Job ID = 4289067 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,759,047 reads read : 29,518,094 reads written : 14,759,047 reads 0-length : 14,759,047 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: 00:02:42 14759047 reads; of these: 14759047 (100.00%) were unpaired; of these: 9459592 (64.09%) aligned 0 times 2845081 (19.28%) aligned exactly 1 time 2454374 (16.63%) aligned >1 times 35.91% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 3709648 / 5299455 = 0.7000 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:35:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.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 @ Tue, 10 Dec 2019 13:35:22: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:35:22: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:35:33: 1000000 INFO @ Tue, 10 Dec 2019 13:35:39: #1 tag size is determined as 101 bps INFO @ Tue, 10 Dec 2019 13:35:39: #1 tag size = 101 INFO @ Tue, 10 Dec 2019 13:35:39: #1 total tags in treatment: 1589807 INFO @ Tue, 10 Dec 2019 13:35:39: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:35:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:35:39: #1 tags after filtering in treatment: 1589807 INFO @ Tue, 10 Dec 2019 13:35:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:35:39: #1 finished! INFO @ Tue, 10 Dec 2019 13:35:39: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:35:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:35:39: #2 number of paired peaks: 175 WARNING @ Tue, 10 Dec 2019 13:35:39: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 10 Dec 2019 13:35:39: start model_add_line... INFO @ Tue, 10 Dec 2019 13:35:39: start X-correlation... INFO @ Tue, 10 Dec 2019 13:35:39: end of X-cor INFO @ Tue, 10 Dec 2019 13:35:39: #2 finished! INFO @ Tue, 10 Dec 2019 13:35:39: #2 predicted fragment length is 261 bps INFO @ Tue, 10 Dec 2019 13:35:39: #2 alternative fragment length(s) may be 261 bps INFO @ Tue, 10 Dec 2019 13:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.05_model.r INFO @ Tue, 10 Dec 2019 13:35:39: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:35:46: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.05_summits.bed INFO @ Tue, 10 Dec 2019 13:35:48: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (914 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:35:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.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 @ Tue, 10 Dec 2019 13:35:52: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:35:52: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:36:00: 1000000 INFO @ Tue, 10 Dec 2019 13:36:05: #1 tag size is determined as 101 bps INFO @ Tue, 10 Dec 2019 13:36:05: #1 tag size = 101 INFO @ Tue, 10 Dec 2019 13:36:05: #1 total tags in treatment: 1589807 INFO @ Tue, 10 Dec 2019 13:36:05: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:36:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:36:05: #1 tags after filtering in treatment: 1589807 INFO @ Tue, 10 Dec 2019 13:36:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:36:05: #1 finished! INFO @ Tue, 10 Dec 2019 13:36:05: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:36:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:36:05: #2 number of paired peaks: 175 WARNING @ Tue, 10 Dec 2019 13:36:05: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 10 Dec 2019 13:36:05: start model_add_line... INFO @ Tue, 10 Dec 2019 13:36:05: start X-correlation... INFO @ Tue, 10 Dec 2019 13:36:05: end of X-cor INFO @ Tue, 10 Dec 2019 13:36:05: #2 finished! INFO @ Tue, 10 Dec 2019 13:36:05: #2 predicted fragment length is 261 bps INFO @ Tue, 10 Dec 2019 13:36:05: #2 alternative fragment length(s) may be 261 bps INFO @ Tue, 10 Dec 2019 13:36:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.10_model.r INFO @ Tue, 10 Dec 2019 13:36:05: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:36:12: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:36:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:36:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:36:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.10_summits.bed INFO @ Tue, 10 Dec 2019 13:36:14: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:36:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.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 @ Tue, 10 Dec 2019 13:36:22: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:36:22: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:36:30: 1000000 INFO @ Tue, 10 Dec 2019 13:36:35: #1 tag size is determined as 101 bps INFO @ Tue, 10 Dec 2019 13:36:35: #1 tag size = 101 INFO @ Tue, 10 Dec 2019 13:36:35: #1 total tags in treatment: 1589807 INFO @ Tue, 10 Dec 2019 13:36:35: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:36:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:36:35: #1 tags after filtering in treatment: 1589807 INFO @ Tue, 10 Dec 2019 13:36:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:36:35: #1 finished! INFO @ Tue, 10 Dec 2019 13:36:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:36:35: #2 number of paired peaks: 175 WARNING @ Tue, 10 Dec 2019 13:36:35: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Tue, 10 Dec 2019 13:36:35: start model_add_line... INFO @ Tue, 10 Dec 2019 13:36:35: start X-correlation... INFO @ Tue, 10 Dec 2019 13:36:35: end of X-cor INFO @ Tue, 10 Dec 2019 13:36:35: #2 finished! INFO @ Tue, 10 Dec 2019 13:36:35: #2 predicted fragment length is 261 bps INFO @ Tue, 10 Dec 2019 13:36:35: #2 alternative fragment length(s) may be 261 bps INFO @ Tue, 10 Dec 2019 13:36:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.20_model.r INFO @ Tue, 10 Dec 2019 13:36:35: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:36:41: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5086837/SRX5086837.20_summits.bed INFO @ Tue, 10 Dec 2019 13:36:44: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (372 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。