Job ID = 2011891 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,310,151 reads read : 8,620,302 reads written : 8,620,302 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: 00:02:54 4310151 reads; of these: 4310151 (100.00%) were paired; of these: 653511 (15.16%) aligned concordantly 0 times 3169689 (73.54%) aligned concordantly exactly 1 time 486951 (11.30%) aligned concordantly >1 times ---- 653511 pairs aligned concordantly 0 times; of these: 416168 (63.68%) aligned discordantly 1 time ---- 237343 pairs aligned 0 times concordantly or discordantly; of these: 474686 mates make up the pairs; of these: 234941 (49.49%) aligned 0 times 97457 (20.53%) aligned exactly 1 time 142288 (29.98%) aligned >1 times 97.27% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 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] 127862 / 4071386 = 0.0314 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 @ Sat, 06 Jul 2019 03:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.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, 06 Jul 2019 03:08:14: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:08:14: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.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, 06 Jul 2019 03:08:14: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:08:14: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.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, 06 Jul 2019 03:08:16: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:08:16: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:08:21: 1000000 INFO @ Sat, 06 Jul 2019 03:08:22: 1000000 INFO @ Sat, 06 Jul 2019 03:08:22: 1000000 INFO @ Sat, 06 Jul 2019 03:08:28: 2000000 INFO @ Sat, 06 Jul 2019 03:08:29: 2000000 INFO @ Sat, 06 Jul 2019 03:08:30: 2000000 INFO @ Sat, 06 Jul 2019 03:08:35: 3000000 INFO @ Sat, 06 Jul 2019 03:08:36: 3000000 INFO @ Sat, 06 Jul 2019 03:08:38: 3000000 INFO @ Sat, 06 Jul 2019 03:08:42: 4000000 INFO @ Sat, 06 Jul 2019 03:08:43: 4000000 INFO @ Sat, 06 Jul 2019 03:08:45: 4000000 INFO @ Sat, 06 Jul 2019 03:08:49: 5000000 INFO @ Sat, 06 Jul 2019 03:08:50: 5000000 INFO @ Sat, 06 Jul 2019 03:08:52: 5000000 INFO @ Sat, 06 Jul 2019 03:08:56: 6000000 INFO @ Sat, 06 Jul 2019 03:08:57: 6000000 INFO @ Sat, 06 Jul 2019 03:08:59: 6000000 INFO @ Sat, 06 Jul 2019 03:09:04: 7000000 INFO @ Sat, 06 Jul 2019 03:09:04: 7000000 INFO @ Sat, 06 Jul 2019 03:09:06: 7000000 INFO @ Sat, 06 Jul 2019 03:09:11: 8000000 INFO @ Sat, 06 Jul 2019 03:09:11: 8000000 INFO @ Sat, 06 Jul 2019 03:09:12: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:09:12: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:09:12: #1 total tags in treatment: 3537879 INFO @ Sat, 06 Jul 2019 03:09:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:09:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:09:12: #1 tags after filtering in treatment: 2878381 INFO @ Sat, 06 Jul 2019 03:09:12: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 06 Jul 2019 03:09:12: #1 finished! INFO @ Sat, 06 Jul 2019 03:09:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:09:12: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:09:12: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:09:12: start model_add_line... INFO @ Sat, 06 Jul 2019 03:09:12: start X-correlation... INFO @ Sat, 06 Jul 2019 03:09:12: end of X-cor INFO @ Sat, 06 Jul 2019 03:09:12: #2 finished! INFO @ Sat, 06 Jul 2019 03:09:12: #2 predicted fragment length is 323 bps INFO @ Sat, 06 Jul 2019 03:09:12: #2 alternative fragment length(s) may be 0,47,79,97,120,155,178,193,200,226,255,263,271,294,303,323,345,363,388,449,487,559,584 bps INFO @ Sat, 06 Jul 2019 03:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.05_model.r INFO @ Sat, 06 Jul 2019 03:09:12: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:09:12: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:09:12: #1 total tags in treatment: 3537879 INFO @ Sat, 06 Jul 2019 03:09:12: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:09:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:09:12: #1 tags after filtering in treatment: 2878381 INFO @ Sat, 06 Jul 2019 03:09:12: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 06 Jul 2019 03:09:12: #1 finished! INFO @ Sat, 06 Jul 2019 03:09:12: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:09:12: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:09:12: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:09:12: start model_add_line... INFO @ Sat, 06 Jul 2019 03:09:12: start X-correlation... INFO @ Sat, 06 Jul 2019 03:09:12: end of X-cor INFO @ Sat, 06 Jul 2019 03:09:12: #2 finished! INFO @ Sat, 06 Jul 2019 03:09:12: #2 predicted fragment length is 323 bps INFO @ Sat, 06 Jul 2019 03:09:12: #2 alternative fragment length(s) may be 0,47,79,97,120,155,178,193,200,226,255,263,271,294,303,323,345,363,388,449,487,559,584 bps INFO @ Sat, 06 Jul 2019 03:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.10_model.r INFO @ Sat, 06 Jul 2019 03:09:14: 8000000 INFO @ Sat, 06 Jul 2019 03:09:14: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:09:14: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:09:14: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:09:14: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:09:14: #1 total tags in treatment: 3537879 INFO @ Sat, 06 Jul 2019 03:09:14: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:09:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 06 Jul 2019 03:09:14: #1 tags after filtering in treatment: 2878381 INFO @ Sat, 06 Jul 2019 03:09:14: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 06 Jul 2019 03:09:14: #1 finished! INFO @ Sat, 06 Jul 2019 03:09:14: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:09:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:09:15: #2 number of paired peaks: 170 WARNING @ Sat, 06 Jul 2019 03:09:15: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Sat, 06 Jul 2019 03:09:15: start model_add_line... INFO @ Sat, 06 Jul 2019 03:09:15: start X-correlation... INFO @ Sat, 06 Jul 2019 03:09:15: end of X-cor INFO @ Sat, 06 Jul 2019 03:09:15: #2 finished! INFO @ Sat, 06 Jul 2019 03:09:15: #2 predicted fragment length is 323 bps INFO @ Sat, 06 Jul 2019 03:09:15: #2 alternative fragment length(s) may be 0,47,79,97,120,155,178,193,200,226,255,263,271,294,303,323,345,363,388,449,487,559,584 bps INFO @ Sat, 06 Jul 2019 03:09:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.20_model.r INFO @ Sat, 06 Jul 2019 03:09:15: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:09:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:09:22: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:09:22: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:09:23: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:09:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:09:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:09:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.10_summits.bed INFO @ Sat, 06 Jul 2019 03:09:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:09:25: Done! INFO @ Sat, 06 Jul 2019 03:09:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:09:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.05_summits.bed INFO @ Sat, 06 Jul 2019 03:09:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:09:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:09:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:09:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383667/SRX5383667.20_summits.bed INFO @ Sat, 06 Jul 2019 03:09:26: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。