Job ID = 1292919 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,760,716 reads read : 8,760,716 reads written : 8,760,716 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: 00:02:15 8760716 reads; of these: 8760716 (100.00%) were unpaired; of these: 224515 (2.56%) aligned 0 times 7015108 (80.07%) aligned exactly 1 time 1521093 (17.36%) aligned >1 times 97.44% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 518556 / 8536201 = 0.0607 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 21:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.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 21:09:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.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 21:09:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.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 21:09:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:20: 1000000 INFO @ Sun, 02 Jun 2019 21:09:21: 1000000 INFO @ Sun, 02 Jun 2019 21:09:21: 1000000 INFO @ Sun, 02 Jun 2019 21:09:29: 2000000 INFO @ Sun, 02 Jun 2019 21:09:29: 2000000 INFO @ Sun, 02 Jun 2019 21:09:32: 2000000 INFO @ Sun, 02 Jun 2019 21:09:37: 3000000 INFO @ Sun, 02 Jun 2019 21:09:38: 3000000 INFO @ Sun, 02 Jun 2019 21:09:42: 3000000 INFO @ Sun, 02 Jun 2019 21:09:45: 4000000 INFO @ Sun, 02 Jun 2019 21:09:46: 4000000 INFO @ Sun, 02 Jun 2019 21:09:52: 4000000 INFO @ Sun, 02 Jun 2019 21:09:52: 5000000 INFO @ Sun, 02 Jun 2019 21:09:55: 5000000 INFO @ Sun, 02 Jun 2019 21:10:00: 6000000 INFO @ Sun, 02 Jun 2019 21:10:02: 5000000 INFO @ Sun, 02 Jun 2019 21:10:04: 6000000 INFO @ Sun, 02 Jun 2019 21:10:07: 7000000 INFO @ Sun, 02 Jun 2019 21:10:12: 7000000 INFO @ Sun, 02 Jun 2019 21:10:12: 6000000 INFO @ Sun, 02 Jun 2019 21:10:14: 8000000 INFO @ Sun, 02 Jun 2019 21:10:15: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:15: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:15: #1 total tags in treatment: 8017645 INFO @ Sun, 02 Jun 2019 21:10:15: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:15: #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 21:10:15: #1 tags after filtering in treatment: 8017645 INFO @ Sun, 02 Jun 2019 21:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:15: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:16: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 21:10:16: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:16: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:16: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:16: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:16: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:16: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:10:16: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 02 Jun 2019 21:10:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.05_model.r WARNING @ Sun, 02 Jun 2019 21:10:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:10:16: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 02 Jun 2019 21:10:16: #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 21:10:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:20: 8000000 INFO @ Sun, 02 Jun 2019 21:10:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:20: #1 total tags in treatment: 8017645 INFO @ Sun, 02 Jun 2019 21:10:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:20: #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 21:10:21: #1 tags after filtering in treatment: 8017645 INFO @ Sun, 02 Jun 2019 21:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:21: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:21: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 21:10:21: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:21: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:21: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:21: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:21: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:21: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:10:21: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 02 Jun 2019 21:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.10_model.r WARNING @ Sun, 02 Jun 2019 21:10:21: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:10:21: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 02 Jun 2019 21:10:21: #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 21:10:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:22: 7000000 INFO @ Sun, 02 Jun 2019 21:10:31: 8000000 INFO @ Sun, 02 Jun 2019 21:10:31: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:31: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:31: #1 total tags in treatment: 8017645 INFO @ Sun, 02 Jun 2019 21:10:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:31: #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 21:10:31: #1 tags after filtering in treatment: 8017645 INFO @ Sun, 02 Jun 2019 21:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:31: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:32: #2 number of paired peaks: 319 WARNING @ Sun, 02 Jun 2019 21:10:32: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:32: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:32: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:32: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:32: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:32: #2 predicted fragment length is 48 bps INFO @ Sun, 02 Jun 2019 21:10:32: #2 alternative fragment length(s) may be 4,48 bps INFO @ Sun, 02 Jun 2019 21:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.20_model.r WARNING @ Sun, 02 Jun 2019 21:10:32: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:10:32: #2 You may need to consider one of the other alternative d(s): 4,48 WARNING @ Sun, 02 Jun 2019 21:10:32: #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 21:10:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:10:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.05_summits.bed INFO @ Sun, 02 Jun 2019 21:10:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (581 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:10:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:10:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.10_summits.bed INFO @ Sun, 02 Jun 2019 21:10:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:10:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:11:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020713/SRX5020713.20_summits.bed INFO @ Sun, 02 Jun 2019 21:11:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (151 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。