Job ID = 1292957 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,222,456 reads read : 4,222,456 reads written : 4,222,456 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: 00:01:03 4222456 reads; of these: 4222456 (100.00%) were unpaired; of these: 771050 (18.26%) aligned 0 times 2835779 (67.16%) aligned exactly 1 time 615627 (14.58%) aligned >1 times 81.74% overall alignment rate Time searching: 00:01:03 Overall time: 00:01:03 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] 230321 / 3451406 = 0.0667 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 21:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.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 21:12:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:12:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.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 21:12:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:12:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.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 21:12:08: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:12:08: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:12:18: 1000000 INFO @ Sun, 02 Jun 2019 21:12:19: 1000000 INFO @ Sun, 02 Jun 2019 21:12:19: 1000000 INFO @ Sun, 02 Jun 2019 21:12:28: 2000000 INFO @ Sun, 02 Jun 2019 21:12:30: 2000000 INFO @ Sun, 02 Jun 2019 21:12:30: 2000000 INFO @ Sun, 02 Jun 2019 21:12:38: 3000000 INFO @ Sun, 02 Jun 2019 21:12:40: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:12:40: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:12:40: #1 total tags in treatment: 3221085 INFO @ Sun, 02 Jun 2019 21:12:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:12:40: #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 21:12:40: #1 tags after filtering in treatment: 3221085 INFO @ Sun, 02 Jun 2019 21:12:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:12:40: #1 finished! INFO @ Sun, 02 Jun 2019 21:12:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:12:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:12:40: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 21:12:40: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 02 Jun 2019 21:12:40: start model_add_line... INFO @ Sun, 02 Jun 2019 21:12:41: start X-correlation... INFO @ Sun, 02 Jun 2019 21:12:41: end of X-cor INFO @ Sun, 02 Jun 2019 21:12:41: #2 finished! INFO @ Sun, 02 Jun 2019 21:12:41: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 21:12:41: #2 alternative fragment length(s) may be 53,573 bps INFO @ Sun, 02 Jun 2019 21:12:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.05_model.r WARNING @ Sun, 02 Jun 2019 21:12:41: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:12:41: #2 You may need to consider one of the other alternative d(s): 53,573 WARNING @ Sun, 02 Jun 2019 21:12:41: #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 21:12:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:12:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:12:41: 3000000 INFO @ Sun, 02 Jun 2019 21:12:41: 3000000 INFO @ Sun, 02 Jun 2019 21:12:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:12:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:12:43: #1 total tags in treatment: 3221085 INFO @ Sun, 02 Jun 2019 21:12:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:12:43: #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 21:12:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:12:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:12:43: #1 total tags in treatment: 3221085 INFO @ Sun, 02 Jun 2019 21:12:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:12:43: #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 21:12:43: #1 tags after filtering in treatment: 3221085 INFO @ Sun, 02 Jun 2019 21:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:12:43: #1 finished! INFO @ Sun, 02 Jun 2019 21:12:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:12:43: #1 tags after filtering in treatment: 3221085 INFO @ Sun, 02 Jun 2019 21:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:12:43: #1 finished! INFO @ Sun, 02 Jun 2019 21:12:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:12:43: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 21:12:43: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 02 Jun 2019 21:12:43: start model_add_line... INFO @ Sun, 02 Jun 2019 21:12:44: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 21:12:44: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Sun, 02 Jun 2019 21:12:44: start model_add_line... INFO @ Sun, 02 Jun 2019 21:12:44: start X-correlation... INFO @ Sun, 02 Jun 2019 21:12:44: end of X-cor INFO @ Sun, 02 Jun 2019 21:12:44: #2 finished! INFO @ Sun, 02 Jun 2019 21:12:44: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 21:12:44: #2 alternative fragment length(s) may be 53,573 bps INFO @ Sun, 02 Jun 2019 21:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.20_model.r INFO @ Sun, 02 Jun 2019 21:12:44: start X-correlation... WARNING @ Sun, 02 Jun 2019 21:12:44: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:12:44: #2 You may need to consider one of the other alternative d(s): 53,573 WARNING @ Sun, 02 Jun 2019 21:12:44: #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 21:12:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:12:44: end of X-cor INFO @ Sun, 02 Jun 2019 21:12:44: #2 finished! INFO @ Sun, 02 Jun 2019 21:12:44: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 21:12:44: #2 alternative fragment length(s) may be 53,573 bps INFO @ Sun, 02 Jun 2019 21:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.10_model.r WARNING @ Sun, 02 Jun 2019 21:12:44: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:12:44: #2 You may need to consider one of the other alternative d(s): 53,573 WARNING @ Sun, 02 Jun 2019 21:12:44: #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 21:12:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:12:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:12:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:12:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:12:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:12:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:12:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.05_summits.bed INFO @ Sun, 02 Jun 2019 21:12:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.20_summits.bed INFO @ Sun, 02 Jun 2019 21:12:59: Done! INFO @ Sun, 02 Jun 2019 21:12:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:12:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.10_peaks.narrowPeak pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (88 records, 4 fields): 2 millis INFO @ Sun, 02 Jun 2019 21:12:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020739/SRX5020739.10_summits.bed INFO @ Sun, 02 Jun 2019 21:12:59: Done! CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。