Job ID = 1292902 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,738,369 reads read : 5,738,369 reads written : 5,738,369 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: 00:01:26 5738369 reads; of these: 5738369 (100.00%) were unpaired; of these: 54183 (0.94%) aligned 0 times 4747013 (82.72%) aligned exactly 1 time 937173 (16.33%) aligned >1 times 99.06% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 301015 / 5684186 = 0.0530 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 21:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.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 21:02:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:02:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.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 21:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.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 21:02:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:02:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:02:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:02:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:03:05: 1000000 INFO @ Sun, 02 Jun 2019 21:03:05: 1000000 INFO @ Sun, 02 Jun 2019 21:03:05: 1000000 INFO @ Sun, 02 Jun 2019 21:03:13: 2000000 INFO @ Sun, 02 Jun 2019 21:03:14: 2000000 INFO @ Sun, 02 Jun 2019 21:03:14: 2000000 INFO @ Sun, 02 Jun 2019 21:03:21: 3000000 INFO @ Sun, 02 Jun 2019 21:03:22: 3000000 INFO @ Sun, 02 Jun 2019 21:03:22: 3000000 INFO @ Sun, 02 Jun 2019 21:03:30: 4000000 INFO @ Sun, 02 Jun 2019 21:03:31: 4000000 INFO @ Sun, 02 Jun 2019 21:03:31: 4000000 INFO @ Sun, 02 Jun 2019 21:03:38: 5000000 INFO @ Sun, 02 Jun 2019 21:03:40: 5000000 INFO @ Sun, 02 Jun 2019 21:03:41: 5000000 INFO @ Sun, 02 Jun 2019 21:03:42: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:03:42: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:03:42: #1 total tags in treatment: 5383171 INFO @ Sun, 02 Jun 2019 21:03:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:03:42: #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 21:03:42: #1 tags after filtering in treatment: 5383171 INFO @ Sun, 02 Jun 2019 21:03:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:03:42: #1 finished! INFO @ Sun, 02 Jun 2019 21:03:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:03:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:03:42: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 21:03:42: 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 21:03:42: start model_add_line... INFO @ Sun, 02 Jun 2019 21:03:42: start X-correlation... INFO @ Sun, 02 Jun 2019 21:03:42: end of X-cor INFO @ Sun, 02 Jun 2019 21:03:42: #2 finished! INFO @ Sun, 02 Jun 2019 21:03:42: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 21:03:42: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 02 Jun 2019 21:03:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.10_model.r WARNING @ Sun, 02 Jun 2019 21:03:42: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:03:42: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 02 Jun 2019 21:03:42: #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 21:03:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:03:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:03:44: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:03:44: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:03:44: #1 total tags in treatment: 5383171 INFO @ Sun, 02 Jun 2019 21:03:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:03:44: #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 21:03:44: #1 tags after filtering in treatment: 5383171 INFO @ Sun, 02 Jun 2019 21:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:03:44: #1 finished! INFO @ Sun, 02 Jun 2019 21:03:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:03:44: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:03:44: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:03:44: #1 total tags in treatment: 5383171 INFO @ Sun, 02 Jun 2019 21:03:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:03:44: #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 21:03:44: #1 tags after filtering in treatment: 5383171 INFO @ Sun, 02 Jun 2019 21:03:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:03:44: #1 finished! INFO @ Sun, 02 Jun 2019 21:03:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:03:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:03:45: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 21:03:45: 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 21:03:45: start model_add_line... INFO @ Sun, 02 Jun 2019 21:03:45: start X-correlation... INFO @ Sun, 02 Jun 2019 21:03:45: end of X-cor INFO @ Sun, 02 Jun 2019 21:03:45: #2 finished! INFO @ Sun, 02 Jun 2019 21:03:45: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 21:03:45: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 02 Jun 2019 21:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.20_model.r WARNING @ Sun, 02 Jun 2019 21:03:45: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:03:45: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 02 Jun 2019 21:03:45: #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 21:03:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:03:45: #2 number of paired peaks: 363 WARNING @ Sun, 02 Jun 2019 21:03:45: 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 21:03:45: start model_add_line... INFO @ Sun, 02 Jun 2019 21:03:45: start X-correlation... INFO @ Sun, 02 Jun 2019 21:03:45: end of X-cor INFO @ Sun, 02 Jun 2019 21:03:45: #2 finished! INFO @ Sun, 02 Jun 2019 21:03:45: #2 predicted fragment length is 54 bps INFO @ Sun, 02 Jun 2019 21:03:45: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 02 Jun 2019 21:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.05_model.r WARNING @ Sun, 02 Jun 2019 21:03:45: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:03:45: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 02 Jun 2019 21:03:45: #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 21:03:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:03:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:04:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:04:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.10_summits.bed INFO @ Sun, 02 Jun 2019 21:04:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (259 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.20_summits.bed INFO @ Sun, 02 Jun 2019 21:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020702/SRX5020702.05_summits.bed INFO @ Sun, 02 Jun 2019 21:04:09: Done! INFO @ Sun, 02 Jun 2019 21:04:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (614 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。