Job ID = 1292363 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,005,065 reads read : 29,005,065 reads written : 29,005,065 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: 00:03:47 29005065 reads; of these: 29005065 (100.00%) were unpaired; of these: 25106865 (86.56%) aligned 0 times 3214767 (11.08%) aligned exactly 1 time 683433 (2.36%) aligned >1 times 13.44% overall alignment rate Time searching: 00:03:47 Overall time: 00:03:47 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] 205537 / 3898200 = 0.0527 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 18:21:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.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 18:21:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.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 18:21:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.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 18:21:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:21:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:21:52: 1000000 INFO @ Sun, 02 Jun 2019 18:21:52: 1000000 INFO @ Sun, 02 Jun 2019 18:21:54: 1000000 INFO @ Sun, 02 Jun 2019 18:21:59: 2000000 INFO @ Sun, 02 Jun 2019 18:21:59: 2000000 INFO @ Sun, 02 Jun 2019 18:22:02: 2000000 INFO @ Sun, 02 Jun 2019 18:22:06: 3000000 INFO @ Sun, 02 Jun 2019 18:22:06: 3000000 INFO @ Sun, 02 Jun 2019 18:22:10: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:22:10: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:22:10: #1 total tags in treatment: 3692663 INFO @ Sun, 02 Jun 2019 18:22:10: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:22:10: #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 18:22:10: #1 tags after filtering in treatment: 3692663 INFO @ Sun, 02 Jun 2019 18:22:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:22:10: #1 finished! INFO @ Sun, 02 Jun 2019 18:22:10: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:22:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:22:11: #2 number of paired peaks: 361 WARNING @ Sun, 02 Jun 2019 18:22:11: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 02 Jun 2019 18:22:11: start model_add_line... INFO @ Sun, 02 Jun 2019 18:22:11: start X-correlation... INFO @ Sun, 02 Jun 2019 18:22:11: end of X-cor INFO @ Sun, 02 Jun 2019 18:22:11: #2 finished! INFO @ Sun, 02 Jun 2019 18:22:11: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 18:22:11: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 02 Jun 2019 18:22:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.10_model.r WARNING @ Sun, 02 Jun 2019 18:22:11: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:22:11: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 02 Jun 2019 18:22:11: #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 18:22:11: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:22:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:22:11: 3000000 INFO @ Sun, 02 Jun 2019 18:22:12: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:22:12: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:22:12: #1 total tags in treatment: 3692663 INFO @ Sun, 02 Jun 2019 18:22:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:22:12: #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 18:22:12: #1 tags after filtering in treatment: 3692663 INFO @ Sun, 02 Jun 2019 18:22:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:22:12: #1 finished! INFO @ Sun, 02 Jun 2019 18:22:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:22:12: #2 number of paired peaks: 361 WARNING @ Sun, 02 Jun 2019 18:22:12: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 02 Jun 2019 18:22:12: start model_add_line... INFO @ Sun, 02 Jun 2019 18:22:12: start X-correlation... INFO @ Sun, 02 Jun 2019 18:22:12: end of X-cor INFO @ Sun, 02 Jun 2019 18:22:12: #2 finished! INFO @ Sun, 02 Jun 2019 18:22:12: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 18:22:12: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 02 Jun 2019 18:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.05_model.r WARNING @ Sun, 02 Jun 2019 18:22:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:22:12: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 02 Jun 2019 18:22:12: #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 18:22:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:22:17: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:22:17: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:22:17: #1 total tags in treatment: 3692663 INFO @ Sun, 02 Jun 2019 18:22:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:22:17: #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 18:22:18: #1 tags after filtering in treatment: 3692663 INFO @ Sun, 02 Jun 2019 18:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:22:18: #1 finished! INFO @ Sun, 02 Jun 2019 18:22:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:22:18: #2 number of paired peaks: 361 WARNING @ Sun, 02 Jun 2019 18:22:18: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 02 Jun 2019 18:22:18: start model_add_line... INFO @ Sun, 02 Jun 2019 18:22:18: start X-correlation... INFO @ Sun, 02 Jun 2019 18:22:18: end of X-cor INFO @ Sun, 02 Jun 2019 18:22:18: #2 finished! INFO @ Sun, 02 Jun 2019 18:22:18: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 18:22:18: #2 alternative fragment length(s) may be 50 bps INFO @ Sun, 02 Jun 2019 18:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.20_model.r WARNING @ Sun, 02 Jun 2019 18:22:18: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:22:18: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sun, 02 Jun 2019 18:22:18: #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 18:22:18: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:22:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:22:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:22:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:22:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:22:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.10_summits.bed INFO @ Sun, 02 Jun 2019 18:22:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.05_summits.bed INFO @ Sun, 02 Jun 2019 18:22:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:22:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373278/SRX373278.20_summits.bed INFO @ Sun, 02 Jun 2019 18:22:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。