Job ID = 2640808 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,609,794 reads read : 29,219,588 reads written : 14,609,794 reads 0-length : 14,609,794 rm: cannot remove ‘[DSE]RR*’: 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: 00:06:54 14609794 reads; of these: 14609794 (100.00%) were unpaired; of these: 746964 (5.11%) aligned 0 times 12529082 (85.76%) aligned exactly 1 time 1333748 (9.13%) aligned >1 times 94.89% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 12039134 / 13862830 = 0.8684 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 19:43:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 19:43:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:43:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:43:48: 1000000 INFO @ Sat, 24 Aug 2019 19:43:57: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 19:43:57: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 19:43:57: #1 total tags in treatment: 1823696 INFO @ Sat, 24 Aug 2019 19:43:57: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:43:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:43:57: #1 tags after filtering in treatment: 1823696 INFO @ Sat, 24 Aug 2019 19:43:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:43:57: #1 finished! INFO @ Sat, 24 Aug 2019 19:43:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:43:57: #2 number of paired peaks: 202 WARNING @ Sat, 24 Aug 2019 19:43:57: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 24 Aug 2019 19:43:57: start model_add_line... INFO @ Sat, 24 Aug 2019 19:43:57: start X-correlation... INFO @ Sat, 24 Aug 2019 19:43:57: end of X-cor INFO @ Sat, 24 Aug 2019 19:43:57: #2 finished! INFO @ Sat, 24 Aug 2019 19:43:57: #2 predicted fragment length is 163 bps INFO @ Sat, 24 Aug 2019 19:43:57: #2 alternative fragment length(s) may be 1,163,551,583 bps INFO @ Sat, 24 Aug 2019 19:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.05_model.r WARNING @ Sat, 24 Aug 2019 19:43:57: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:43:57: #2 You may need to consider one of the other alternative d(s): 1,163,551,583 WARNING @ Sat, 24 Aug 2019 19:43:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:43:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:43:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:44:03: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:44:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.05_peaks.xls INFO @ Sat, 24 Aug 2019 19:44:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:44:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.05_summits.bed INFO @ Sat, 24 Aug 2019 19:44:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:44:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 19:44:07: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:44:07: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:44:17: 1000000 INFO @ Sat, 24 Aug 2019 19:44:26: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 19:44:26: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 19:44:26: #1 total tags in treatment: 1823696 INFO @ Sat, 24 Aug 2019 19:44:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:44:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:44:26: #1 tags after filtering in treatment: 1823696 INFO @ Sat, 24 Aug 2019 19:44:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:44:26: #1 finished! INFO @ Sat, 24 Aug 2019 19:44:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:44:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:44:27: #2 number of paired peaks: 202 WARNING @ Sat, 24 Aug 2019 19:44:27: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 24 Aug 2019 19:44:27: start model_add_line... INFO @ Sat, 24 Aug 2019 19:44:27: start X-correlation... INFO @ Sat, 24 Aug 2019 19:44:27: end of X-cor INFO @ Sat, 24 Aug 2019 19:44:27: #2 finished! INFO @ Sat, 24 Aug 2019 19:44:27: #2 predicted fragment length is 163 bps INFO @ Sat, 24 Aug 2019 19:44:27: #2 alternative fragment length(s) may be 1,163,551,583 bps INFO @ Sat, 24 Aug 2019 19:44:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.10_model.r WARNING @ Sat, 24 Aug 2019 19:44:27: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:44:27: #2 You may need to consider one of the other alternative d(s): 1,163,551,583 WARNING @ Sat, 24 Aug 2019 19:44:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:44:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:44:33: #3 Call peaks for each chromosome... BedGraph に変換中... INFO @ Sat, 24 Aug 2019 19:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.10_peaks.xls INFO @ Sat, 24 Aug 2019 19:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:44:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.10_summits.bed INFO @ Sat, 24 Aug 2019 19:44:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 19:44:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 24 Aug 2019 19:44:37: #1 read tag files... INFO @ Sat, 24 Aug 2019 19:44:37: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 19:44:46: 1000000 INFO @ Sat, 24 Aug 2019 19:44:53: #1 tag size is determined as 101 bps INFO @ Sat, 24 Aug 2019 19:44:53: #1 tag size = 101 INFO @ Sat, 24 Aug 2019 19:44:53: #1 total tags in treatment: 1823696 INFO @ Sat, 24 Aug 2019 19:44:53: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 19:44:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 19:44:53: #1 tags after filtering in treatment: 1823696 INFO @ Sat, 24 Aug 2019 19:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 19:44:53: #1 finished! INFO @ Sat, 24 Aug 2019 19:44:53: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 19:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 19:44:54: #2 number of paired peaks: 202 WARNING @ Sat, 24 Aug 2019 19:44:54: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 24 Aug 2019 19:44:54: start model_add_line... INFO @ Sat, 24 Aug 2019 19:44:54: start X-correlation... INFO @ Sat, 24 Aug 2019 19:44:54: end of X-cor INFO @ Sat, 24 Aug 2019 19:44:54: #2 finished! INFO @ Sat, 24 Aug 2019 19:44:54: #2 predicted fragment length is 163 bps INFO @ Sat, 24 Aug 2019 19:44:54: #2 alternative fragment length(s) may be 1,163,551,583 bps INFO @ Sat, 24 Aug 2019 19:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.20_model.r WARNING @ Sat, 24 Aug 2019 19:44:54: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 19:44:54: #2 You may need to consider one of the other alternative d(s): 1,163,551,583 WARNING @ Sat, 24 Aug 2019 19:44:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 19:44:54: #3 Call peaks... INFO @ Sat, 24 Aug 2019 19:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 19:45:00: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 19:45:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.20_peaks.xls INFO @ Sat, 24 Aug 2019 19:45:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 19:45:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2439295/SRX2439295.20_summits.bed INFO @ Sat, 24 Aug 2019 19:45:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (47 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。