Job ID = 2008066 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,684,262 reads read : 3,368,524 reads written : 3,368,524 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: 00:02:11 1684262 reads; of these: 1684262 (100.00%) were paired; of these: 308004 (18.29%) aligned concordantly 0 times 1260825 (74.86%) aligned concordantly exactly 1 time 115433 (6.85%) aligned concordantly >1 times ---- 308004 pairs aligned concordantly 0 times; of these: 33826 (10.98%) aligned discordantly 1 time ---- 274178 pairs aligned 0 times concordantly or discordantly; of these: 548356 mates make up the pairs; of these: 520124 (94.85%) aligned 0 times 18217 (3.32%) aligned exactly 1 time 10015 (1.83%) aligned >1 times 84.56% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 258726 / 1405380 = 0.1841 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 17:31:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.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 17:31:31: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:31:31: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.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 17:31:32: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:31:32: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:31:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.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 17:31:33: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:31:33: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:31:43: 1000000 INFO @ Fri, 05 Jul 2019 17:31:45: 1000000 INFO @ Fri, 05 Jul 2019 17:31:45: 1000000 INFO @ Fri, 05 Jul 2019 17:31:53: 2000000 INFO @ Fri, 05 Jul 2019 17:31:56: 2000000 INFO @ Fri, 05 Jul 2019 17:31:59: 2000000 INFO @ Fri, 05 Jul 2019 17:32:03: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:32:03: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:32:03: #1 total tags in treatment: 1121137 INFO @ Fri, 05 Jul 2019 17:32:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:32:03: #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 17:32:03: #1 tags after filtering in treatment: 1069906 INFO @ Fri, 05 Jul 2019 17:32:03: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:32:03: #1 finished! INFO @ Fri, 05 Jul 2019 17:32:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:32:03: #2 number of paired peaks: 167 WARNING @ Fri, 05 Jul 2019 17:32:03: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 05 Jul 2019 17:32:03: start model_add_line... INFO @ Fri, 05 Jul 2019 17:32:03: start X-correlation... INFO @ Fri, 05 Jul 2019 17:32:03: end of X-cor INFO @ Fri, 05 Jul 2019 17:32:03: #2 finished! INFO @ Fri, 05 Jul 2019 17:32:03: #2 predicted fragment length is 225 bps INFO @ Fri, 05 Jul 2019 17:32:03: #2 alternative fragment length(s) may be 1,131,176,198,225,238,266,561,582,584 bps INFO @ Fri, 05 Jul 2019 17:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.10_model.r INFO @ Fri, 05 Jul 2019 17:32:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:32:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:32:04: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:32:04: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:32:04: #1 total tags in treatment: 1121137 INFO @ Fri, 05 Jul 2019 17:32:04: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:32:04: #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 17:32:04: #1 tags after filtering in treatment: 1069906 INFO @ Fri, 05 Jul 2019 17:32:04: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:32:04: #1 finished! INFO @ Fri, 05 Jul 2019 17:32:04: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:32:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:32:04: #2 number of paired peaks: 167 WARNING @ Fri, 05 Jul 2019 17:32:04: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 05 Jul 2019 17:32:04: start model_add_line... INFO @ Fri, 05 Jul 2019 17:32:04: start X-correlation... INFO @ Fri, 05 Jul 2019 17:32:04: end of X-cor INFO @ Fri, 05 Jul 2019 17:32:04: #2 finished! INFO @ Fri, 05 Jul 2019 17:32:04: #2 predicted fragment length is 225 bps INFO @ Fri, 05 Jul 2019 17:32:04: #2 alternative fragment length(s) may be 1,131,176,198,225,238,266,561,582,584 bps INFO @ Fri, 05 Jul 2019 17:32:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.20_model.r INFO @ Fri, 05 Jul 2019 17:32:04: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:32:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:32:05: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:32:05: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:32:05: #1 total tags in treatment: 1121137 INFO @ Fri, 05 Jul 2019 17:32:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:32:05: #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 17:32:05: #1 tags after filtering in treatment: 1069906 INFO @ Fri, 05 Jul 2019 17:32:05: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:32:05: #1 finished! INFO @ Fri, 05 Jul 2019 17:32:05: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:32:05: #2 number of paired peaks: 167 WARNING @ Fri, 05 Jul 2019 17:32:05: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Fri, 05 Jul 2019 17:32:05: start model_add_line... INFO @ Fri, 05 Jul 2019 17:32:05: start X-correlation... INFO @ Fri, 05 Jul 2019 17:32:05: end of X-cor INFO @ Fri, 05 Jul 2019 17:32:05: #2 finished! INFO @ Fri, 05 Jul 2019 17:32:05: #2 predicted fragment length is 225 bps INFO @ Fri, 05 Jul 2019 17:32:05: #2 alternative fragment length(s) may be 1,131,176,198,225,238,266,561,582,584 bps INFO @ Fri, 05 Jul 2019 17:32:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.05_model.r INFO @ Fri, 05 Jul 2019 17:32:05: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:32:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:32:07: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:32:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:32:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.10_summits.bed INFO @ Fri, 05 Jul 2019 17:32:09: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (34 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:32:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:32:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:32:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.20_summits.bed INFO @ Fri, 05 Jul 2019 17:32:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471849/ERX471849.05_summits.bed INFO @ Fri, 05 Jul 2019 17:32:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。