Job ID = 14520493 SRX = SRX11781166 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:13:39 prefetch.2.10.7: 1) Downloading 'SRR15481109'... 2022-01-15T10:13:39 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:14:00 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:14:01 prefetch.2.10.7: 'SRR15481109' is valid 2022-01-15T10:14:01 prefetch.2.10.7: 1) 'SRR15481109' was downloaded successfully 2022-01-15T10:14:02 prefetch.2.10.7: 'SRR15481109' has 0 unresolved dependencies Read 7206720 spots for SRR15481109/SRR15481109.sra Written 7206720 spots for SRR15481109/SRR15481109.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: 00:11:31 7206720 reads; of these: 7206720 (100.00%) were paired; of these: 4973878 (69.02%) aligned concordantly 0 times 1344613 (18.66%) aligned concordantly exactly 1 time 888229 (12.33%) aligned concordantly >1 times ---- 4973878 pairs aligned concordantly 0 times; of these: 26402 (0.53%) aligned discordantly 1 time ---- 4947476 pairs aligned 0 times concordantly or discordantly; of these: 9894952 mates make up the pairs; of these: 5631815 (56.92%) aligned 0 times 2600439 (26.28%) aligned exactly 1 time 1662698 (16.80%) aligned >1 times 60.93% overall alignment rate Time searching: 00:11:31 Overall time: 00:11:32 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] 163765 / 2258591 = 0.0725 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 19:31:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.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 19:31:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:31:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:31:25: 1000000 INFO @ Sat, 15 Jan 2022 19:31:31: 2000000 INFO @ Sat, 15 Jan 2022 19:31:37: 3000000 INFO @ Sat, 15 Jan 2022 19:31:43: 4000000 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 19:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.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 19:31:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:31:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:31:49: 5000000 INFO @ Sat, 15 Jan 2022 19:31:55: 1000000 INFO @ Sat, 15 Jan 2022 19:31:55: 6000000 INFO @ Sat, 15 Jan 2022 19:32:02: 7000000 INFO @ Sat, 15 Jan 2022 19:32:03: 2000000 INFO @ Sat, 15 Jan 2022 19:32:10: 8000000 INFO @ Sat, 15 Jan 2022 19:32:11: 3000000 INFO @ Sat, 15 Jan 2022 19:32:13: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:32:13: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:32:13: #1 total tags in treatment: 2070346 INFO @ Sat, 15 Jan 2022 19:32:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:32:13: #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 19:32:13: #1 tags after filtering in treatment: 1367637 INFO @ Sat, 15 Jan 2022 19:32:13: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 19:32:13: #1 finished! INFO @ Sat, 15 Jan 2022 19:32:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:32:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:32:13: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:32:13: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:32:13: start model_add_line... INFO @ Sat, 15 Jan 2022 19:32:13: start X-correlation... INFO @ Sat, 15 Jan 2022 19:32:13: end of X-cor INFO @ Sat, 15 Jan 2022 19:32:13: #2 finished! INFO @ Sat, 15 Jan 2022 19:32:13: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:32:13: #2 alternative fragment length(s) may be 2,241,254 bps INFO @ Sat, 15 Jan 2022 19:32:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.05_model.r INFO @ Sat, 15 Jan 2022 19:32:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:32:13: #3 Pre-compute pvalue-qvalue table... 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 19:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.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 19:32:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:32:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:32:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:32:20: 4000000 INFO @ Sat, 15 Jan 2022 19:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.05_summits.bed INFO @ Sat, 15 Jan 2022 19:32:22: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:32:23: 1000000 INFO @ Sat, 15 Jan 2022 19:32:28: 5000000 INFO @ Sat, 15 Jan 2022 19:32:30: 2000000 INFO @ Sat, 15 Jan 2022 19:32:37: 6000000 INFO @ Sat, 15 Jan 2022 19:32:37: 3000000 INFO @ Sat, 15 Jan 2022 19:32:44: 4000000 INFO @ Sat, 15 Jan 2022 19:32:47: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:32:53: 5000000 INFO @ Sat, 15 Jan 2022 19:32:57: 8000000 INFO @ Sat, 15 Jan 2022 19:33:02: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:33:02: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:33:02: #1 total tags in treatment: 2070346 INFO @ Sat, 15 Jan 2022 19:33:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:33:02: #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 19:33:02: #1 tags after filtering in treatment: 1367637 INFO @ Sat, 15 Jan 2022 19:33:02: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 19:33:02: #1 finished! INFO @ Sat, 15 Jan 2022 19:33:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:33:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:33:03: 6000000 INFO @ Sat, 15 Jan 2022 19:33:03: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:33:03: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:33:03: start model_add_line... INFO @ Sat, 15 Jan 2022 19:33:03: start X-correlation... INFO @ Sat, 15 Jan 2022 19:33:03: end of X-cor INFO @ Sat, 15 Jan 2022 19:33:03: #2 finished! INFO @ Sat, 15 Jan 2022 19:33:03: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:33:03: #2 alternative fragment length(s) may be 2,241,254 bps INFO @ Sat, 15 Jan 2022 19:33:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.10_model.r INFO @ Sat, 15 Jan 2022 19:33:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:33:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:33:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:33:11: 7000000 INFO @ Sat, 15 Jan 2022 19:33:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:33:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:33:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.10_summits.bed INFO @ Sat, 15 Jan 2022 19:33:12: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:33:20: 8000000 INFO @ Sat, 15 Jan 2022 19:33:24: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:33:24: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:33:24: #1 total tags in treatment: 2070346 INFO @ Sat, 15 Jan 2022 19:33:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:33:24: #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 19:33:24: #1 tags after filtering in treatment: 1367637 INFO @ Sat, 15 Jan 2022 19:33:24: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 15 Jan 2022 19:33:24: #1 finished! INFO @ Sat, 15 Jan 2022 19:33:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:33:25: #2 number of paired peaks: 181 WARNING @ Sat, 15 Jan 2022 19:33:25: Fewer paired peaks (181) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 181 pairs to build model! INFO @ Sat, 15 Jan 2022 19:33:25: start model_add_line... INFO @ Sat, 15 Jan 2022 19:33:25: start X-correlation... INFO @ Sat, 15 Jan 2022 19:33:25: end of X-cor INFO @ Sat, 15 Jan 2022 19:33:25: #2 finished! INFO @ Sat, 15 Jan 2022 19:33:25: #2 predicted fragment length is 254 bps INFO @ Sat, 15 Jan 2022 19:33:25: #2 alternative fragment length(s) may be 2,241,254 bps INFO @ Sat, 15 Jan 2022 19:33:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.20_model.r INFO @ Sat, 15 Jan 2022 19:33:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:33:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:33:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:33:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:33:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:33:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781166/SRX11781166.20_summits.bed INFO @ Sat, 15 Jan 2022 19:33:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 55 millis CompletedMACS2peakCalling