Job ID = 1292468 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,555,555 reads read : 19,555,555 reads written : 19,555,555 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: 00:02:44 19555555 reads; of these: 19555555 (100.00%) were unpaired; of these: 8713191 (44.56%) aligned 0 times 9073593 (46.40%) aligned exactly 1 time 1768771 (9.04%) aligned >1 times 55.44% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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] 648227 / 10842364 = 0.0598 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 19:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.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 19:08:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:08:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.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 19:08:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:08:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.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 19:08:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:08:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:08:41: 1000000 INFO @ Sun, 02 Jun 2019 19:08:41: 1000000 INFO @ Sun, 02 Jun 2019 19:08:41: 1000000 INFO @ Sun, 02 Jun 2019 19:08:48: 2000000 INFO @ Sun, 02 Jun 2019 19:08:49: 2000000 INFO @ Sun, 02 Jun 2019 19:08:50: 2000000 INFO @ Sun, 02 Jun 2019 19:08:56: 3000000 INFO @ Sun, 02 Jun 2019 19:08:57: 3000000 INFO @ Sun, 02 Jun 2019 19:08:59: 3000000 INFO @ Sun, 02 Jun 2019 19:09:03: 4000000 INFO @ Sun, 02 Jun 2019 19:09:04: 4000000 INFO @ Sun, 02 Jun 2019 19:09:08: 4000000 INFO @ Sun, 02 Jun 2019 19:09:10: 5000000 INFO @ Sun, 02 Jun 2019 19:09:12: 5000000 INFO @ Sun, 02 Jun 2019 19:09:17: 6000000 INFO @ Sun, 02 Jun 2019 19:09:17: 5000000 INFO @ Sun, 02 Jun 2019 19:09:20: 6000000 INFO @ Sun, 02 Jun 2019 19:09:24: 7000000 INFO @ Sun, 02 Jun 2019 19:09:26: 6000000 INFO @ Sun, 02 Jun 2019 19:09:27: 7000000 INFO @ Sun, 02 Jun 2019 19:09:31: 8000000 INFO @ Sun, 02 Jun 2019 19:09:35: 8000000 INFO @ Sun, 02 Jun 2019 19:09:35: 7000000 INFO @ Sun, 02 Jun 2019 19:09:38: 9000000 INFO @ Sun, 02 Jun 2019 19:09:42: 9000000 INFO @ Sun, 02 Jun 2019 19:09:44: 8000000 INFO @ Sun, 02 Jun 2019 19:09:45: 10000000 INFO @ Sun, 02 Jun 2019 19:09:46: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:09:46: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:09:46: #1 total tags in treatment: 10194137 INFO @ Sun, 02 Jun 2019 19:09:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:09:46: #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 19:09:46: #1 tags after filtering in treatment: 10194137 INFO @ Sun, 02 Jun 2019 19:09:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:09:46: #1 finished! INFO @ Sun, 02 Jun 2019 19:09:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:09:47: #2 number of paired peaks: 253 WARNING @ Sun, 02 Jun 2019 19:09:47: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 02 Jun 2019 19:09:47: start model_add_line... INFO @ Sun, 02 Jun 2019 19:09:47: start X-correlation... INFO @ Sun, 02 Jun 2019 19:09:47: end of X-cor INFO @ Sun, 02 Jun 2019 19:09:47: #2 finished! INFO @ Sun, 02 Jun 2019 19:09:47: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 19:09:47: #2 alternative fragment length(s) may be 0,32,563 bps INFO @ Sun, 02 Jun 2019 19:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.05_model.r WARNING @ Sun, 02 Jun 2019 19:09:47: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:09:47: #2 You may need to consider one of the other alternative d(s): 0,32,563 WARNING @ Sun, 02 Jun 2019 19:09:47: #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 19:09:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:09:49: 10000000 INFO @ Sun, 02 Jun 2019 19:09:51: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:09:51: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:09:51: #1 total tags in treatment: 10194137 INFO @ Sun, 02 Jun 2019 19:09:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:09:51: #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 19:09:51: #1 tags after filtering in treatment: 10194137 INFO @ Sun, 02 Jun 2019 19:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:09:51: #1 finished! INFO @ Sun, 02 Jun 2019 19:09:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:09:52: #2 number of paired peaks: 253 WARNING @ Sun, 02 Jun 2019 19:09:52: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 02 Jun 2019 19:09:52: start model_add_line... INFO @ Sun, 02 Jun 2019 19:09:52: start X-correlation... INFO @ Sun, 02 Jun 2019 19:09:52: end of X-cor INFO @ Sun, 02 Jun 2019 19:09:52: #2 finished! INFO @ Sun, 02 Jun 2019 19:09:52: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 19:09:52: #2 alternative fragment length(s) may be 0,32,563 bps INFO @ Sun, 02 Jun 2019 19:09:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.10_model.r WARNING @ Sun, 02 Jun 2019 19:09:52: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:09:52: #2 You may need to consider one of the other alternative d(s): 0,32,563 WARNING @ Sun, 02 Jun 2019 19:09:52: #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 19:09:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:09:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:09:52: 9000000 INFO @ Sun, 02 Jun 2019 19:10:01: 10000000 INFO @ Sun, 02 Jun 2019 19:10:03: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 19:10:03: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 19:10:03: #1 total tags in treatment: 10194137 INFO @ Sun, 02 Jun 2019 19:10:03: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:10:03: #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 19:10:03: #1 tags after filtering in treatment: 10194137 INFO @ Sun, 02 Jun 2019 19:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:10:03: #1 finished! INFO @ Sun, 02 Jun 2019 19:10:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:10:04: #2 number of paired peaks: 253 WARNING @ Sun, 02 Jun 2019 19:10:04: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sun, 02 Jun 2019 19:10:04: start model_add_line... INFO @ Sun, 02 Jun 2019 19:10:04: start X-correlation... INFO @ Sun, 02 Jun 2019 19:10:04: end of X-cor INFO @ Sun, 02 Jun 2019 19:10:04: #2 finished! INFO @ Sun, 02 Jun 2019 19:10:04: #2 predicted fragment length is 32 bps INFO @ Sun, 02 Jun 2019 19:10:04: #2 alternative fragment length(s) may be 0,32,563 bps INFO @ Sun, 02 Jun 2019 19:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.20_model.r WARNING @ Sun, 02 Jun 2019 19:10:04: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:10:04: #2 You may need to consider one of the other alternative d(s): 0,32,563 WARNING @ Sun, 02 Jun 2019 19:10:04: #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 19:10:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:10:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.05_summits.bed INFO @ Sun, 02 Jun 2019 19:10:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:10:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.10_summits.bed INFO @ Sun, 02 Jun 2019 19:10:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX463081/SRX463081.20_summits.bed INFO @ Sun, 02 Jun 2019 19:10:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (61 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。