Job ID = 2011903 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,243,241 reads read : 6,486,482 reads written : 6,486,482 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: 00:02:13 3243241 reads; of these: 3243241 (100.00%) were paired; of these: 446910 (13.78%) aligned concordantly 0 times 2389962 (73.69%) aligned concordantly exactly 1 time 406369 (12.53%) aligned concordantly >1 times ---- 446910 pairs aligned concordantly 0 times; of these: 266525 (59.64%) aligned discordantly 1 time ---- 180385 pairs aligned 0 times concordantly or discordantly; of these: 360770 mates make up the pairs; of these: 189784 (52.61%) aligned 0 times 68172 (18.90%) aligned exactly 1 time 102814 (28.50%) aligned >1 times 97.07% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 110961 / 3062254 = 0.0362 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 03:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.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 03:13:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:13:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:13:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.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 03:13:09: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:13:09: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.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 03:13:11: #1 read tag files... INFO @ Sat, 06 Jul 2019 03:13:11: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 03:13:15: 1000000 INFO @ Sat, 06 Jul 2019 03:13:16: 1000000 INFO @ Sat, 06 Jul 2019 03:13:16: 1000000 INFO @ Sat, 06 Jul 2019 03:13:20: 2000000 INFO @ Sat, 06 Jul 2019 03:13:23: 2000000 INFO @ Sat, 06 Jul 2019 03:13:23: 2000000 INFO @ Sat, 06 Jul 2019 03:13:26: 3000000 INFO @ Sat, 06 Jul 2019 03:13:29: 3000000 INFO @ Sat, 06 Jul 2019 03:13:29: 3000000 INFO @ Sat, 06 Jul 2019 03:13:32: 4000000 INFO @ Sat, 06 Jul 2019 03:13:34: 4000000 INFO @ Sat, 06 Jul 2019 03:13:36: 4000000 INFO @ Sat, 06 Jul 2019 03:13:38: 5000000 INFO @ Sat, 06 Jul 2019 03:13:40: 5000000 INFO @ Sat, 06 Jul 2019 03:13:42: 5000000 INFO @ Sat, 06 Jul 2019 03:13:43: 6000000 INFO @ Sat, 06 Jul 2019 03:13:44: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:13:44: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:13:44: #1 total tags in treatment: 2691786 INFO @ Sat, 06 Jul 2019 03:13:44: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:13:44: #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 03:13:44: #1 tags after filtering in treatment: 2277864 INFO @ Sat, 06 Jul 2019 03:13:44: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:13:44: #1 finished! INFO @ Sat, 06 Jul 2019 03:13:44: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:13:44: #2 number of paired peaks: 125 WARNING @ Sat, 06 Jul 2019 03:13:44: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Sat, 06 Jul 2019 03:13:44: start model_add_line... INFO @ Sat, 06 Jul 2019 03:13:44: start X-correlation... INFO @ Sat, 06 Jul 2019 03:13:44: end of X-cor INFO @ Sat, 06 Jul 2019 03:13:44: #2 finished! INFO @ Sat, 06 Jul 2019 03:13:44: #2 predicted fragment length is 249 bps INFO @ Sat, 06 Jul 2019 03:13:44: #2 alternative fragment length(s) may be 3,218,249,266,289 bps INFO @ Sat, 06 Jul 2019 03:13:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.05_model.r INFO @ Sat, 06 Jul 2019 03:13:44: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:13:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:13:46: 6000000 INFO @ Sat, 06 Jul 2019 03:13:47: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:13:47: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:13:47: #1 total tags in treatment: 2691786 INFO @ Sat, 06 Jul 2019 03:13:47: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:13:47: #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 03:13:47: #1 tags after filtering in treatment: 2277864 INFO @ Sat, 06 Jul 2019 03:13:47: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:13:47: #1 finished! INFO @ Sat, 06 Jul 2019 03:13:47: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:13:47: #2 number of paired peaks: 125 WARNING @ Sat, 06 Jul 2019 03:13:47: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Sat, 06 Jul 2019 03:13:47: start model_add_line... INFO @ Sat, 06 Jul 2019 03:13:47: start X-correlation... INFO @ Sat, 06 Jul 2019 03:13:47: end of X-cor INFO @ Sat, 06 Jul 2019 03:13:47: #2 finished! INFO @ Sat, 06 Jul 2019 03:13:47: #2 predicted fragment length is 249 bps INFO @ Sat, 06 Jul 2019 03:13:47: #2 alternative fragment length(s) may be 3,218,249,266,289 bps INFO @ Sat, 06 Jul 2019 03:13:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.20_model.r INFO @ Sat, 06 Jul 2019 03:13:47: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:13:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:13:48: 6000000 INFO @ Sat, 06 Jul 2019 03:13:49: #1 tag size is determined as 37 bps INFO @ Sat, 06 Jul 2019 03:13:49: #1 tag size = 37 INFO @ Sat, 06 Jul 2019 03:13:49: #1 total tags in treatment: 2691786 INFO @ Sat, 06 Jul 2019 03:13:49: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 03:13:49: #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 03:13:49: #1 tags after filtering in treatment: 2277864 INFO @ Sat, 06 Jul 2019 03:13:49: #1 Redundant rate of treatment: 0.15 INFO @ Sat, 06 Jul 2019 03:13:49: #1 finished! INFO @ Sat, 06 Jul 2019 03:13:49: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 03:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 03:13:49: #2 number of paired peaks: 125 WARNING @ Sat, 06 Jul 2019 03:13:49: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Sat, 06 Jul 2019 03:13:49: start model_add_line... INFO @ Sat, 06 Jul 2019 03:13:49: start X-correlation... INFO @ Sat, 06 Jul 2019 03:13:49: end of X-cor INFO @ Sat, 06 Jul 2019 03:13:49: #2 finished! INFO @ Sat, 06 Jul 2019 03:13:49: #2 predicted fragment length is 249 bps INFO @ Sat, 06 Jul 2019 03:13:49: #2 alternative fragment length(s) may be 3,218,249,266,289 bps INFO @ Sat, 06 Jul 2019 03:13:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.10_model.r INFO @ Sat, 06 Jul 2019 03:13:49: #3 Call peaks... INFO @ Sat, 06 Jul 2019 03:13:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 03:13:52: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:13:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.05_peaks.xls INFO @ Sat, 06 Jul 2019 03:13:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:13:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.05_summits.bed INFO @ Sat, 06 Jul 2019 03:13:55: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:13:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (942 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:13:58: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 03:13:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.20_peaks.xls INFO @ Sat, 06 Jul 2019 03:13:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:13:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.20_summits.bed INFO @ Sat, 06 Jul 2019 03:13:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (350 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 06 Jul 2019 03:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.10_peaks.xls INFO @ Sat, 06 Jul 2019 03:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 03:14:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5383676/SRX5383676.10_summits.bed INFO @ Sat, 06 Jul 2019 03:14:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。