Job ID = 2010629 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,821,976 reads read : 5,643,952 reads written : 5,643,952 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: 00:01:34 2821976 reads; of these: 2821976 (100.00%) were paired; of these: 1606306 (56.92%) aligned concordantly 0 times 702779 (24.90%) aligned concordantly exactly 1 time 512891 (18.17%) aligned concordantly >1 times ---- 1606306 pairs aligned concordantly 0 times; of these: 1820 (0.11%) aligned discordantly 1 time ---- 1604486 pairs aligned 0 times concordantly or discordantly; of these: 3208972 mates make up the pairs; of these: 3151280 (98.20%) aligned 0 times 29792 (0.93%) aligned exactly 1 time 27900 (0.87%) aligned >1 times 44.17% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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] 139641 / 1216786 = 0.1148 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 23:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.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 23:44:54: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:54: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.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 23:44:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.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 23:44:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:44:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:45:05: 1000000 INFO @ Fri, 05 Jul 2019 23:45:06: 1000000 INFO @ Fri, 05 Jul 2019 23:45:07: 1000000 INFO @ Fri, 05 Jul 2019 23:45:17: 2000000 INFO @ Fri, 05 Jul 2019 23:45:18: 2000000 INFO @ Fri, 05 Jul 2019 23:45:19: 2000000 INFO @ Fri, 05 Jul 2019 23:45:20: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 23:45:20: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 23:45:20: #1 total tags in treatment: 1076110 INFO @ Fri, 05 Jul 2019 23:45:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:45:20: #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 23:45:20: #1 tags after filtering in treatment: 664715 INFO @ Fri, 05 Jul 2019 23:45:20: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:45:20: #1 finished! INFO @ Fri, 05 Jul 2019 23:45:20: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:45:20: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 23:45:20: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 23:45:20: start model_add_line... INFO @ Fri, 05 Jul 2019 23:45:20: start X-correlation... INFO @ Fri, 05 Jul 2019 23:45:20: end of X-cor INFO @ Fri, 05 Jul 2019 23:45:20: #2 finished! INFO @ Fri, 05 Jul 2019 23:45:20: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 23:45:20: #2 alternative fragment length(s) may be 2,26,158,190,587 bps INFO @ Fri, 05 Jul 2019 23:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.05_model.r INFO @ Fri, 05 Jul 2019 23:45:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:45:20: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 23:45:20: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 23:45:20: #1 total tags in treatment: 1076110 INFO @ Fri, 05 Jul 2019 23:45:20: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:45:20: #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 23:45:21: #1 tags after filtering in treatment: 664715 INFO @ Fri, 05 Jul 2019 23:45:21: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:45:21: #1 finished! INFO @ Fri, 05 Jul 2019 23:45:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:45:21: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 23:45:21: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 23:45:21: start model_add_line... INFO @ Fri, 05 Jul 2019 23:45:21: start X-correlation... INFO @ Fri, 05 Jul 2019 23:45:21: end of X-cor INFO @ Fri, 05 Jul 2019 23:45:21: #2 finished! INFO @ Fri, 05 Jul 2019 23:45:21: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 23:45:21: #2 alternative fragment length(s) may be 2,26,158,190,587 bps INFO @ Fri, 05 Jul 2019 23:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.20_model.r INFO @ Fri, 05 Jul 2019 23:45:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:45:21: #1 tag size is determined as 76 bps INFO @ Fri, 05 Jul 2019 23:45:21: #1 tag size = 76 INFO @ Fri, 05 Jul 2019 23:45:21: #1 total tags in treatment: 1076110 INFO @ Fri, 05 Jul 2019 23:45:21: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:45:21: #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 23:45:21: #1 tags after filtering in treatment: 664715 INFO @ Fri, 05 Jul 2019 23:45:21: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 05 Jul 2019 23:45:21: #1 finished! INFO @ Fri, 05 Jul 2019 23:45:21: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:45:21: #2 number of paired peaks: 158 WARNING @ Fri, 05 Jul 2019 23:45:21: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Fri, 05 Jul 2019 23:45:21: start model_add_line... INFO @ Fri, 05 Jul 2019 23:45:21: start X-correlation... INFO @ Fri, 05 Jul 2019 23:45:21: end of X-cor INFO @ Fri, 05 Jul 2019 23:45:21: #2 finished! INFO @ Fri, 05 Jul 2019 23:45:21: #2 predicted fragment length is 158 bps INFO @ Fri, 05 Jul 2019 23:45:21: #2 alternative fragment length(s) may be 2,26,158,190,587 bps INFO @ Fri, 05 Jul 2019 23:45:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.10_model.r INFO @ Fri, 05 Jul 2019 23:45:21: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:45:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:45:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:45:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:45:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.05_summits.bed INFO @ Fri, 05 Jul 2019 23:45:23: Done! INFO @ Fri, 05 Jul 2019 23:45:23: #3 Call peaks for each chromosome... pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (65 records, 4 fields): 196 millis INFO @ Fri, 05 Jul 2019 23:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.20_summits.bed INFO @ Fri, 05 Jul 2019 23:45:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (22 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX3828987/SRX3828987.10_summits.bed INFO @ Fri, 05 Jul 2019 23:45:24: Done! CompletedMACS2peakCalling pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (35 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。