Job ID = 2010565 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 9,809,731 reads read : 19,619,462 reads written : 19,619,462 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: 00:03:44 9809731 reads; of these: 9809731 (100.00%) were paired; of these: 7602332 (77.50%) aligned concordantly 0 times 1630498 (16.62%) aligned concordantly exactly 1 time 576901 (5.88%) aligned concordantly >1 times ---- 7602332 pairs aligned concordantly 0 times; of these: 19265 (0.25%) aligned discordantly 1 time ---- 7583067 pairs aligned 0 times concordantly or discordantly; of these: 15166134 mates make up the pairs; of these: 15021988 (99.05%) aligned 0 times 74053 (0.49%) aligned exactly 1 time 70093 (0.46%) aligned >1 times 23.43% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 511172 / 2223630 = 0.2299 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 23:20:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.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 23:20:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.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 23:20:58: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:58: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:20:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.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 23:20:59: #1 read tag files... INFO @ Fri, 05 Jul 2019 23:20:59: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 23:21:07: 1000000 INFO @ Fri, 05 Jul 2019 23:21:07: 1000000 INFO @ Fri, 05 Jul 2019 23:21:08: 1000000 INFO @ Fri, 05 Jul 2019 23:21:14: 2000000 INFO @ Fri, 05 Jul 2019 23:21:17: 2000000 INFO @ Fri, 05 Jul 2019 23:21:18: 2000000 INFO @ Fri, 05 Jul 2019 23:21:21: 3000000 INFO @ Fri, 05 Jul 2019 23:21:25: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:21:25: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:21:25: #1 total tags in treatment: 1698352 INFO @ Fri, 05 Jul 2019 23:21:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:21:25: #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 23:21:25: #1 tags after filtering in treatment: 999514 INFO @ Fri, 05 Jul 2019 23:21:25: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:21:25: #1 finished! INFO @ Fri, 05 Jul 2019 23:21:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:21:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:21:25: #2 number of paired peaks: 1078 INFO @ Fri, 05 Jul 2019 23:21:25: start model_add_line... INFO @ Fri, 05 Jul 2019 23:21:25: start X-correlation... INFO @ Fri, 05 Jul 2019 23:21:25: end of X-cor INFO @ Fri, 05 Jul 2019 23:21:25: #2 finished! INFO @ Fri, 05 Jul 2019 23:21:25: #2 predicted fragment length is 209 bps INFO @ Fri, 05 Jul 2019 23:21:25: #2 alternative fragment length(s) may be 2,190,209,231 bps INFO @ Fri, 05 Jul 2019 23:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.20_model.r INFO @ Fri, 05 Jul 2019 23:21:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:21:26: 3000000 INFO @ Fri, 05 Jul 2019 23:21:27: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 23:21:31: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:21:31: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:21:31: #1 total tags in treatment: 1698352 INFO @ Fri, 05 Jul 2019 23:21:31: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:21:31: #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 23:21:31: #1 tags after filtering in treatment: 999514 INFO @ Fri, 05 Jul 2019 23:21:31: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:21:31: #1 finished! INFO @ Fri, 05 Jul 2019 23:21:31: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:21:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:21:31: #2 number of paired peaks: 1078 INFO @ Fri, 05 Jul 2019 23:21:31: start model_add_line... INFO @ Fri, 05 Jul 2019 23:21:31: start X-correlation... INFO @ Fri, 05 Jul 2019 23:21:31: end of X-cor INFO @ Fri, 05 Jul 2019 23:21:31: #2 finished! INFO @ Fri, 05 Jul 2019 23:21:31: #2 predicted fragment length is 209 bps INFO @ Fri, 05 Jul 2019 23:21:31: #2 alternative fragment length(s) may be 2,190,209,231 bps INFO @ Fri, 05 Jul 2019 23:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.05_model.r INFO @ Fri, 05 Jul 2019 23:21:31: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:21:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 23:21:32: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 23:21:32: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 23:21:32: #1 total tags in treatment: 1698352 INFO @ Fri, 05 Jul 2019 23:21:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 23:21:32: #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 23:21:32: #1 tags after filtering in treatment: 999514 INFO @ Fri, 05 Jul 2019 23:21:32: #1 Redundant rate of treatment: 0.41 INFO @ Fri, 05 Jul 2019 23:21:32: #1 finished! INFO @ Fri, 05 Jul 2019 23:21:32: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 23:21:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 23:21:32: #2 number of paired peaks: 1078 INFO @ Fri, 05 Jul 2019 23:21:32: start model_add_line... INFO @ Fri, 05 Jul 2019 23:21:32: start X-correlation... INFO @ Fri, 05 Jul 2019 23:21:32: end of X-cor INFO @ Fri, 05 Jul 2019 23:21:32: #2 finished! INFO @ Fri, 05 Jul 2019 23:21:32: #2 predicted fragment length is 209 bps INFO @ Fri, 05 Jul 2019 23:21:32: #2 alternative fragment length(s) may be 2,190,209,231 bps INFO @ Fri, 05 Jul 2019 23:21:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.10_model.r INFO @ Fri, 05 Jul 2019 23:21:32: #3 Call peaks... INFO @ Fri, 05 Jul 2019 23:21:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 23:21:32: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.20_peaks.xls INFO @ Fri, 05 Jul 2019 23:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.20_summits.bed INFO @ Fri, 05 Jul 2019 23:21:33: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (250 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 23:21:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:21:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 23:21:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.05_peaks.xls INFO @ Fri, 05 Jul 2019 23:21:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:21:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.05_summits.bed INFO @ Fri, 05 Jul 2019 23:21:40: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 23:21:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.10_peaks.xls INFO @ Fri, 05 Jul 2019 23:21:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 23:21:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX381266/SRX381266.10_summits.bed INFO @ Fri, 05 Jul 2019 23:21:41: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling