Job ID = 2641243 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 995,740 reads read : 1,991,480 reads written : 1,991,480 spots read : 980,633 reads read : 1,961,266 reads written : 1,961,266 spots read : 996,869 reads read : 1,993,738 reads written : 1,993,738 spots read : 985,191 reads read : 1,970,382 reads written : 1,970,382 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: 00:01:53 3958433 reads; of these: 3958433 (100.00%) were paired; of these: 1469801 (37.13%) aligned concordantly 0 times 2186355 (55.23%) aligned concordantly exactly 1 time 302277 (7.64%) aligned concordantly >1 times ---- 1469801 pairs aligned concordantly 0 times; of these: 7487 (0.51%) aligned discordantly 1 time ---- 1462314 pairs aligned 0 times concordantly or discordantly; of these: 2924628 mates make up the pairs; of these: 2444155 (83.57%) aligned 0 times 408007 (13.95%) aligned exactly 1 time 72466 (2.48%) aligned >1 times 69.13% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 50225 / 2492998 = 0.0201 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 22:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.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, 24 Aug 2019 22:18:02: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:18:02: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:18:08: 1000000 INFO @ Sat, 24 Aug 2019 22:18:14: 2000000 INFO @ Sat, 24 Aug 2019 22:18:20: 3000000 INFO @ Sat, 24 Aug 2019 22:18:26: 4000000 INFO @ Sat, 24 Aug 2019 22:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.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, 24 Aug 2019 22:18:31: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:18:31: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:18:32: 5000000 INFO @ Sat, 24 Aug 2019 22:18:34: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:18:34: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:18:34: #1 total tags in treatment: 2438460 INFO @ Sat, 24 Aug 2019 22:18:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:18:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:18:34: #1 tags after filtering in treatment: 2170362 INFO @ Sat, 24 Aug 2019 22:18:34: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:18:34: #1 finished! INFO @ Sat, 24 Aug 2019 22:18:34: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:18:34: #2 number of paired peaks: 100 WARNING @ Sat, 24 Aug 2019 22:18:34: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 24 Aug 2019 22:18:34: start model_add_line... INFO @ Sat, 24 Aug 2019 22:18:34: start X-correlation... INFO @ Sat, 24 Aug 2019 22:18:34: end of X-cor INFO @ Sat, 24 Aug 2019 22:18:34: #2 finished! INFO @ Sat, 24 Aug 2019 22:18:34: #2 predicted fragment length is 245 bps INFO @ Sat, 24 Aug 2019 22:18:34: #2 alternative fragment length(s) may be 2,50,208,245,261,264,288,326 bps INFO @ Sat, 24 Aug 2019 22:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.05_model.r INFO @ Sat, 24 Aug 2019 22:18:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:18:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:18:38: 1000000 INFO @ Sat, 24 Aug 2019 22:18:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:18:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.05_peaks.xls INFO @ Sat, 24 Aug 2019 22:18:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:18:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.05_summits.bed INFO @ Sat, 24 Aug 2019 22:18:43: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:18:45: 2000000 INFO @ Sat, 24 Aug 2019 22:18:52: 3000000 INFO @ Sat, 24 Aug 2019 22:18:58: 4000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 22:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.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, 24 Aug 2019 22:19:01: #1 read tag files... INFO @ Sat, 24 Aug 2019 22:19:01: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 22:19:05: 5000000 INFO @ Sat, 24 Aug 2019 22:19:07: 1000000 INFO @ Sat, 24 Aug 2019 22:19:08: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:19:08: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:19:08: #1 total tags in treatment: 2438460 INFO @ Sat, 24 Aug 2019 22:19:08: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:19:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:19:08: #1 tags after filtering in treatment: 2170362 INFO @ Sat, 24 Aug 2019 22:19:08: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:19:08: #1 finished! INFO @ Sat, 24 Aug 2019 22:19:08: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:19:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:19:08: #2 number of paired peaks: 100 WARNING @ Sat, 24 Aug 2019 22:19:08: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 24 Aug 2019 22:19:08: start model_add_line... INFO @ Sat, 24 Aug 2019 22:19:08: start X-correlation... INFO @ Sat, 24 Aug 2019 22:19:08: end of X-cor INFO @ Sat, 24 Aug 2019 22:19:08: #2 finished! INFO @ Sat, 24 Aug 2019 22:19:08: #2 predicted fragment length is 245 bps INFO @ Sat, 24 Aug 2019 22:19:08: #2 alternative fragment length(s) may be 2,50,208,245,261,264,288,326 bps INFO @ Sat, 24 Aug 2019 22:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.10_model.r INFO @ Sat, 24 Aug 2019 22:19:08: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:19:13: 2000000 INFO @ Sat, 24 Aug 2019 22:19:14: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:19:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.10_peaks.xls INFO @ Sat, 24 Aug 2019 22:19:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:19:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.10_summits.bed INFO @ Sat, 24 Aug 2019 22:19:16: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 22:19:19: 3000000 INFO @ Sat, 24 Aug 2019 22:19:25: 4000000 INFO @ Sat, 24 Aug 2019 22:19:31: 5000000 INFO @ Sat, 24 Aug 2019 22:19:33: #1 tag size is determined as 35 bps INFO @ Sat, 24 Aug 2019 22:19:33: #1 tag size = 35 INFO @ Sat, 24 Aug 2019 22:19:33: #1 total tags in treatment: 2438460 INFO @ Sat, 24 Aug 2019 22:19:33: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 22:19:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 22:19:33: #1 tags after filtering in treatment: 2170362 INFO @ Sat, 24 Aug 2019 22:19:33: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 24 Aug 2019 22:19:33: #1 finished! INFO @ Sat, 24 Aug 2019 22:19:33: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 22:19:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 22:19:33: #2 number of paired peaks: 100 WARNING @ Sat, 24 Aug 2019 22:19:33: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Sat, 24 Aug 2019 22:19:33: start model_add_line... INFO @ Sat, 24 Aug 2019 22:19:33: start X-correlation... INFO @ Sat, 24 Aug 2019 22:19:33: end of X-cor INFO @ Sat, 24 Aug 2019 22:19:33: #2 finished! INFO @ Sat, 24 Aug 2019 22:19:33: #2 predicted fragment length is 245 bps INFO @ Sat, 24 Aug 2019 22:19:33: #2 alternative fragment length(s) may be 2,50,208,245,261,264,288,326 bps INFO @ Sat, 24 Aug 2019 22:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.20_model.r INFO @ Sat, 24 Aug 2019 22:19:33: #3 Call peaks... INFO @ Sat, 24 Aug 2019 22:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 22:19:40: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 22:19:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.20_peaks.xls INFO @ Sat, 24 Aug 2019 22:19:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 22:19:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6403220/SRX6403220.20_summits.bed INFO @ Sat, 24 Aug 2019 22:19:42: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。