Job ID = 2010558 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,477,884 reads read : 22,955,768 reads written : 22,955,768 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: 00:02:56 11477884 reads; of these: 11477884 (100.00%) were paired; of these: 9966853 (86.84%) aligned concordantly 0 times 1001856 (8.73%) aligned concordantly exactly 1 time 509175 (4.44%) aligned concordantly >1 times ---- 9966853 pairs aligned concordantly 0 times; of these: 43756 (0.44%) aligned discordantly 1 time ---- 9923097 pairs aligned 0 times concordantly or discordantly; of these: 19846194 mates make up the pairs; of these: 19716069 (99.34%) aligned 0 times 39504 (0.20%) aligned exactly 1 time 90621 (0.46%) aligned >1 times 14.11% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 240821 / 1551894 = 0.1552 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 23:15:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.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 23:15:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:15:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:15:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.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 23:15:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:15:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:15:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.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 23:15:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:15:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:15:49: 1000000 INFO @ Fri, 05 Jul 2019 23:15:51: 1000000 INFO @ Fri, 05 Jul 2019 23:15:55: 2000000 INFO @ Fri, 05 Jul 2019 23:15:56: 1000000 INFO @ Fri, 05 Jul 2019 23:15:59: 2000000 INFO @ Fri, 05 Jul 2019 23:16:00: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:16:00: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:16:00: #1 total tags in treatment: 1277777 INFO @ Fri, 05 Jul 2019 23:16:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:16:00: #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 23:16:00: #1 tags after filtering in treatment: 765093 INFO @ Fri, 05 Jul 2019 23:16:00: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:16:00: #1 finished! INFO @ Fri, 05 Jul 2019 23:16:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:16:00: #2 number of paired peaks: 836 WARNING @ Fri, 05 Jul 2019 23:16:00: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Fri, 05 Jul 2019 23:16:00: start model_add_line... INFO @ Fri, 05 Jul 2019 23:16:00: start X-correlation... INFO @ Fri, 05 Jul 2019 23:16:00: end of X-cor INFO @ Fri, 05 Jul 2019 23:16:00: #2 finished! INFO @ Fri, 05 Jul 2019 23:16:00: #2 predicted fragment length is 250 bps INFO @ Fri, 05 Jul 2019 23:16:00: #2 alternative fragment length(s) may be 2,250,300 bps INFO @ Fri, 05 Jul 2019 23:16:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.05_model.r INFO @ Fri, 05 Jul 2019 23:16:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:16:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:16:03: 2000000 INFO @ Fri, 05 Jul 2019 23:16:04: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:16:04: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:16:04: #1 total tags in treatment: 1277777 INFO @ Fri, 05 Jul 2019 23:16:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:16:04: #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 23:16:04: #1 tags after filtering in treatment: 765093 INFO @ Fri, 05 Jul 2019 23:16:04: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:16:04: #1 finished! INFO @ Fri, 05 Jul 2019 23:16:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:16:05: #2 number of paired peaks: 836 WARNING @ Fri, 05 Jul 2019 23:16:05: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Fri, 05 Jul 2019 23:16:05: start model_add_line... INFO @ Fri, 05 Jul 2019 23:16:05: start X-correlation... INFO @ Fri, 05 Jul 2019 23:16:05: end of X-cor INFO @ Fri, 05 Jul 2019 23:16:05: #2 finished! INFO @ Fri, 05 Jul 2019 23:16:05: #2 predicted fragment length is 250 bps INFO @ Fri, 05 Jul 2019 23:16:05: #2 alternative fragment length(s) may be 2,250,300 bps INFO @ Fri, 05 Jul 2019 23:16:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.10_model.r INFO @ Fri, 05 Jul 2019 23:16:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:16:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:16:05: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:16:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.05_summits.bed INFO @ Fri, 05 Jul 2019 23:16:07: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 23:16:07: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:16:07: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:16:07: #1 total tags in treatment: 1277777 INFO @ Fri, 05 Jul 2019 23:16:07: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:16:07: #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 23:16:07: #1 tags after filtering in treatment: 765093 INFO @ Fri, 05 Jul 2019 23:16:07: #1 Redundant rate of treatment: 0.40 INFO @ Fri, 05 Jul 2019 23:16:07: #1 finished! INFO @ Fri, 05 Jul 2019 23:16:07: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:16:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:16:07: #2 number of paired peaks: 836 WARNING @ Fri, 05 Jul 2019 23:16:07: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Fri, 05 Jul 2019 23:16:07: start model_add_line... INFO @ Fri, 05 Jul 2019 23:16:07: start X-correlation... INFO @ Fri, 05 Jul 2019 23:16:07: end of X-cor INFO @ Fri, 05 Jul 2019 23:16:07: #2 finished! INFO @ Fri, 05 Jul 2019 23:16:07: #2 predicted fragment length is 250 bps INFO @ Fri, 05 Jul 2019 23:16:07: #2 alternative fragment length(s) may be 2,250,300 bps INFO @ Fri, 05 Jul 2019 23:16:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.20_model.r INFO @ Fri, 05 Jul 2019 23:16:07: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:16:07: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:16:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:16:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:16:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:16:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.10_summits.bed INFO @ Fri, 05 Jul 2019 23:16:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 23:16:13: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381259/SRX381259.20_summits.bed INFO @ Fri, 05 Jul 2019 23:16:14: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 2 millis BigWig に変換しました。 CompletedMACS2peakCalling