Job ID = 2007993 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,986,456 reads read : 3,972,912 reads written : 3,972,912 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: 00:02:15 1986456 reads; of these: 1986456 (100.00%) were paired; of these: 186730 (9.40%) aligned concordantly 0 times 1667660 (83.95%) aligned concordantly exactly 1 time 132066 (6.65%) aligned concordantly >1 times ---- 186730 pairs aligned concordantly 0 times; of these: 85389 (45.73%) aligned discordantly 1 time ---- 101341 pairs aligned 0 times concordantly or discordantly; of these: 202682 mates make up the pairs; of these: 164485 (81.15%) aligned 0 times 20878 (10.30%) aligned exactly 1 time 17319 (8.54%) aligned >1 times 95.86% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 12057 / 1883778 = 0.0064 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 17:08:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.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 17:08:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:08:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:08:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.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 17:08:16: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:08:16: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:08:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.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 17:08:17: #1 read tag files... INFO @ Fri, 05 Jul 2019 17:08:17: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 17:08:26: 1000000 INFO @ Fri, 05 Jul 2019 17:08:29: 1000000 INFO @ Fri, 05 Jul 2019 17:08:29: 1000000 INFO @ Fri, 05 Jul 2019 17:08:38: 2000000 INFO @ Fri, 05 Jul 2019 17:08:40: 2000000 INFO @ Fri, 05 Jul 2019 17:08:41: 2000000 INFO @ Fri, 05 Jul 2019 17:08:49: 3000000 INFO @ Fri, 05 Jul 2019 17:08:51: 3000000 INFO @ Fri, 05 Jul 2019 17:08:54: 3000000 INFO @ Fri, 05 Jul 2019 17:08:58: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:08:58: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:08:58: #1 total tags in treatment: 1787950 INFO @ Fri, 05 Jul 2019 17:08:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:08:58: #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 17:08:58: #1 tags after filtering in treatment: 1668831 INFO @ Fri, 05 Jul 2019 17:08:58: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:08:58: #1 finished! INFO @ Fri, 05 Jul 2019 17:08:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:08:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:08:58: #2 number of paired peaks: 174 WARNING @ Fri, 05 Jul 2019 17:08:58: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 05 Jul 2019 17:08:58: start model_add_line... INFO @ Fri, 05 Jul 2019 17:08:58: start X-correlation... INFO @ Fri, 05 Jul 2019 17:08:58: end of X-cor INFO @ Fri, 05 Jul 2019 17:08:58: #2 finished! INFO @ Fri, 05 Jul 2019 17:08:58: #2 predicted fragment length is 253 bps INFO @ Fri, 05 Jul 2019 17:08:58: #2 alternative fragment length(s) may be 38,68,93,108,148,164,189,212,253,286,317,350,392,410,439,471,494,516,534,563 bps INFO @ Fri, 05 Jul 2019 17:08:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.05_model.r INFO @ Fri, 05 Jul 2019 17:08:58: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:08:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:09:00: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:09:00: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:09:00: #1 total tags in treatment: 1787950 INFO @ Fri, 05 Jul 2019 17:09:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:09:00: #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 17:09:00: #1 tags after filtering in treatment: 1668831 INFO @ Fri, 05 Jul 2019 17:09:00: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:09:00: #1 finished! INFO @ Fri, 05 Jul 2019 17:09:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:09:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:09:00: #2 number of paired peaks: 174 WARNING @ Fri, 05 Jul 2019 17:09:00: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 05 Jul 2019 17:09:00: start model_add_line... INFO @ Fri, 05 Jul 2019 17:09:00: start X-correlation... INFO @ Fri, 05 Jul 2019 17:09:00: end of X-cor INFO @ Fri, 05 Jul 2019 17:09:00: #2 finished! INFO @ Fri, 05 Jul 2019 17:09:00: #2 predicted fragment length is 253 bps INFO @ Fri, 05 Jul 2019 17:09:00: #2 alternative fragment length(s) may be 38,68,93,108,148,164,189,212,253,286,317,350,392,410,439,471,494,516,534,563 bps INFO @ Fri, 05 Jul 2019 17:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.20_model.r INFO @ Fri, 05 Jul 2019 17:09:00: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:09:03: #1 tag size is determined as 100 bps INFO @ Fri, 05 Jul 2019 17:09:03: #1 tag size = 100 INFO @ Fri, 05 Jul 2019 17:09:03: #1 total tags in treatment: 1787950 INFO @ Fri, 05 Jul 2019 17:09:03: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 17:09:03: #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 17:09:03: #1 tags after filtering in treatment: 1668831 INFO @ Fri, 05 Jul 2019 17:09:03: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 05 Jul 2019 17:09:03: #1 finished! INFO @ Fri, 05 Jul 2019 17:09:03: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 17:09:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 17:09:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:09:03: #2 number of paired peaks: 174 WARNING @ Fri, 05 Jul 2019 17:09:03: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Fri, 05 Jul 2019 17:09:03: start model_add_line... INFO @ Fri, 05 Jul 2019 17:09:03: start X-correlation... INFO @ Fri, 05 Jul 2019 17:09:03: end of X-cor INFO @ Fri, 05 Jul 2019 17:09:03: #2 finished! INFO @ Fri, 05 Jul 2019 17:09:03: #2 predicted fragment length is 253 bps INFO @ Fri, 05 Jul 2019 17:09:03: #2 alternative fragment length(s) may be 38,68,93,108,148,164,189,212,253,286,317,350,392,410,439,471,494,516,534,563 bps INFO @ Fri, 05 Jul 2019 17:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.10_model.r INFO @ Fri, 05 Jul 2019 17:09:03: #3 Call peaks... INFO @ Fri, 05 Jul 2019 17:09:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 17:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.05_peaks.xls INFO @ Fri, 05 Jul 2019 17:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.05_summits.bed INFO @ Fri, 05 Jul 2019 17:09:05: Done! INFO @ Fri, 05 Jul 2019 17:09:05: #3 Call peaks for each chromosome... pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 17:09:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.20_peaks.xls INFO @ Fri, 05 Jul 2019 17:09:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:09:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.20_summits.bed INFO @ Fri, 05 Jul 2019 17:09:07: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 17:09:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 17:09:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.10_peaks.xls INFO @ Fri, 05 Jul 2019 17:09:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 17:09:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX471783/ERX471783.10_summits.bed INFO @ Fri, 05 Jul 2019 17:09:10: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。