Job ID = 2010770 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,022,242 reads read : 3,022,242 reads written : 3,022,242 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: 00:00:33 3022242 reads; of these: 3022242 (100.00%) were unpaired; of these: 239042 (7.91%) aligned 0 times 2443989 (80.87%) aligned exactly 1 time 339211 (11.22%) aligned >1 times 92.09% overall alignment rate Time searching: 00:00:33 Overall time: 00:00:33 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] 600313 / 2783200 = 0.2157 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 00:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.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 00:34:15: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:34:15: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:34:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.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 00:34:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:34:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.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 00:34:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 00:34:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 00:34:24: 1000000 INFO @ Sat, 06 Jul 2019 00:34:24: 1000000 INFO @ Sat, 06 Jul 2019 00:34:26: 1000000 INFO @ Sat, 06 Jul 2019 00:34:32: 2000000 INFO @ Sat, 06 Jul 2019 00:34:33: 2000000 INFO @ Sat, 06 Jul 2019 00:34:33: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:34:34: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:34:34: #1 total tags in treatment: 2182887 INFO @ Sat, 06 Jul 2019 00:34:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:34:34: #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 00:34:34: #1 tags after filtering in treatment: 2182887 INFO @ Sat, 06 Jul 2019 00:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:34:34: #1 finished! INFO @ Sat, 06 Jul 2019 00:34:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:34:34: #2 number of paired peaks: 114 WARNING @ Sat, 06 Jul 2019 00:34:34: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 06 Jul 2019 00:34:34: start model_add_line... INFO @ Sat, 06 Jul 2019 00:34:34: start X-correlation... INFO @ Sat, 06 Jul 2019 00:34:34: end of X-cor INFO @ Sat, 06 Jul 2019 00:34:34: #2 finished! INFO @ Sat, 06 Jul 2019 00:34:34: #2 predicted fragment length is 228 bps INFO @ Sat, 06 Jul 2019 00:34:34: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 06 Jul 2019 00:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.05_model.r INFO @ Sat, 06 Jul 2019 00:34:34: 2000000 INFO @ Sat, 06 Jul 2019 00:34:34: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:34:34: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:34:34: #1 total tags in treatment: 2182887 INFO @ Sat, 06 Jul 2019 00:34:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:34:34: #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 00:34:34: #1 tags after filtering in treatment: 2182887 INFO @ Sat, 06 Jul 2019 00:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:34:34: #1 finished! INFO @ Sat, 06 Jul 2019 00:34:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:34:35: #2 number of paired peaks: 114 WARNING @ Sat, 06 Jul 2019 00:34:35: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 06 Jul 2019 00:34:35: start model_add_line... INFO @ Sat, 06 Jul 2019 00:34:35: start X-correlation... INFO @ Sat, 06 Jul 2019 00:34:35: end of X-cor INFO @ Sat, 06 Jul 2019 00:34:35: #2 finished! INFO @ Sat, 06 Jul 2019 00:34:35: #2 predicted fragment length is 228 bps INFO @ Sat, 06 Jul 2019 00:34:35: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 06 Jul 2019 00:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.10_model.r INFO @ Sat, 06 Jul 2019 00:34:35: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 00:34:35: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 00:34:35: #1 total tags in treatment: 2182887 INFO @ Sat, 06 Jul 2019 00:34:35: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 00:34:35: #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 00:34:35: #1 tags after filtering in treatment: 2182887 INFO @ Sat, 06 Jul 2019 00:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 00:34:35: #1 finished! INFO @ Sat, 06 Jul 2019 00:34:35: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 00:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 00:34:35: #2 number of paired peaks: 114 WARNING @ Sat, 06 Jul 2019 00:34:35: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Sat, 06 Jul 2019 00:34:35: start model_add_line... INFO @ Sat, 06 Jul 2019 00:34:35: start X-correlation... INFO @ Sat, 06 Jul 2019 00:34:35: end of X-cor INFO @ Sat, 06 Jul 2019 00:34:35: #2 finished! INFO @ Sat, 06 Jul 2019 00:34:35: #2 predicted fragment length is 228 bps INFO @ Sat, 06 Jul 2019 00:34:35: #2 alternative fragment length(s) may be 228 bps INFO @ Sat, 06 Jul 2019 00:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 00:34:55: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:34:55: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 00:34:55: #3 Call peaks... INFO @ Sat, 06 Jul 2019 00:34:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 06 Jul 2019 00:35:04: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:35:04: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:35:04: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.05_peaks.xls INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.20_peaks.xls INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.05_summits.bed INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:35:07: Done! INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.20_summits.bed INFO @ Sat, 06 Jul 2019 00:35:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1105 records, 4 fields): 6 millis pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (2325 records, 4 fields): 10 millis INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.10_peaks.xls CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 00:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX390616/SRX390616.10_summits.bed INFO @ Sat, 06 Jul 2019 00:35:07: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (1777 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling