Job ID = 2011735 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,846,662 reads read : 5,693,324 reads written : 5,693,324 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: 00:01:07 2846662 reads; of these: 2846662 (100.00%) were paired; of these: 2152849 (75.63%) aligned concordantly 0 times 527125 (18.52%) aligned concordantly exactly 1 time 166688 (5.86%) aligned concordantly >1 times ---- 2152849 pairs aligned concordantly 0 times; of these: 13116 (0.61%) aligned discordantly 1 time ---- 2139733 pairs aligned 0 times concordantly or discordantly; of these: 4279466 mates make up the pairs; of these: 4072651 (95.17%) aligned 0 times 157136 (3.67%) aligned exactly 1 time 49679 (1.16%) aligned >1 times 28.47% overall alignment rate Time searching: 00:01:07 Overall time: 00:01:07 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] 313582 / 701098 = 0.4473 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 02:20:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.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 02:20:10: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:20:10: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:20:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.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 02:20:11: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:20:11: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:20:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.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 02:20:12: #1 read tag files... INFO @ Sat, 06 Jul 2019 02:20:12: #1 read treatment tags... INFO @ Sat, 06 Jul 2019 02:20:19: #1 tag size is determined as 70 bps INFO @ Sat, 06 Jul 2019 02:20:19: #1 tag size = 70 INFO @ Sat, 06 Jul 2019 02:20:19: #1 total tags in treatment: 382975 INFO @ Sat, 06 Jul 2019 02:20:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:20:19: #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 02:20:19: #1 tags after filtering in treatment: 281652 INFO @ Sat, 06 Jul 2019 02:20:19: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 02:20:19: #1 finished! INFO @ Sat, 06 Jul 2019 02:20:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:20:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:20:19: #2 number of paired peaks: 264 WARNING @ Sat, 06 Jul 2019 02:20:19: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 06 Jul 2019 02:20:19: start model_add_line... INFO @ Sat, 06 Jul 2019 02:20:19: start X-correlation... INFO @ Sat, 06 Jul 2019 02:20:19: end of X-cor INFO @ Sat, 06 Jul 2019 02:20:19: #2 finished! INFO @ Sat, 06 Jul 2019 02:20:19: #2 predicted fragment length is 262 bps INFO @ Sat, 06 Jul 2019 02:20:19: #2 alternative fragment length(s) may be 262 bps INFO @ Sat, 06 Jul 2019 02:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.05_model.r INFO @ Sat, 06 Jul 2019 02:20:19: #1 tag size is determined as 70 bps INFO @ Sat, 06 Jul 2019 02:20:19: #1 tag size = 70 INFO @ Sat, 06 Jul 2019 02:20:19: #1 total tags in treatment: 382975 INFO @ Sat, 06 Jul 2019 02:20:19: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:20:19: #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 02:20:19: #1 tags after filtering in treatment: 281652 INFO @ Sat, 06 Jul 2019 02:20:19: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 02:20:19: #1 finished! INFO @ Sat, 06 Jul 2019 02:20:19: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:20:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:20:19: #2 number of paired peaks: 264 WARNING @ Sat, 06 Jul 2019 02:20:19: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 06 Jul 2019 02:20:19: start model_add_line... INFO @ Sat, 06 Jul 2019 02:20:19: start X-correlation... INFO @ Sat, 06 Jul 2019 02:20:19: end of X-cor INFO @ Sat, 06 Jul 2019 02:20:19: #2 finished! INFO @ Sat, 06 Jul 2019 02:20:19: #2 predicted fragment length is 262 bps INFO @ Sat, 06 Jul 2019 02:20:19: #2 alternative fragment length(s) may be 262 bps INFO @ Sat, 06 Jul 2019 02:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.10_model.r INFO @ Sat, 06 Jul 2019 02:20:20: #1 tag size is determined as 70 bps INFO @ Sat, 06 Jul 2019 02:20:20: #1 tag size = 70 INFO @ Sat, 06 Jul 2019 02:20:20: #1 total tags in treatment: 382975 INFO @ Sat, 06 Jul 2019 02:20:20: #1 user defined the maximum tags... INFO @ Sat, 06 Jul 2019 02:20:20: #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 02:20:20: #1 tags after filtering in treatment: 281652 INFO @ Sat, 06 Jul 2019 02:20:20: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 06 Jul 2019 02:20:20: #1 finished! INFO @ Sat, 06 Jul 2019 02:20:20: #2 Build Peak Model... INFO @ Sat, 06 Jul 2019 02:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 06 Jul 2019 02:20:20: #2 number of paired peaks: 264 WARNING @ Sat, 06 Jul 2019 02:20:20: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 06 Jul 2019 02:20:20: start model_add_line... INFO @ Sat, 06 Jul 2019 02:20:20: start X-correlation... INFO @ Sat, 06 Jul 2019 02:20:20: end of X-cor INFO @ Sat, 06 Jul 2019 02:20:20: #2 finished! INFO @ Sat, 06 Jul 2019 02:20:20: #2 predicted fragment length is 262 bps INFO @ Sat, 06 Jul 2019 02:20:20: #2 alternative fragment length(s) may be 262 bps INFO @ Sat, 06 Jul 2019 02:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 06 Jul 2019 02:20:37: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:20:37: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:20:37: #3 Call peaks... INFO @ Sat, 06 Jul 2019 02:20:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 06 Jul 2019 02:20:39: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:20:39: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:20:39: #3 Call peaks for each chromosome... INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.05_peaks.xls INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.10_peaks.xls INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.10_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.05_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.10_summits.bed INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.05_summits.bed INFO @ Sat, 06 Jul 2019 02:20:39: Done! INFO @ Sat, 06 Jul 2019 02:20:39: Done! INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.20_peaks.xls INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.20_peaks.narrowPeak INFO @ Sat, 06 Jul 2019 02:20:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX480356/SRX480356.20_summits.bed INFO @ Sat, 06 Jul 2019 02:20:39: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 3 millis pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (353 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 CompletedMACS2peakCalling