Job ID = 1292362 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,946,188 reads read : 19,946,188 reads written : 19,946,188 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: 00:03:00 19946188 reads; of these: 19946188 (100.00%) were unpaired; of these: 14221821 (71.30%) aligned 0 times 4705747 (23.59%) aligned exactly 1 time 1018620 (5.11%) aligned >1 times 28.70% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 649225 / 5724367 = 0.1134 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 18:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.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 18:15:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:15:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.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 18:15:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:15:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.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 18:15:15: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:15:15: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:15:22: 1000000 INFO @ Sun, 02 Jun 2019 18:15:22: 1000000 INFO @ Sun, 02 Jun 2019 18:15:23: 1000000 INFO @ Sun, 02 Jun 2019 18:15:30: 2000000 INFO @ Sun, 02 Jun 2019 18:15:30: 2000000 INFO @ Sun, 02 Jun 2019 18:15:31: 2000000 INFO @ Sun, 02 Jun 2019 18:15:37: 3000000 INFO @ Sun, 02 Jun 2019 18:15:37: 3000000 INFO @ Sun, 02 Jun 2019 18:15:38: 3000000 INFO @ Sun, 02 Jun 2019 18:15:44: 4000000 INFO @ Sun, 02 Jun 2019 18:15:44: 4000000 INFO @ Sun, 02 Jun 2019 18:15:46: 4000000 INFO @ Sun, 02 Jun 2019 18:15:51: 5000000 INFO @ Sun, 02 Jun 2019 18:15:51: 5000000 INFO @ Sun, 02 Jun 2019 18:15:51: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:15:51: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:15:51: #1 total tags in treatment: 5075142 INFO @ Sun, 02 Jun 2019 18:15:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:15:51: #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 18:15:51: #1 tags after filtering in treatment: 5075142 INFO @ Sun, 02 Jun 2019 18:15:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:15:51: #1 finished! INFO @ Sun, 02 Jun 2019 18:15:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:15:51: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:15:51: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:15:51: #1 total tags in treatment: 5075142 INFO @ Sun, 02 Jun 2019 18:15:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:15:51: #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 18:15:52: #1 tags after filtering in treatment: 5075142 INFO @ Sun, 02 Jun 2019 18:15:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:15:52: #1 finished! INFO @ Sun, 02 Jun 2019 18:15:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:15:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:15:52: #2 number of paired peaks: 406 WARNING @ Sun, 02 Jun 2019 18:15:52: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sun, 02 Jun 2019 18:15:52: start model_add_line... INFO @ Sun, 02 Jun 2019 18:15:52: start X-correlation... INFO @ Sun, 02 Jun 2019 18:15:52: end of X-cor INFO @ Sun, 02 Jun 2019 18:15:52: #2 finished! INFO @ Sun, 02 Jun 2019 18:15:52: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 18:15:52: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 02 Jun 2019 18:15:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.20_model.r WARNING @ Sun, 02 Jun 2019 18:15:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:15:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 02 Jun 2019 18:15:52: #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 18:15:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:15:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:15:52: #2 number of paired peaks: 406 WARNING @ Sun, 02 Jun 2019 18:15:52: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sun, 02 Jun 2019 18:15:52: start model_add_line... INFO @ Sun, 02 Jun 2019 18:15:52: start X-correlation... INFO @ Sun, 02 Jun 2019 18:15:52: end of X-cor INFO @ Sun, 02 Jun 2019 18:15:52: #2 finished! INFO @ Sun, 02 Jun 2019 18:15:52: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 18:15:52: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 02 Jun 2019 18:15:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.10_model.r WARNING @ Sun, 02 Jun 2019 18:15:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:15:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 02 Jun 2019 18:15:52: #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 18:15:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:15:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:15:53: 5000000 INFO @ Sun, 02 Jun 2019 18:15:54: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:15:54: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:15:54: #1 total tags in treatment: 5075142 INFO @ Sun, 02 Jun 2019 18:15:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:15:54: #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 18:15:54: #1 tags after filtering in treatment: 5075142 INFO @ Sun, 02 Jun 2019 18:15:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:15:54: #1 finished! INFO @ Sun, 02 Jun 2019 18:15:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:15:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:15:54: #2 number of paired peaks: 406 WARNING @ Sun, 02 Jun 2019 18:15:54: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Sun, 02 Jun 2019 18:15:54: start model_add_line... INFO @ Sun, 02 Jun 2019 18:15:54: start X-correlation... INFO @ Sun, 02 Jun 2019 18:15:54: end of X-cor INFO @ Sun, 02 Jun 2019 18:15:54: #2 finished! INFO @ Sun, 02 Jun 2019 18:15:54: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 18:15:54: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 02 Jun 2019 18:15:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.05_model.r WARNING @ Sun, 02 Jun 2019 18:15:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:15:54: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 02 Jun 2019 18:15:54: #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 18:15:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:15:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:16:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:16:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:16:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.20_summits.bed INFO @ Sun, 02 Jun 2019 18:16:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.10_summits.bed INFO @ Sun, 02 Jun 2019 18:16:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:16:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:16:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:16:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373277/SRX373277.05_summits.bed INFO @ Sun, 02 Jun 2019 18:16:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (484 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。