Job ID = 14520463 SRX = SRX11781153 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:09:51 prefetch.2.10.7: 1) Downloading 'SRR15481096'... 2022-01-15T10:09:51 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:10:04 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:10:05 prefetch.2.10.7: 'SRR15481096' is valid 2022-01-15T10:10:05 prefetch.2.10.7: 1) 'SRR15481096' was downloaded successfully 2022-01-15T10:10:05 prefetch.2.10.7: 'SRR15481096' has 0 unresolved dependencies Read 5659965 spots for SRR15481096/SRR15481096.sra Written 5659965 spots for SRR15481096/SRR15481096.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: 00:02:22 5659965 reads; of these: 5659965 (100.00%) were paired; of these: 3556227 (62.83%) aligned concordantly 0 times 1838151 (32.48%) aligned concordantly exactly 1 time 265587 (4.69%) aligned concordantly >1 times ---- 3556227 pairs aligned concordantly 0 times; of these: 56283 (1.58%) aligned discordantly 1 time ---- 3499944 pairs aligned 0 times concordantly or discordantly; of these: 6999888 mates make up the pairs; of these: 3846208 (54.95%) aligned 0 times 2727425 (38.96%) aligned exactly 1 time 426255 (6.09%) aligned >1 times 66.02% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 334864 / 2159168 = 0.1551 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 19:14:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.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 19:14:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:14:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:14:55: 1000000 INFO @ Sat, 15 Jan 2022 19:14:59: 2000000 INFO @ Sat, 15 Jan 2022 19:15:03: 3000000 INFO @ Sat, 15 Jan 2022 19:15:07: 4000000 INFO @ Sat, 15 Jan 2022 19:15:11: 5000000 INFO @ Sat, 15 Jan 2022 19:15:15: 6000000 INFO @ Sat, 15 Jan 2022 19:15:18: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:15:18: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:15:18: #1 total tags in treatment: 1773872 INFO @ Sat, 15 Jan 2022 19:15:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:15:18: #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 19:15:18: #1 tags after filtering in treatment: 1243551 INFO @ Sat, 15 Jan 2022 19:15:18: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 19:15:18: #1 finished! INFO @ Sat, 15 Jan 2022 19:15:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:15:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:15:18: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 19:15:18: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 19:15:18: start model_add_line... INFO @ Sat, 15 Jan 2022 19:15:18: start X-correlation... INFO @ Sat, 15 Jan 2022 19:15:18: end of X-cor INFO @ Sat, 15 Jan 2022 19:15:18: #2 finished! INFO @ Sat, 15 Jan 2022 19:15:18: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 19:15:18: #2 alternative fragment length(s) may be 1,209,234,269 bps INFO @ Sat, 15 Jan 2022 19:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.05_model.r INFO @ Sat, 15 Jan 2022 19:15:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:15:18: #3 Pre-compute pvalue-qvalue table... 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 19:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.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 19:15:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:15:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:15:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.05_summits.bed INFO @ Sat, 15 Jan 2022 19:15:23: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:15:24: 1000000 INFO @ Sat, 15 Jan 2022 19:15:28: 2000000 INFO @ Sat, 15 Jan 2022 19:15:33: 3000000 INFO @ Sat, 15 Jan 2022 19:15:37: 4000000 INFO @ Sat, 15 Jan 2022 19:15:41: 5000000 INFO @ Sat, 15 Jan 2022 19:15:45: 6000000 INFO @ Sat, 15 Jan 2022 19:15:48: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:15:48: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:15:48: #1 total tags in treatment: 1773872 INFO @ Sat, 15 Jan 2022 19:15:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:15:48: #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 19:15:48: #1 tags after filtering in treatment: 1243551 INFO @ Sat, 15 Jan 2022 19:15:48: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 19:15:48: #1 finished! INFO @ Sat, 15 Jan 2022 19:15:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:15:48: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 19:15:48: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 19:15:48: start model_add_line... INFO @ Sat, 15 Jan 2022 19:15:48: start X-correlation... BedGraph に変換中... INFO @ Sat, 15 Jan 2022 19:15:48: end of X-cor INFO @ Sat, 15 Jan 2022 19:15:48: #2 finished! INFO @ Sat, 15 Jan 2022 19:15:48: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 19:15:48: #2 alternative fragment length(s) may be 1,209,234,269 bps INFO @ Sat, 15 Jan 2022 19:15:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.10_model.r INFO @ Sat, 15 Jan 2022 19:15:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:15:48: #3 Pre-compute pvalue-qvalue table... 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 19:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.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 19:15:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:15:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:15:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:15:53: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:15:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:15:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.10_summits.bed INFO @ Sat, 15 Jan 2022 19:15:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:15:54: 1000000 INFO @ Sat, 15 Jan 2022 19:15:58: 2000000 INFO @ Sat, 15 Jan 2022 19:16:02: 3000000 INFO @ Sat, 15 Jan 2022 19:16:06: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:16:10: 5000000 INFO @ Sat, 15 Jan 2022 19:16:15: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:16:19: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:16:19: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:16:19: #1 total tags in treatment: 1773872 INFO @ Sat, 15 Jan 2022 19:16:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:16:19: #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 19:16:19: #1 tags after filtering in treatment: 1243551 INFO @ Sat, 15 Jan 2022 19:16:19: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 15 Jan 2022 19:16:19: #1 finished! INFO @ Sat, 15 Jan 2022 19:16:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:16:19: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 19:16:19: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 19:16:19: start model_add_line... INFO @ Sat, 15 Jan 2022 19:16:19: start X-correlation... INFO @ Sat, 15 Jan 2022 19:16:19: end of X-cor INFO @ Sat, 15 Jan 2022 19:16:19: #2 finished! INFO @ Sat, 15 Jan 2022 19:16:19: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 19:16:19: #2 alternative fragment length(s) may be 1,209,234,269 bps INFO @ Sat, 15 Jan 2022 19:16:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.20_model.r INFO @ Sat, 15 Jan 2022 19:16:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:16:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:16:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:16:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:16:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:16:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781153/SRX11781153.20_summits.bed INFO @ Sat, 15 Jan 2022 19:16:23: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis CompletedMACS2peakCalling