Job ID = 10224075 SRX = SRX8952631 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10679257 spots for SRR12458255/SRR12458255.sra Written 10679257 spots for SRR12458255/SRR12458255.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: 00:03:18 10679257 reads; of these: 10679257 (100.00%) were paired; of these: 7427677 (69.55%) aligned concordantly 0 times 2843654 (26.63%) aligned concordantly exactly 1 time 407926 (3.82%) aligned concordantly >1 times ---- 7427677 pairs aligned concordantly 0 times; of these: 510393 (6.87%) aligned discordantly 1 time ---- 6917284 pairs aligned 0 times concordantly or discordantly; of these: 13834568 mates make up the pairs; of these: 10992692 (79.46%) aligned 0 times 2484113 (17.96%) aligned exactly 1 time 357763 (2.59%) aligned >1 times 48.53% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1091345 / 3745886 = 0.2913 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 09:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.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 09:27:22: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:22: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:29: 1000000 INFO @ Fri, 16 Oct 2020 09:27:35: 2000000 INFO @ Fri, 16 Oct 2020 09:27:41: 3000000 INFO @ Fri, 16 Oct 2020 09:27:48: 4000000 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 09:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.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 09:27:52: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:27:52: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:27:54: 5000000 INFO @ Fri, 16 Oct 2020 09:27:59: 1000000 INFO @ Fri, 16 Oct 2020 09:28:01: 6000000 INFO @ Fri, 16 Oct 2020 09:28:06: 2000000 INFO @ Fri, 16 Oct 2020 09:28:08: 7000000 INFO @ Fri, 16 Oct 2020 09:28:13: 3000000 INFO @ Fri, 16 Oct 2020 09:28:16: 8000000 INFO @ Fri, 16 Oct 2020 09:28:17: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:28:17: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:28:17: #1 total tags in treatment: 2475277 INFO @ Fri, 16 Oct 2020 09:28:17: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:28:17: #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 09:28:17: #1 tags after filtering in treatment: 2136114 INFO @ Fri, 16 Oct 2020 09:28:17: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 09:28:17: #1 finished! INFO @ Fri, 16 Oct 2020 09:28:17: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:28:17: #2 number of paired peaks: 164 WARNING @ Fri, 16 Oct 2020 09:28:17: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 16 Oct 2020 09:28:17: start model_add_line... INFO @ Fri, 16 Oct 2020 09:28:17: start X-correlation... INFO @ Fri, 16 Oct 2020 09:28:17: end of X-cor INFO @ Fri, 16 Oct 2020 09:28:17: #2 finished! INFO @ Fri, 16 Oct 2020 09:28:17: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 09:28:17: #2 alternative fragment length(s) may be 2,204,217,259 bps INFO @ Fri, 16 Oct 2020 09:28:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.05_model.r INFO @ Fri, 16 Oct 2020 09:28:17: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:28:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:28:19: 4000000 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 09:28:22: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.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 09:28:22: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:28:22: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.05_summits.bed INFO @ Fri, 16 Oct 2020 09:28:24: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (370 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:28:26: 5000000 INFO @ Fri, 16 Oct 2020 09:28:29: 1000000 INFO @ Fri, 16 Oct 2020 09:28:34: 6000000 INFO @ Fri, 16 Oct 2020 09:28:36: 2000000 INFO @ Fri, 16 Oct 2020 09:28:41: 7000000 INFO @ Fri, 16 Oct 2020 09:28:42: 3000000 INFO @ Fri, 16 Oct 2020 09:28:48: 8000000 INFO @ Fri, 16 Oct 2020 09:28:49: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:28:49: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:28:49: #1 total tags in treatment: 2475277 INFO @ Fri, 16 Oct 2020 09:28:49: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:28:49: #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 09:28:49: #1 tags after filtering in treatment: 2136114 INFO @ Fri, 16 Oct 2020 09:28:49: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 09:28:49: #1 finished! INFO @ Fri, 16 Oct 2020 09:28:49: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:28:49: #2 number of paired peaks: 164 WARNING @ Fri, 16 Oct 2020 09:28:49: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 16 Oct 2020 09:28:49: start model_add_line... INFO @ Fri, 16 Oct 2020 09:28:49: start X-correlation... INFO @ Fri, 16 Oct 2020 09:28:49: end of X-cor INFO @ Fri, 16 Oct 2020 09:28:49: #2 finished! INFO @ Fri, 16 Oct 2020 09:28:49: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 09:28:49: #2 alternative fragment length(s) may be 2,204,217,259 bps INFO @ Fri, 16 Oct 2020 09:28:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.10_model.r INFO @ Fri, 16 Oct 2020 09:28:49: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:28:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:28:49: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:28:54: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:28:56: 5000000 INFO @ Fri, 16 Oct 2020 09:28:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:28:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:28:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.10_summits.bed INFO @ Fri, 16 Oct 2020 09:28:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:29:03: 6000000 INFO @ Fri, 16 Oct 2020 09:29:09: 7000000 INFO @ Fri, 16 Oct 2020 09:29:16: 8000000 INFO @ Fri, 16 Oct 2020 09:29:17: #1 tag size is determined as 41 bps INFO @ Fri, 16 Oct 2020 09:29:17: #1 tag size = 41 INFO @ Fri, 16 Oct 2020 09:29:17: #1 total tags in treatment: 2475277 INFO @ Fri, 16 Oct 2020 09:29:17: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:29:17: #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 09:29:17: #1 tags after filtering in treatment: 2136114 INFO @ Fri, 16 Oct 2020 09:29:17: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 16 Oct 2020 09:29:17: #1 finished! INFO @ Fri, 16 Oct 2020 09:29:17: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:29:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:29:17: #2 number of paired peaks: 164 WARNING @ Fri, 16 Oct 2020 09:29:17: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 16 Oct 2020 09:29:17: start model_add_line... INFO @ Fri, 16 Oct 2020 09:29:17: start X-correlation... INFO @ Fri, 16 Oct 2020 09:29:17: end of X-cor INFO @ Fri, 16 Oct 2020 09:29:17: #2 finished! INFO @ Fri, 16 Oct 2020 09:29:17: #2 predicted fragment length is 217 bps INFO @ Fri, 16 Oct 2020 09:29:17: #2 alternative fragment length(s) may be 2,204,217,259 bps INFO @ Fri, 16 Oct 2020 09:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.20_model.r INFO @ Fri, 16 Oct 2020 09:29:17: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:29:22: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952631/SRX8952631.20_summits.bed INFO @ Fri, 16 Oct 2020 09:29:24: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling