Job ID = 10224067 SRX = SRX8952624 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5111855 spots for SRR12458262/SRR12458262.sra Written 5111855 spots for SRR12458262/SRR12458262.sra 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: 00:01:53 5111855 reads; of these: 5111855 (100.00%) were paired; of these: 3534762 (69.15%) aligned concordantly 0 times 1329687 (26.01%) aligned concordantly exactly 1 time 247406 (4.84%) aligned concordantly >1 times ---- 3534762 pairs aligned concordantly 0 times; of these: 762029 (21.56%) aligned discordantly 1 time ---- 2772733 pairs aligned 0 times concordantly or discordantly; of these: 5545466 mates make up the pairs; of these: 3866923 (69.73%) aligned 0 times 1317177 (23.75%) aligned exactly 1 time 361366 (6.52%) aligned >1 times 62.18% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 420583 / 1809011 = 0.2325 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:20:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.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, 16 Oct 2020 09:20:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:20:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:20:53: 1000000 INFO @ Fri, 16 Oct 2020 09:20:58: 2000000 INFO @ Fri, 16 Oct 2020 09:21:03: 3000000 INFO @ Fri, 16 Oct 2020 09:21:08: 4000000 INFO @ Fri, 16 Oct 2020 09:21:13: 5000000 INFO @ Fri, 16 Oct 2020 09:21:15: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:21:15: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:21:15: #1 total tags in treatment: 1241611 INFO @ Fri, 16 Oct 2020 09:21:15: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:21:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:21:15: #1 tags after filtering in treatment: 1081457 INFO @ Fri, 16 Oct 2020 09:21:15: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 09:21:15: #1 finished! INFO @ Fri, 16 Oct 2020 09:21:15: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:21:16: #2 number of paired peaks: 190 WARNING @ Fri, 16 Oct 2020 09:21:16: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 16 Oct 2020 09:21:16: start model_add_line... INFO @ Fri, 16 Oct 2020 09:21:16: start X-correlation... INFO @ Fri, 16 Oct 2020 09:21:16: end of X-cor INFO @ Fri, 16 Oct 2020 09:21:16: #2 finished! INFO @ Fri, 16 Oct 2020 09:21:16: #2 predicted fragment length is 210 bps INFO @ Fri, 16 Oct 2020 09:21:16: #2 alternative fragment length(s) may be 210,228 bps INFO @ Fri, 16 Oct 2020 09:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.05_model.r INFO @ Fri, 16 Oct 2020 09:21:16: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:21:16: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:21:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.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, 16 Oct 2020 09:21:18: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:21:18: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:21:19: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.05_summits.bed INFO @ Fri, 16 Oct 2020 09:21:20: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:21:24: 1000000 INFO @ Fri, 16 Oct 2020 09:21:29: 2000000 INFO @ Fri, 16 Oct 2020 09:21:34: 3000000 INFO @ Fri, 16 Oct 2020 09:21:39: 4000000 INFO @ Fri, 16 Oct 2020 09:21:44: 5000000 INFO @ Fri, 16 Oct 2020 09:21:46: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:21:46: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:21:46: #1 total tags in treatment: 1241611 INFO @ Fri, 16 Oct 2020 09:21:46: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:21:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:21:46: #1 tags after filtering in treatment: 1081457 INFO @ Fri, 16 Oct 2020 09:21:46: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 09:21:46: #1 finished! INFO @ Fri, 16 Oct 2020 09:21:46: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:21:46: #2 number of paired peaks: 190 WARNING @ Fri, 16 Oct 2020 09:21:46: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 16 Oct 2020 09:21:46: start model_add_line... INFO @ Fri, 16 Oct 2020 09:21:46: start X-correlation... INFO @ Fri, 16 Oct 2020 09:21:46: end of X-cor INFO @ Fri, 16 Oct 2020 09:21:46: #2 finished! INFO @ Fri, 16 Oct 2020 09:21:46: #2 predicted fragment length is 210 bps INFO @ Fri, 16 Oct 2020 09:21:46: #2 alternative fragment length(s) may be 210,228 bps INFO @ Fri, 16 Oct 2020 09:21:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.10_model.r INFO @ Fri, 16 Oct 2020 09:21:46: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:21:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 09:21:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.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, 16 Oct 2020 09:21:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:21:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:21:49: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.10_summits.bed INFO @ Fri, 16 Oct 2020 09:21:50: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (426 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:21:53: 1000000 INFO @ Fri, 16 Oct 2020 09:21:58: 2000000 INFO @ Fri, 16 Oct 2020 09:22:03: 3000000 INFO @ Fri, 16 Oct 2020 09:22:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:22:12: 5000000 INFO @ Fri, 16 Oct 2020 09:22:15: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:22:15: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:22:15: #1 total tags in treatment: 1241611 INFO @ Fri, 16 Oct 2020 09:22:15: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:22:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:22:15: #1 tags after filtering in treatment: 1081457 INFO @ Fri, 16 Oct 2020 09:22:15: #1 Redundant rate of treatment: 0.13 INFO @ Fri, 16 Oct 2020 09:22:15: #1 finished! INFO @ Fri, 16 Oct 2020 09:22:15: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:22:15: #2 number of paired peaks: 190 WARNING @ Fri, 16 Oct 2020 09:22:15: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 16 Oct 2020 09:22:15: start model_add_line... INFO @ Fri, 16 Oct 2020 09:22:15: start X-correlation... INFO @ Fri, 16 Oct 2020 09:22:15: end of X-cor INFO @ Fri, 16 Oct 2020 09:22:15: #2 finished! INFO @ Fri, 16 Oct 2020 09:22:15: #2 predicted fragment length is 210 bps INFO @ Fri, 16 Oct 2020 09:22:15: #2 alternative fragment length(s) may be 210,228 bps INFO @ Fri, 16 Oct 2020 09:22:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.20_model.r INFO @ Fri, 16 Oct 2020 09:22:15: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:22:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:22:18: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:22:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:22:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:22:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952624/SRX8952624.20_summits.bed INFO @ Fri, 16 Oct 2020 09:22:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 1 millis CompletedMACS2peakCalling