Job ID = 14520461 SRX = SRX11781151 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5479975 spots for SRR15481094/SRR15481094.sra Written 5479975 spots for SRR15481094/SRR15481094.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: 00:02:06 5479975 reads; of these: 5479975 (100.00%) were paired; of these: 3651693 (66.64%) aligned concordantly 0 times 1649821 (30.11%) aligned concordantly exactly 1 time 178461 (3.26%) aligned concordantly >1 times ---- 3651693 pairs aligned concordantly 0 times; of these: 57795 (1.58%) aligned discordantly 1 time ---- 3593898 pairs aligned 0 times concordantly or discordantly; of these: 7187796 mates make up the pairs; of these: 3970931 (55.25%) aligned 0 times 2841357 (39.53%) aligned exactly 1 time 375508 (5.22%) aligned >1 times 63.77% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 290851 / 1885243 = 0.1543 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.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, 15 Jan 2022 19:13:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:13:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:13:52: 1000000 INFO @ Sat, 15 Jan 2022 19:13:56: 2000000 INFO @ Sat, 15 Jan 2022 19:14:00: 3000000 INFO @ Sat, 15 Jan 2022 19:14:03: 4000000 INFO @ Sat, 15 Jan 2022 19:14:07: 5000000 INFO @ Sat, 15 Jan 2022 19:14:11: 6000000 INFO @ Sat, 15 Jan 2022 19:14:13: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:14:13: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:14:13: #1 total tags in treatment: 1542836 INFO @ Sat, 15 Jan 2022 19:14:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:14:13: #1 tags after filtering in treatment: 992040 INFO @ Sat, 15 Jan 2022 19:14:13: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 19:14:13: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:13: #2 number of paired peaks: 182 WARNING @ Sat, 15 Jan 2022 19:14:13: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sat, 15 Jan 2022 19:14:13: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:13: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:13: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:13: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:13: #2 predicted fragment length is 264 bps INFO @ Sat, 15 Jan 2022 19:14:13: #2 alternative fragment length(s) may be 88,183,242,264,294,330,412,513,591 bps INFO @ Sat, 15 Jan 2022 19:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.05_model.r INFO @ Sat, 15 Jan 2022 19:14:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.05_summits.bed INFO @ Sat, 15 Jan 2022 19:14:16: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (15 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.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, 15 Jan 2022 19:14:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:22: 1000000 INFO @ Sat, 15 Jan 2022 19:14:26: 2000000 INFO @ Sat, 15 Jan 2022 19:14:30: 3000000 INFO @ Sat, 15 Jan 2022 19:14:33: 4000000 INFO @ Sat, 15 Jan 2022 19:14:37: 5000000 INFO @ Sat, 15 Jan 2022 19:14:41: 6000000 INFO @ Sat, 15 Jan 2022 19:14:43: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:14:43: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:14:43: #1 total tags in treatment: 1542836 INFO @ Sat, 15 Jan 2022 19:14:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:14:43: #1 tags after filtering in treatment: 992040 INFO @ Sat, 15 Jan 2022 19:14:43: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 19:14:43: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:43: #2 number of paired peaks: 182 WARNING @ Sat, 15 Jan 2022 19:14:43: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sat, 15 Jan 2022 19:14:43: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:43: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:43: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:43: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:43: #2 predicted fragment length is 264 bps INFO @ Sat, 15 Jan 2022 19:14:43: #2 alternative fragment length(s) may be 88,183,242,264,294,330,412,513,591 bps INFO @ Sat, 15 Jan 2022 19:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.10_model.r INFO @ Sat, 15 Jan 2022 19:14:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.10_summits.bed INFO @ Sat, 15 Jan 2022 19:14:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 19:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.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, 15 Jan 2022 19:14:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:53: 1000000 INFO @ Sat, 15 Jan 2022 19:14:57: 2000000 INFO @ Sat, 15 Jan 2022 19:15:02: 3000000 INFO @ Sat, 15 Jan 2022 19:15:06: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:15:11: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:15:15: 6000000 INFO @ Sat, 15 Jan 2022 19:15:17: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:15:17: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:15:17: #1 total tags in treatment: 1542836 INFO @ Sat, 15 Jan 2022 19:15:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:15:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 19:15:17: #1 tags after filtering in treatment: 992040 INFO @ Sat, 15 Jan 2022 19:15:17: #1 Redundant rate of treatment: 0.36 INFO @ Sat, 15 Jan 2022 19:15:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:15:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:15:17: #2 number of paired peaks: 182 WARNING @ Sat, 15 Jan 2022 19:15:17: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sat, 15 Jan 2022 19:15:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:15:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:15:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:15:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:15:17: #2 predicted fragment length is 264 bps INFO @ Sat, 15 Jan 2022 19:15:17: #2 alternative fragment length(s) may be 88,183,242,264,294,330,412,513,591 bps INFO @ Sat, 15 Jan 2022 19:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.20_model.r INFO @ Sat, 15 Jan 2022 19:15:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:15:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781151/SRX11781151.20_summits.bed INFO @ Sat, 15 Jan 2022 19:15:21: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 269 millis CompletedMACS2peakCalling