Job ID = 2007990 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,656,404 reads read : 3,312,808 reads written : 3,312,808 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: 00:01:51 1656404 reads; of these: 1656404 (100.00%) were paired; of these: 181928 (10.98%) aligned concordantly 0 times 1362164 (82.24%) aligned concordantly exactly 1 time 112312 (6.78%) aligned concordantly >1 times ---- 181928 pairs aligned concordantly 0 times; of these: 30974 (17.03%) aligned discordantly 1 time ---- 150954 pairs aligned 0 times concordantly or discordantly; of these: 301908 mates make up the pairs; of these: 279055 (92.43%) aligned 0 times 14201 (4.70%) aligned exactly 1 time 8652 (2.87%) aligned >1 times 91.58% overall alignment rate Time searching: 00:01:51 Overall time: 00:01:51 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] 214942 / 1503438 = 0.1430 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 17:06:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.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 17:06:48: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:48: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.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 17:06:49: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:49: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.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 17:06:50: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:06:50: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:06:56: 1000000 INFO @ Fri, 05 Jul 2019 17:06:58: 1000000 INFO @ Fri, 05 Jul 2019 17:07:00: 1000000 INFO @ Fri, 05 Jul 2019 17:07:05: 2000000 INFO @ Fri, 05 Jul 2019 17:07:06: 2000000 INFO @ Fri, 05 Jul 2019 17:07:10: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:10: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:10: #1 total tags in treatment: 1261649 INFO @ Fri, 05 Jul 2019 17:07:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:10: #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 17:07:10: #1 tags after filtering in treatment: 1198252 INFO @ Fri, 05 Jul 2019 17:07:10: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:10: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:10: #2 number of paired peaks: 166 WARNING @ Fri, 05 Jul 2019 17:07:10: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:10: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:10: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:10: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:10: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:10: #2 predicted fragment length is 251 bps INFO @ Fri, 05 Jul 2019 17:07:10: #2 alternative fragment length(s) may be 1,154,178,200,251,273,506,511,541,597 bps INFO @ Fri, 05 Jul 2019 17:07:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.05_model.r INFO @ Fri, 05 Jul 2019 17:07:10: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:10: 2000000 INFO @ Fri, 05 Jul 2019 17:07:11: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:11: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:11: #1 total tags in treatment: 1261649 INFO @ Fri, 05 Jul 2019 17:07:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:11: #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 17:07:11: #1 tags after filtering in treatment: 1198252 INFO @ Fri, 05 Jul 2019 17:07:11: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:11: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:11: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:11: #2 number of paired peaks: 166 WARNING @ Fri, 05 Jul 2019 17:07:11: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:11: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:11: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:11: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:11: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:11: #2 predicted fragment length is 251 bps INFO @ Fri, 05 Jul 2019 17:07:11: #2 alternative fragment length(s) may be 1,154,178,200,251,273,506,511,541,597 bps INFO @ Fri, 05 Jul 2019 17:07:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.10_model.r INFO @ Fri, 05 Jul 2019 17:07:11: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:07:14: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:15: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.05_summits.bed INFO @ Fri, 05 Jul 2019 17:07:16: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 3 millis INFO @ Fri, 05 Jul 2019 17:07:16: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:07:16: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:07:16: #1 total tags in treatment: 1261649 INFO @ Fri, 05 Jul 2019 17:07:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:07:16: #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 17:07:16: #1 tags after filtering in treatment: 1198252 INFO @ Fri, 05 Jul 2019 17:07:16: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 05 Jul 2019 17:07:16: #1 finished! INFO @ Fri, 05 Jul 2019 17:07:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:07:16: #2 number of paired peaks: 166 WARNING @ Fri, 05 Jul 2019 17:07:16: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Fri, 05 Jul 2019 17:07:16: start model_add_line... INFO @ Fri, 05 Jul 2019 17:07:16: start X-correlation... INFO @ Fri, 05 Jul 2019 17:07:16: end of X-cor INFO @ Fri, 05 Jul 2019 17:07:16: #2 finished! INFO @ Fri, 05 Jul 2019 17:07:16: #2 predicted fragment length is 251 bps INFO @ Fri, 05 Jul 2019 17:07:16: #2 alternative fragment length(s) may be 1,154,178,200,251,273,506,511,541,597 bps INFO @ Fri, 05 Jul 2019 17:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.20_model.r INFO @ Fri, 05 Jul 2019 17:07:16: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:07:16: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:07:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.10_summits.bed INFO @ Fri, 05 Jul 2019 17:07:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (59 records, 4 fields): 2 millis INFO @ Fri, 05 Jul 2019 17:07:20: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471780/ERX471780.20_summits.bed INFO @ Fri, 05 Jul 2019 17:07:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (21 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。