Job ID = 2009748 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,743,774 reads read : 5,743,774 reads written : 5,743,774 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: 00:00:16 5743774 reads; of these: 5743774 (100.00%) were unpaired; of these: 5681493 (98.92%) aligned 0 times 4628 (0.08%) aligned exactly 1 time 57653 (1.00%) aligned >1 times 1.08% overall alignment rate Time searching: 00:00:16 Overall time: 00:00:16 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_rmdupse_core] 57705 / 62281 = 0.9265 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Fri, 05 Jul 2019 19:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.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 @ Fri, 05 Jul 2019 19:43:51: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:43:51: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:43:51: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:43:51: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:43:51: #1 total tags in treatment: 4576 INFO @ Fri, 05 Jul 2019 19:43:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:43:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:43:51: #1 tags after filtering in treatment: 4576 INFO @ Fri, 05 Jul 2019 19:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:43:51: #1 finished! INFO @ Fri, 05 Jul 2019 19:43:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:43:51: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 19:43:51: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 19:43:51: start model_add_line... INFO @ Fri, 05 Jul 2019 19:43:51: start X-correlation... INFO @ Fri, 05 Jul 2019 19:43:51: end of X-cor INFO @ Fri, 05 Jul 2019 19:43:51: #2 finished! INFO @ Fri, 05 Jul 2019 19:43:51: #2 predicted fragment length is 28 bps INFO @ Fri, 05 Jul 2019 19:43:51: #2 alternative fragment length(s) may be 28,87,131,157,205,240,273,363,512,549,597 bps INFO @ Fri, 05 Jul 2019 19:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.05_model.r WARNING @ Fri, 05 Jul 2019 19:43:51: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:43:51: #2 You may need to consider one of the other alternative d(s): 28,87,131,157,205,240,273,363,512,549,597 WARNING @ Fri, 05 Jul 2019 19:43:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 19:43:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:43:51: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:43:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:43:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:43:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.05_summits.bed INFO @ Fri, 05 Jul 2019 19:43:51: Done! BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 19:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.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 @ Fri, 05 Jul 2019 19:43:52: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:43:52: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:43:52: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:43:52: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:43:52: #1 total tags in treatment: 4576 INFO @ Fri, 05 Jul 2019 19:43:52: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:43:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:43:52: #1 tags after filtering in treatment: 4576 INFO @ Fri, 05 Jul 2019 19:43:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:43:52: #1 finished! INFO @ Fri, 05 Jul 2019 19:43:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:43:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:43:52: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 19:43:52: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 19:43:52: start model_add_line... INFO @ Fri, 05 Jul 2019 19:43:52: start X-correlation... INFO @ Fri, 05 Jul 2019 19:43:52: end of X-cor INFO @ Fri, 05 Jul 2019 19:43:52: #2 finished! INFO @ Fri, 05 Jul 2019 19:43:52: #2 predicted fragment length is 28 bps INFO @ Fri, 05 Jul 2019 19:43:52: #2 alternative fragment length(s) may be 28,87,131,157,205,240,273,363,512,549,597 bps INFO @ Fri, 05 Jul 2019 19:43:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.10_model.r WARNING @ Fri, 05 Jul 2019 19:43:52: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:43:52: #2 You may need to consider one of the other alternative d(s): 28,87,131,157,205,240,273,363,512,549,597 WARNING @ Fri, 05 Jul 2019 19:43:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 19:43:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:43:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:43:52: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:43:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.10_peaks.xls pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 20 millis INFO @ Fri, 05 Jul 2019 19:43:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:43:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.10_summits.bed INFO @ Fri, 05 Jul 2019 19:43:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.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 @ Fri, 05 Jul 2019 19:43:53: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:43:53: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:43:53: #1 tag size is determined as 30 bps INFO @ Fri, 05 Jul 2019 19:43:53: #1 tag size = 30 INFO @ Fri, 05 Jul 2019 19:43:53: #1 total tags in treatment: 4576 INFO @ Fri, 05 Jul 2019 19:43:53: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:43:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 19:43:53: #1 tags after filtering in treatment: 4576 INFO @ Fri, 05 Jul 2019 19:43:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:43:53: #1 finished! INFO @ Fri, 05 Jul 2019 19:43:53: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:43:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:43:53: #2 number of paired peaks: 154 WARNING @ Fri, 05 Jul 2019 19:43:53: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Fri, 05 Jul 2019 19:43:53: start model_add_line... INFO @ Fri, 05 Jul 2019 19:43:53: start X-correlation... INFO @ Fri, 05 Jul 2019 19:43:53: end of X-cor INFO @ Fri, 05 Jul 2019 19:43:53: #2 finished! INFO @ Fri, 05 Jul 2019 19:43:53: #2 predicted fragment length is 28 bps INFO @ Fri, 05 Jul 2019 19:43:53: #2 alternative fragment length(s) may be 28,87,131,157,205,240,273,363,512,549,597 bps INFO @ Fri, 05 Jul 2019 19:43:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.20_model.r CompletedMACS2peakCalling WARNING @ Fri, 05 Jul 2019 19:44:19: #2 Since the d (28) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 19:44:19: #2 You may need to consider one of the other alternative d(s): 28,87,131,157,205,240,273,363,512,549,597 WARNING @ Fri, 05 Jul 2019 19:44:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 19:44:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:44:19: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:44:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:44:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX148604/SRX148604.20_summits.bed INFO @ Fri, 05 Jul 2019 19:44:21: Done! pass1 - making usageList (9 chroms): 0 millis INFO @ Fri, 05 Jul 2019 19:44:21: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 2795 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (84 records, 4 fields): 8665 millis CompletedMACS2peakCalling