Job ID = 14520529 SRX = SRX11781178 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:18:38 prefetch.2.10.7: 1) Downloading 'SRR15481121'... 2022-01-15T10:18:38 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:18:57 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:18:57 prefetch.2.10.7: 'SRR15481121' is valid 2022-01-15T10:18:57 prefetch.2.10.7: 1) 'SRR15481121' was downloaded successfully 2022-01-15T10:18:57 prefetch.2.10.7: 'SRR15481121' has 0 unresolved dependencies Read 6816134 spots for SRR15481121/SRR15481121.sra Written 6816134 spots for SRR15481121/SRR15481121.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: 00:07:24 6816134 reads; of these: 6816134 (100.00%) were paired; of these: 4428754 (64.97%) aligned concordantly 0 times 1113253 (16.33%) aligned concordantly exactly 1 time 1274127 (18.69%) aligned concordantly >1 times ---- 4428754 pairs aligned concordantly 0 times; of these: 35808 (0.81%) aligned discordantly 1 time ---- 4392946 pairs aligned 0 times concordantly or discordantly; of these: 8785892 mates make up the pairs; of these: 5399523 (61.46%) aligned 0 times 1613148 (18.36%) aligned exactly 1 time 1773221 (20.18%) aligned >1 times 60.39% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 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] 204642 / 2422376 = 0.0845 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 19:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.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 19:29:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:29:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:29:23: 1000000 INFO @ Sat, 15 Jan 2022 19:29:27: 2000000 INFO @ Sat, 15 Jan 2022 19:29:31: 3000000 INFO @ Sat, 15 Jan 2022 19:29:34: 4000000 INFO @ Sat, 15 Jan 2022 19:29:38: 5000000 INFO @ Sat, 15 Jan 2022 19:29:42: 6000000 INFO @ Sat, 15 Jan 2022 19:29:45: 7000000 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 19:29:48: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:29:48: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:29:48: #1 total tags in treatment: 2184607 INFO @ Sat, 15 Jan 2022 19:29:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:29:48: #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 19:29:49: #1 tags after filtering in treatment: 1191325 INFO @ Sat, 15 Jan 2022 19:29:49: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 19:29:49: #1 finished! INFO @ Sat, 15 Jan 2022 19:29:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:29:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:29:49: #2 number of paired peaks: 192 WARNING @ Sat, 15 Jan 2022 19:29:49: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 15 Jan 2022 19:29:49: start model_add_line... INFO @ Sat, 15 Jan 2022 19:29:49: start X-correlation... INFO @ Sat, 15 Jan 2022 19:29:49: end of X-cor INFO @ Sat, 15 Jan 2022 19:29:49: #2 finished! INFO @ Sat, 15 Jan 2022 19:29:49: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 19:29:49: #2 alternative fragment length(s) may be 2,214,216,247,269 bps INFO @ Sat, 15 Jan 2022 19:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.05_model.r INFO @ Sat, 15 Jan 2022 19:29:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.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 19:29:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:29:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:29:53: 1000000 INFO @ Sat, 15 Jan 2022 19:29:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:29:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:29:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:29:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.05_summits.bed INFO @ Sat, 15 Jan 2022 19:29:55: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:29:57: 2000000 INFO @ Sat, 15 Jan 2022 19:30:01: 3000000 INFO @ Sat, 15 Jan 2022 19:30:04: 4000000 INFO @ Sat, 15 Jan 2022 19:30:08: 5000000 INFO @ Sat, 15 Jan 2022 19:30:12: 6000000 INFO @ Sat, 15 Jan 2022 19:30:16: 7000000 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 19:30:19: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:30:19: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:30:19: #1 total tags in treatment: 2184607 INFO @ Sat, 15 Jan 2022 19:30:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:30:19: #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 19:30:19: #1 tags after filtering in treatment: 1191325 INFO @ Sat, 15 Jan 2022 19:30:19: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 19:30:19: #1 finished! INFO @ Sat, 15 Jan 2022 19:30:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:30:19: #2 number of paired peaks: 192 WARNING @ Sat, 15 Jan 2022 19:30:19: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 15 Jan 2022 19:30:19: start model_add_line... INFO @ Sat, 15 Jan 2022 19:30:19: start X-correlation... INFO @ Sat, 15 Jan 2022 19:30:19: end of X-cor INFO @ Sat, 15 Jan 2022 19:30:19: #2 finished! INFO @ Sat, 15 Jan 2022 19:30:19: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 19:30:19: #2 alternative fragment length(s) may be 2,214,216,247,269 bps INFO @ Sat, 15 Jan 2022 19:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.10_model.r INFO @ Sat, 15 Jan 2022 19:30:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.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 19:30:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:30:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:30:23: 1000000 INFO @ Sat, 15 Jan 2022 19:30:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.10_summits.bed INFO @ Sat, 15 Jan 2022 19:30:25: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (246 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:30:27: 2000000 INFO @ Sat, 15 Jan 2022 19:30:31: 3000000 INFO @ Sat, 15 Jan 2022 19:30:35: 4000000 INFO @ Sat, 15 Jan 2022 19:30:39: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:30:43: 6000000 INFO @ Sat, 15 Jan 2022 19:30:46: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:30:50: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:30:50: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:30:50: #1 total tags in treatment: 2184607 INFO @ Sat, 15 Jan 2022 19:30:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:30:50: #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 19:30:50: #1 tags after filtering in treatment: 1191325 INFO @ Sat, 15 Jan 2022 19:30:50: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 19:30:50: #1 finished! INFO @ Sat, 15 Jan 2022 19:30:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:30:50: #2 number of paired peaks: 192 WARNING @ Sat, 15 Jan 2022 19:30:50: Fewer paired peaks (192) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 192 pairs to build model! INFO @ Sat, 15 Jan 2022 19:30:50: start model_add_line... INFO @ Sat, 15 Jan 2022 19:30:50: start X-correlation... INFO @ Sat, 15 Jan 2022 19:30:50: end of X-cor INFO @ Sat, 15 Jan 2022 19:30:50: #2 finished! INFO @ Sat, 15 Jan 2022 19:30:50: #2 predicted fragment length is 269 bps INFO @ Sat, 15 Jan 2022 19:30:50: #2 alternative fragment length(s) may be 2,214,216,247,269 bps INFO @ Sat, 15 Jan 2022 19:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.20_model.r INFO @ Sat, 15 Jan 2022 19:30:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:30:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:30:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:30:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:30:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781178/SRX11781178.20_summits.bed INFO @ Sat, 15 Jan 2022 19:30:56: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 12 millis CompletedMACS2peakCalling