Job ID = 2011789 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,489,063 reads read : 12,978,126 reads written : 6,489,063 reads 0-length : 6,489,063 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: 00:01:23 6489063 reads; of these: 6489063 (100.00%) were unpaired; of these: 1389618 (21.41%) aligned 0 times 4643200 (71.55%) aligned exactly 1 time 456245 (7.03%) aligned >1 times 78.59% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 3927328 / 5099445 = 0.7701 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 02:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.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 02:41:17: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:41:17: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:41:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.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 02:41:18: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:41:18: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:41:27: 1000000 INFO @ Sat, 06 Jul 2019 02:41:27: 1000000 INFO @ Sat, 06 Jul 2019 02:41:28: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:41:28: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:41:28: #1 total tags in treatment: 1172117 INFO @ Sat, 06 Jul 2019 02:41:28: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:41:28: #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 02:41:28: #1 tags after filtering in treatment: 1172117 INFO @ Sat, 06 Jul 2019 02:41:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:41:28: #1 finished! INFO @ Sat, 06 Jul 2019 02:41:28: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:41:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:41:28: #2 number of paired peaks: 122 WARNING @ Sat, 06 Jul 2019 02:41:28: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 06 Jul 2019 02:41:28: start model_add_line... INFO @ Sat, 06 Jul 2019 02:41:28: start X-correlation... INFO @ Sat, 06 Jul 2019 02:41:28: end of X-cor INFO @ Sat, 06 Jul 2019 02:41:28: #2 finished! INFO @ Sat, 06 Jul 2019 02:41:28: #2 predicted fragment length is 130 bps INFO @ Sat, 06 Jul 2019 02:41:28: #2 alternative fragment length(s) may be 3,38,75,113,130,146,208 bps INFO @ Sat, 06 Jul 2019 02:41:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.05_model.r INFO @ Sat, 06 Jul 2019 02:41:29: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:41:29: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:41:29: #1 total tags in treatment: 1172117 INFO @ Sat, 06 Jul 2019 02:41:29: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:41:29: #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 02:41:29: #1 tags after filtering in treatment: 1172117 INFO @ Sat, 06 Jul 2019 02:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:41:29: #1 finished! INFO @ Sat, 06 Jul 2019 02:41:29: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:41:29: #2 number of paired peaks: 122 WARNING @ Sat, 06 Jul 2019 02:41:29: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 06 Jul 2019 02:41:29: start model_add_line... INFO @ Sat, 06 Jul 2019 02:41:29: start X-correlation... INFO @ Sat, 06 Jul 2019 02:41:29: end of X-cor INFO @ Sat, 06 Jul 2019 02:41:29: #2 finished! INFO @ Sat, 06 Jul 2019 02:41:29: #2 predicted fragment length is 130 bps INFO @ Sat, 06 Jul 2019 02:41:29: #2 alternative fragment length(s) may be 3,38,75,113,130,146,208 bps INFO @ Sat, 06 Jul 2019 02:41:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.10_model.r INFO @ Sat, 06 Jul 2019 02:41:38: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:41:38: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:41:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:41:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.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 02:41:40: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:41:40: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:41:42: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:41:42: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.05_summits.bed INFO @ Sat, 06 Jul 2019 02:41:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (533 records, 4 fields): 4 millis INFO @ Sat, 06 Jul 2019 02:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.10_summits.bed INFO @ Sat, 06 Jul 2019 02:41:43: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 02:41:48: 1000000 INFO @ Sat, 06 Jul 2019 02:41:50: #1 tag size is determined as 51 bps INFO @ Sat, 06 Jul 2019 02:41:50: #1 tag size = 51 INFO @ Sat, 06 Jul 2019 02:41:50: #1 total tags in treatment: 1172117 INFO @ Sat, 06 Jul 2019 02:41:50: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:41:50: #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 02:41:50: #1 tags after filtering in treatment: 1172117 INFO @ Sat, 06 Jul 2019 02:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 06 Jul 2019 02:41:50: #1 finished! INFO @ Sat, 06 Jul 2019 02:41:50: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:41:50: #2 number of paired peaks: 122 WARNING @ Sat, 06 Jul 2019 02:41:50: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 06 Jul 2019 02:41:50: start model_add_line... INFO @ Sat, 06 Jul 2019 02:41:50: start X-correlation... INFO @ Sat, 06 Jul 2019 02:41:50: end of X-cor INFO @ Sat, 06 Jul 2019 02:41:50: #2 finished! INFO @ Sat, 06 Jul 2019 02:41:50: #2 predicted fragment length is 130 bps INFO @ Sat, 06 Jul 2019 02:41:50: #2 alternative fragment length(s) may be 3,38,75,113,130,146,208 bps INFO @ Sat, 06 Jul 2019 02:41:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.20_model.r INFO @ Sat, 06 Jul 2019 02:41:50: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:41:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:41:53: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:41:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:41:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:41:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5028220/SRX5028220.20_summits.bed INFO @ Sat, 06 Jul 2019 02:41:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (108 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。