Job ID = 2011776 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,943,480 reads read : 13,886,960 reads written : 6,943,480 reads 0-length : 6,943,480 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: 00:01:27 6943480 reads; of these: 6943480 (100.00%) were unpaired; of these: 1398821 (20.15%) aligned 0 times 5057293 (72.84%) aligned exactly 1 time 487366 (7.02%) aligned >1 times 79.85% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 4773033 / 5544659 = 0.8608 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 @ Sat, 06 Jul 2019 02:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.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, 06 Jul 2019 02:39:23: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:23: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.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, 06 Jul 2019 02:39:24: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:24: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.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, 06 Jul 2019 02:39:25: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:39:25: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:39:30: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:39:30: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:39:30: #1 total tags in treatment: 771626 INFO @ Sat, 06 Jul 2019 02:39:30: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:39:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:39:30: #1 tags after filtering in treatment: 771626 INFO @ Sat, 06 Jul 2019 02:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:39:30: #1 finished! INFO @ Sat, 06 Jul 2019 02:39:30: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:39:30: #2 number of paired peaks: 236 WARNING @ Sat, 06 Jul 2019 02:39:30: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 06 Jul 2019 02:39:30: start model_add_line... INFO @ Sat, 06 Jul 2019 02:39:30: start X-correlation... INFO @ Sat, 06 Jul 2019 02:39:30: end of X-cor INFO @ Sat, 06 Jul 2019 02:39:30: #2 finished! INFO @ Sat, 06 Jul 2019 02:39:30: #2 predicted fragment length is 145 bps INFO @ Sat, 06 Jul 2019 02:39:30: #2 alternative fragment length(s) may be 4,117,145,179 bps INFO @ Sat, 06 Jul 2019 02:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.05_model.r INFO @ Sat, 06 Jul 2019 02:39:30: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:39:31: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:39:31: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:39:31: #1 total tags in treatment: 771626 INFO @ Sat, 06 Jul 2019 02:39:31: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:39:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:39:31: #1 tags after filtering in treatment: 771626 INFO @ Sat, 06 Jul 2019 02:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:39:31: #1 finished! INFO @ Sat, 06 Jul 2019 02:39:31: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:39:32: #2 number of paired peaks: 236 WARNING @ Sat, 06 Jul 2019 02:39:32: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 06 Jul 2019 02:39:32: start model_add_line... INFO @ Sat, 06 Jul 2019 02:39:32: start X-correlation... INFO @ Sat, 06 Jul 2019 02:39:32: end of X-cor INFO @ Sat, 06 Jul 2019 02:39:32: #2 finished! INFO @ Sat, 06 Jul 2019 02:39:32: #2 predicted fragment length is 145 bps INFO @ Sat, 06 Jul 2019 02:39:32: #2 alternative fragment length(s) may be 4,117,145,179 bps INFO @ Sat, 06 Jul 2019 02:39:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.10_model.r INFO @ Sat, 06 Jul 2019 02:39:32: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:39:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:39:33: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:39:33: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:39:33: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:39:33: #1 total tags in treatment: 771626 INFO @ Sat, 06 Jul 2019 02:39:33: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:39:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 02:39:33: #1 tags after filtering in treatment: 771626 INFO @ Sat, 06 Jul 2019 02:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:39:33: #1 finished! INFO @ Sat, 06 Jul 2019 02:39:33: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:39:33: #2 number of paired peaks: 236 WARNING @ Sat, 06 Jul 2019 02:39:33: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 06 Jul 2019 02:39:33: start model_add_line... INFO @ Sat, 06 Jul 2019 02:39:33: start X-correlation... INFO @ Sat, 06 Jul 2019 02:39:33: end of X-cor INFO @ Sat, 06 Jul 2019 02:39:33: #2 finished! INFO @ Sat, 06 Jul 2019 02:39:33: #2 predicted fragment length is 145 bps INFO @ Sat, 06 Jul 2019 02:39:33: #2 alternative fragment length(s) may be 4,117,145,179 bps INFO @ Sat, 06 Jul 2019 02:39:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.20_model.r INFO @ Sat, 06 Jul 2019 02:39:33: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:39:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:39:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:39:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.05_summits.bed INFO @ Sat, 06 Jul 2019 02:39:34: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (526 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:39:34: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:39:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:39:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:39:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.10_summits.bed INFO @ Sat, 06 Jul 2019 02:39:35: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:39:36: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:39:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:39:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:39:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028207/SRX5028207.20_summits.bed INFO @ Sat, 06 Jul 2019 02:39:37: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (106 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。