Job ID = 2010647 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,824,961 reads read : 7,649,922 reads written : 7,649,922 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: 00:01:18 3824961 reads; of these: 3824961 (100.00%) were paired; of these: 3077480 (80.46%) aligned concordantly 0 times 604644 (15.81%) aligned concordantly exactly 1 time 142837 (3.73%) aligned concordantly >1 times ---- 3077480 pairs aligned concordantly 0 times; of these: 8178 (0.27%) aligned discordantly 1 time ---- 3069302 pairs aligned 0 times concordantly or discordantly; of these: 6138604 mates make up the pairs; of these: 5987133 (97.53%) aligned 0 times 118617 (1.93%) aligned exactly 1 time 32854 (0.54%) aligned >1 times 21.74% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:22 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] 405402 / 751561 = 0.5394 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 23:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.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 23:51:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:51:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:51:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.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 23:51:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:51:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.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 23:51:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:51:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:51:25: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:51:25: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:51:25: #1 total tags in treatment: 343910 INFO @ Fri, 05 Jul 2019 23:51:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:51:25: #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 23:51:25: #1 tags after filtering in treatment: 249931 INFO @ Fri, 05 Jul 2019 23:51:25: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 05 Jul 2019 23:51:25: #1 finished! INFO @ Fri, 05 Jul 2019 23:51:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:51:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:51:25: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 23:51:25: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 23:51:25: start model_add_line... INFO @ Fri, 05 Jul 2019 23:51:25: start X-correlation... INFO @ Fri, 05 Jul 2019 23:51:25: end of X-cor INFO @ Fri, 05 Jul 2019 23:51:25: #2 finished! INFO @ Fri, 05 Jul 2019 23:51:25: #2 predicted fragment length is 235 bps INFO @ Fri, 05 Jul 2019 23:51:25: #2 alternative fragment length(s) may be 235 bps INFO @ Fri, 05 Jul 2019 23:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.05_model.r INFO @ Fri, 05 Jul 2019 23:51:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:51:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:51:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:51:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:51:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.05_summits.bed INFO @ Fri, 05 Jul 2019 23:51:27: Done! INFO @ Fri, 05 Jul 2019 23:51:27: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:51:27: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:51:27: #1 total tags in treatment: 343910 INFO @ Fri, 05 Jul 2019 23:51:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:51:27: #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 23:51:27: #1 tags after filtering in treatment: 249931 INFO @ Fri, 05 Jul 2019 23:51:27: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 05 Jul 2019 23:51:27: #1 finished! INFO @ Fri, 05 Jul 2019 23:51:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:51:27: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (224 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 23:51:27: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 23:51:27: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 23:51:27: start model_add_line... INFO @ Fri, 05 Jul 2019 23:51:27: start X-correlation... INFO @ Fri, 05 Jul 2019 23:51:27: end of X-cor INFO @ Fri, 05 Jul 2019 23:51:27: #2 finished! INFO @ Fri, 05 Jul 2019 23:51:27: #2 predicted fragment length is 235 bps INFO @ Fri, 05 Jul 2019 23:51:27: #2 alternative fragment length(s) may be 235 bps INFO @ Fri, 05 Jul 2019 23:51:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.10_model.r INFO @ Fri, 05 Jul 2019 23:51:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:51:27: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:51:28: #1 tag size is determined as 70 bps INFO @ Fri, 05 Jul 2019 23:51:28: #1 tag size = 70 INFO @ Fri, 05 Jul 2019 23:51:28: #1 total tags in treatment: 343910 INFO @ Fri, 05 Jul 2019 23:51:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:51:28: #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 23:51:28: #1 tags after filtering in treatment: 249931 INFO @ Fri, 05 Jul 2019 23:51:28: #1 Redundant rate of treatment: 0.27 INFO @ Fri, 05 Jul 2019 23:51:28: #1 finished! INFO @ Fri, 05 Jul 2019 23:51:28: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:51:28: #2 number of paired peaks: 172 WARNING @ Fri, 05 Jul 2019 23:51:28: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Fri, 05 Jul 2019 23:51:28: start model_add_line... INFO @ Fri, 05 Jul 2019 23:51:28: start X-correlation... INFO @ Fri, 05 Jul 2019 23:51:28: end of X-cor INFO @ Fri, 05 Jul 2019 23:51:28: #2 finished! INFO @ Fri, 05 Jul 2019 23:51:28: #2 predicted fragment length is 235 bps INFO @ Fri, 05 Jul 2019 23:51:28: #2 alternative fragment length(s) may be 235 bps INFO @ Fri, 05 Jul 2019 23:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.20_model.r INFO @ Fri, 05 Jul 2019 23:51:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:51:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:51:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:51:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:51:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.10_summits.bed INFO @ Fri, 05 Jul 2019 23:51:28: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:51:29: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:51:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX386400/SRX386400.20_summits.bed INFO @ Fri, 05 Jul 2019 23:51:29: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (68 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。