Job ID = 10224039 SRX = SRX8926524 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3848405 spots for SRR12430727/SRR12430727.sra Written 3848405 spots for SRR12430727/SRR12430727.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: 00:01:06 3848405 reads; of these: 3848405 (100.00%) were paired; of these: 2137614 (55.55%) aligned concordantly 0 times 1371080 (35.63%) aligned concordantly exactly 1 time 339711 (8.83%) aligned concordantly >1 times ---- 2137614 pairs aligned concordantly 0 times; of these: 494 (0.02%) aligned discordantly 1 time ---- 2137120 pairs aligned 0 times concordantly or discordantly; of these: 4274240 mates make up the pairs; of these: 4254688 (99.54%) aligned 0 times 13523 (0.32%) aligned exactly 1 time 6029 (0.14%) aligned >1 times 44.72% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 596676 / 1711178 = 0.3487 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 09:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.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 09:13:02: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:13:02: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:13:08: 1000000 INFO @ Fri, 16 Oct 2020 09:13:13: 2000000 INFO @ Fri, 16 Oct 2020 09:13:14: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:13:14: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:13:14: #1 total tags in treatment: 1114186 INFO @ Fri, 16 Oct 2020 09:13:14: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:13:14: #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 09:13:14: #1 tags after filtering in treatment: 951043 INFO @ Fri, 16 Oct 2020 09:13:14: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 16 Oct 2020 09:13:14: #1 finished! INFO @ Fri, 16 Oct 2020 09:13:14: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:13:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:13:14: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 09:13:14: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 09:13:14: start model_add_line... INFO @ Fri, 16 Oct 2020 09:13:14: start X-correlation... INFO @ Fri, 16 Oct 2020 09:13:15: end of X-cor INFO @ Fri, 16 Oct 2020 09:13:15: #2 finished! INFO @ Fri, 16 Oct 2020 09:13:15: #2 predicted fragment length is 156 bps INFO @ Fri, 16 Oct 2020 09:13:15: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 16 Oct 2020 09:13:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.05_model.r INFO @ Fri, 16 Oct 2020 09:13:15: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:13:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:13:17: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:13:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:13:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:13:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.05_summits.bed INFO @ Fri, 16 Oct 2020 09:13:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (816 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 09:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.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 09:13:32: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:13:32: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:13:37: 1000000 INFO @ Fri, 16 Oct 2020 09:13:42: 2000000 INFO @ Fri, 16 Oct 2020 09:13:43: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:13:43: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:13:43: #1 total tags in treatment: 1114186 INFO @ Fri, 16 Oct 2020 09:13:43: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:13:43: #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 09:13:43: #1 tags after filtering in treatment: 951043 INFO @ Fri, 16 Oct 2020 09:13:43: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 16 Oct 2020 09:13:43: #1 finished! INFO @ Fri, 16 Oct 2020 09:13:43: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:13:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:13:43: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 09:13:43: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 09:13:43: start model_add_line... INFO @ Fri, 16 Oct 2020 09:13:43: start X-correlation... INFO @ Fri, 16 Oct 2020 09:13:43: end of X-cor INFO @ Fri, 16 Oct 2020 09:13:43: #2 finished! INFO @ Fri, 16 Oct 2020 09:13:43: #2 predicted fragment length is 156 bps INFO @ Fri, 16 Oct 2020 09:13:43: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 16 Oct 2020 09:13:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.10_model.r INFO @ Fri, 16 Oct 2020 09:13:43: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:13:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:13:45: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:13:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:13:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:13:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.10_summits.bed INFO @ Fri, 16 Oct 2020 09:13:46: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 09:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.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 09:14:02: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:14:02: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:14:08: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:14:13: 2000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:14:15: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:14:15: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:14:15: #1 total tags in treatment: 1114186 INFO @ Fri, 16 Oct 2020 09:14:15: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:14:15: #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 09:14:15: #1 tags after filtering in treatment: 951043 INFO @ Fri, 16 Oct 2020 09:14:15: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 16 Oct 2020 09:14:15: #1 finished! INFO @ Fri, 16 Oct 2020 09:14:15: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:14:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:14:15: #2 number of paired peaks: 115 WARNING @ Fri, 16 Oct 2020 09:14:15: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 16 Oct 2020 09:14:15: start model_add_line... INFO @ Fri, 16 Oct 2020 09:14:15: start X-correlation... INFO @ Fri, 16 Oct 2020 09:14:15: end of X-cor INFO @ Fri, 16 Oct 2020 09:14:15: #2 finished! INFO @ Fri, 16 Oct 2020 09:14:15: #2 predicted fragment length is 156 bps INFO @ Fri, 16 Oct 2020 09:14:15: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 16 Oct 2020 09:14:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.20_model.r INFO @ Fri, 16 Oct 2020 09:14:15: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:14:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:14:17: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:14:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:14:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:14:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926524/SRX8926524.20_summits.bed INFO @ Fri, 16 Oct 2020 09:14:18: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 2 millis CompletedMACS2peakCalling