2019 22:36:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:36:32: 1000000 INFO @ Sun, 02 Jun 2019 22:36:32: #2 number of paired peaks: 196 WARNING @ Sun, 02 Jun 2019 22:36:32: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sun, 02 Jun 2019 22:36:32: start model_add_line... INFO @ Sun, 02 Jun 2019 22:36:32: start X-correlation... INFO @ Sun, 02 Jun 2019 22:36:32: end of X-cor INFO @ Sun, 02 Jun 2019 22:36:32: #2 finished! INFO @ Sun, 02 Jun 2019 22:36:32: #2 predicted fragment length is 102 bps INFO @ Sun, 02 Jun 2019 22:36:32: #2 alternative fragment length(s) may be 102,574 bps INFO @ Sun, 02 Jun 2019 22:36:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.05_model.r WARNING @ Sun, 02 Jun 2019 22:36:32: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:36:32: #2 You may need to consider one of the other alternative d(s): 102,574 WARNING @ Sun, 02 Jun 2019 22:36:32: #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 22:36:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:36:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:36:33: #1 tag size is determined as 101 bps INFO @ Sun, 02 Jun 2019 22:36:33: #1 tag size = 101 INFO @ Sun, 02 Jun 2019 22:36:33: #1 total tags in treatment: 1317174 INFO @ Sun, 02 Jun 2019 22:36:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:36:33: #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 22:36:33: #1 tags after filtering in treatment: 1317174 INFO @ Sun, 02 Jun 2019 22:36:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:36:33: #1 finished! INFO @ Sun, 02 Jun 2019 22:36:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:36:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:36:34: #2 number of paired peaks: 196 WARNING @ Sun, 02 Jun 2019 22:36:34: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sun, 02 Jun 2019 22:36:34: start model_add_line... INFO @ Sun, 02 Jun 2019 22:36:34: start X-correlation... INFO @ Sun, 02 Jun 2019 22:36:34: end of X-cor INFO @ Sun, 02 Jun 2019 22:36:34: #2 finished! INFO @ Sun, 02 Jun 2019 22:36:34: #2 predicted fragment length is 102 bps INFO @ Sun, 02 Jun 2019 22:36:34: #2 alternative fragment length(s) may be 102,574 bps INFO @ Sun, 02 Jun 2019 22:36:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.20_model.r WARNING @ Sun, 02 Jun 2019 22:36:34: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:36:34: #2 You may need to consider one of the other alternative d(s): 102,574 WARNING @ Sun, 02 Jun 2019 22:36:34: #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 22:36:34: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:36:36: #1 tag size is determined as 101 bps INFO @ Sun, 02 Jun 2019 22:36:36: #1 tag size = 101 INFO @ Sun, 02 Jun 2019 22:36:36: #1 total tags in treatment: 1317174 INFO @ Sun, 02 Jun 2019 22:36:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:36:36: #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 22:36:36: #1 tags after filtering in treatment: 1317174 INFO @ Sun, 02 Jun 2019 22:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:36:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:36:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:36:36: #2 number of paired peaks: 196 WARNING @ Sun, 02 Jun 2019 22:36:36: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Sun, 02 Jun 2019 22:36:36: start model_add_line... INFO @ Sun, 02 Jun 2019 22:36:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:36:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:36:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:36:36: #2 predicted fragment length is 102 bps INFO @ Sun, 02 Jun 2019 22:36:36: #2 alternative fragment length(s) may be 102,574 bps INFO @ Sun, 02 Jun 2019 22:36:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.10_model.r WARNING @ Sun, 02 Jun 2019 22:36:36: #2 Since the d (102) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:36:36: #2 You may need to consider one of the other alternative d(s): 102,574 WARNING @ Sun, 02 Jun 2019 22:36:36: #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 22:36:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:36:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:36:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:36:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:36:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:36:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:36:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.05_summits.bed INFO @ Sun, 02 Jun 2019 22:36:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.20_summits.bed INFO @ Sun, 02 Jun 2019 22:36:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:36:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:36:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:36:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:36:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX560679/SRX560679.10_summits.bed INFO @ Sun, 02 Jun 2019 22:36:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (89 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。