Job ID = 2010562 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,715,425 reads read : 13,430,850 reads written : 13,430,850 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: 00:02:02 6715425 reads; of these: 6715425 (100.00%) were paired; of these: 5212414 (77.62%) aligned concordantly 0 times 1082690 (16.12%) aligned concordantly exactly 1 time 420321 (6.26%) aligned concordantly >1 times ---- 5212414 pairs aligned concordantly 0 times; of these: 10529 (0.20%) aligned discordantly 1 time ---- 5201885 pairs aligned 0 times concordantly or discordantly; of these: 10403770 mates make up the pairs; of these: 10334446 (99.33%) aligned 0 times 36196 (0.35%) aligned exactly 1 time 33128 (0.32%) aligned >1 times 23.05% overall alignment rate Time searching: 00:02:02 Overall time: 00:02:02 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 199985 / 1512544 = 0.1322 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 @ Fri, 05 Jul 2019 23:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.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 23:10:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:10:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.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 23:10:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:10:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:10:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.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 23:10:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:10:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:11:04: 1000000 INFO @ Fri, 05 Jul 2019 23:11:05: 1000000 INFO @ Fri, 05 Jul 2019 23:11:06: 1000000 INFO @ Fri, 05 Jul 2019 23:11:12: 2000000 INFO @ Fri, 05 Jul 2019 23:11:12: 2000000 INFO @ Fri, 05 Jul 2019 23:11:13: 2000000 INFO @ Fri, 05 Jul 2019 23:11:17: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:11:17: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:11:17: #1 total tags in treatment: 1303573 INFO @ Fri, 05 Jul 2019 23:11:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:11:17: #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 23:11:17: #1 tags after filtering in treatment: 781368 INFO @ Fri, 05 Jul 2019 23:11:17: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:11:17: #1 finished! INFO @ Fri, 05 Jul 2019 23:11:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:11:17: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:11:17: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:11:17: #1 total tags in treatment: 1303573 INFO @ Fri, 05 Jul 2019 23:11:17: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:11:17: #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 23:11:17: #1 tags after filtering in treatment: 781368 INFO @ Fri, 05 Jul 2019 23:11:17: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:11:17: #1 finished! INFO @ Fri, 05 Jul 2019 23:11:17: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:11:17: #2 number of paired peaks: 1044 INFO @ Fri, 05 Jul 2019 23:11:17: start model_add_line... INFO @ Fri, 05 Jul 2019 23:11:18: start X-correlation... INFO @ Fri, 05 Jul 2019 23:11:18: end of X-cor INFO @ Fri, 05 Jul 2019 23:11:18: #2 finished! INFO @ Fri, 05 Jul 2019 23:11:18: #2 predicted fragment length is 241 bps INFO @ Fri, 05 Jul 2019 23:11:18: #2 alternative fragment length(s) may be 2,191,223,241,260 bps INFO @ Fri, 05 Jul 2019 23:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.05_model.r INFO @ Fri, 05 Jul 2019 23:11:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:11:18: #2 number of paired peaks: 1044 INFO @ Fri, 05 Jul 2019 23:11:18: start model_add_line... INFO @ Fri, 05 Jul 2019 23:11:18: start X-correlation... INFO @ Fri, 05 Jul 2019 23:11:18: end of X-cor INFO @ Fri, 05 Jul 2019 23:11:18: #2 finished! INFO @ Fri, 05 Jul 2019 23:11:18: #2 predicted fragment length is 241 bps INFO @ Fri, 05 Jul 2019 23:11:18: #2 alternative fragment length(s) may be 2,191,223,241,260 bps INFO @ Fri, 05 Jul 2019 23:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.10_model.r INFO @ Fri, 05 Jul 2019 23:11:18: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:11:18: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:11:18: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:11:18: #1 total tags in treatment: 1303573 INFO @ Fri, 05 Jul 2019 23:11:18: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:11:18: #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 23:11:18: #1 tags after filtering in treatment: 781368 INFO @ Fri, 05 Jul 2019 23:11:18: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:11:18: #1 finished! INFO @ Fri, 05 Jul 2019 23:11:18: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:11:18: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:11:19: #2 number of paired peaks: 1044 INFO @ Fri, 05 Jul 2019 23:11:19: start model_add_line... INFO @ Fri, 05 Jul 2019 23:11:19: start X-correlation... INFO @ Fri, 05 Jul 2019 23:11:19: end of X-cor INFO @ Fri, 05 Jul 2019 23:11:19: #2 finished! INFO @ Fri, 05 Jul 2019 23:11:19: #2 predicted fragment length is 241 bps INFO @ Fri, 05 Jul 2019 23:11:19: #2 alternative fragment length(s) may be 2,191,223,241,260 bps INFO @ Fri, 05 Jul 2019 23:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.20_model.r INFO @ Fri, 05 Jul 2019 23:11:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:11:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:11:24: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.05_summits.bed INFO @ Fri, 05 Jul 2019 23:11:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (358 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 23:11:25: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.10_summits.bed INFO @ Fri, 05 Jul 2019 23:11:25: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381263/SRX381263.20_summits.bed INFO @ Fri, 05 Jul 2019 23:11:26: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 4 millis CompletedMACS2peakCalling