Job ID = 2011914 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,079,481 reads read : 4,158,962 reads written : 4,158,962 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: 00:01:27 2079481 reads; of these: 2079481 (100.00%) were paired; of these: 287984 (13.85%) aligned concordantly 0 times 1581204 (76.04%) aligned concordantly exactly 1 time 210293 (10.11%) aligned concordantly >1 times ---- 287984 pairs aligned concordantly 0 times; of these: 185833 (64.53%) aligned discordantly 1 time ---- 102151 pairs aligned 0 times concordantly or discordantly; of these: 204302 mates make up the pairs; of these: 105639 (51.71%) aligned 0 times 44477 (21.77%) aligned exactly 1 time 54186 (26.52%) aligned >1 times 97.46% overall alignment rate Time searching: 00:01:27 Overall time: 00:01:27 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] 51570 / 1976463 = 0.0261 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 03:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.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 03:18:06: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:18:06: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:18:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.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 03:18:07: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:18:07: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:18:13: 1000000 INFO @ Sat, 06 Jul 2019 03:18:13: 1000000 INFO @ Sat, 06 Jul 2019 03:18:20: 2000000 INFO @ Sat, 06 Jul 2019 03:18:21: 2000000 INFO @ Sat, 06 Jul 2019 03:18:26: 3000000 INFO @ Sat, 06 Jul 2019 03:18:28: 3000000 INFO @ Sat, 06 Jul 2019 03:18:32: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:18:32: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:18:32: #1 total tags in treatment: 1743629 INFO @ Sat, 06 Jul 2019 03:18:32: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:32: #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 03:18:32: #1 tags after filtering in treatment: 1561944 INFO @ Sat, 06 Jul 2019 03:18:32: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 06 Jul 2019 03:18:32: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:32: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:32: #2 number of paired peaks: 193 WARNING @ Sat, 06 Jul 2019 03:18:32: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 06 Jul 2019 03:18:32: start model_add_line... INFO @ Sat, 06 Jul 2019 03:18:32: start X-correlation... INFO @ Sat, 06 Jul 2019 03:18:32: end of X-cor INFO @ Sat, 06 Jul 2019 03:18:32: #2 finished! INFO @ Sat, 06 Jul 2019 03:18:32: #2 predicted fragment length is 244 bps INFO @ Sat, 06 Jul 2019 03:18:32: #2 alternative fragment length(s) may be 0,53,196,244,272,291,331,428,467,533 bps INFO @ Sat, 06 Jul 2019 03:18:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.10_model.r INFO @ Sat, 06 Jul 2019 03:18:33: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:18:34: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:18:34: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:18:34: #1 total tags in treatment: 1743629 INFO @ Sat, 06 Jul 2019 03:18:34: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:18:34: #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 03:18:34: #1 tags after filtering in treatment: 1561944 INFO @ Sat, 06 Jul 2019 03:18:34: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 06 Jul 2019 03:18:34: #1 finished! INFO @ Sat, 06 Jul 2019 03:18:34: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:18:35: #2 number of paired peaks: 193 WARNING @ Sat, 06 Jul 2019 03:18:35: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 06 Jul 2019 03:18:35: start model_add_line... INFO @ Sat, 06 Jul 2019 03:18:35: start X-correlation... INFO @ Sat, 06 Jul 2019 03:18:35: end of X-cor INFO @ Sat, 06 Jul 2019 03:18:35: #2 finished! INFO @ Sat, 06 Jul 2019 03:18:35: #2 predicted fragment length is 244 bps INFO @ Sat, 06 Jul 2019 03:18:35: #2 alternative fragment length(s) may be 0,53,196,244,272,291,331,428,467,533 bps INFO @ Sat, 06 Jul 2019 03:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.05_model.r INFO @ Sat, 06 Jul 2019 03:18:35: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:18:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.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 03:18:35: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:18:35: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:18:38: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:18:40: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:18:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:18:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:18:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.10_summits.bed INFO @ Sat, 06 Jul 2019 03:18:40: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.05_summits.bed INFO @ Sat, 06 Jul 2019 03:18:42: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:18:43: 1000000 INFO @ Sat, 06 Jul 2019 03:18:50: 2000000 INFO @ Sat, 06 Jul 2019 03:18:57: 3000000 INFO @ Sat, 06 Jul 2019 03:19:03: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:19:03: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:19:03: #1 total tags in treatment: 1743629 INFO @ Sat, 06 Jul 2019 03:19:03: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:19:03: #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 03:19:03: #1 tags after filtering in treatment: 1561944 INFO @ Sat, 06 Jul 2019 03:19:03: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 06 Jul 2019 03:19:03: #1 finished! INFO @ Sat, 06 Jul 2019 03:19:03: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:19:03: #2 number of paired peaks: 193 WARNING @ Sat, 06 Jul 2019 03:19:03: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 06 Jul 2019 03:19:03: start model_add_line... INFO @ Sat, 06 Jul 2019 03:19:03: start X-correlation... INFO @ Sat, 06 Jul 2019 03:19:03: end of X-cor INFO @ Sat, 06 Jul 2019 03:19:03: #2 finished! INFO @ Sat, 06 Jul 2019 03:19:03: #2 predicted fragment length is 244 bps INFO @ Sat, 06 Jul 2019 03:19:03: #2 alternative fragment length(s) may be 0,53,196,244,272,291,331,428,467,533 bps INFO @ Sat, 06 Jul 2019 03:19:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.20_model.r INFO @ Sat, 06 Jul 2019 03:19:03: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:19:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:19:08: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:19:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:19:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:19:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383687/SRX5383687.20_summits.bed INFO @ Sat, 06 Jul 2019 03:19:10: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 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。