Job ID = 14519728 SRX = SRX8754202 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6048339 spots for SRR12246273/SRR12246273.sra Written 6048339 spots for SRR12246273/SRR12246273.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: 00:01:11 6048339 reads; of these: 6048339 (100.00%) were paired; of these: 4976422 (82.28%) aligned concordantly 0 times 665279 (11.00%) aligned concordantly exactly 1 time 406638 (6.72%) aligned concordantly >1 times ---- 4976422 pairs aligned concordantly 0 times; of these: 3716 (0.07%) aligned discordantly 1 time ---- 4972706 pairs aligned 0 times concordantly or discordantly; of these: 9945412 mates make up the pairs; of these: 9899544 (99.54%) aligned 0 times 16146 (0.16%) aligned exactly 1 time 29722 (0.30%) aligned >1 times 18.16% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 198956 / 1073990 = 0.1852 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 17:34:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.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 17:34:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:34:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:34:19: 1000000 INFO @ Sat, 15 Jan 2022 17:34:24: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:34:24: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:34:24: #1 total tags in treatment: 873133 INFO @ Sat, 15 Jan 2022 17:34:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:34:24: #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 17:34:24: #1 tags after filtering in treatment: 651620 INFO @ Sat, 15 Jan 2022 17:34:24: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 17:34:24: #1 finished! INFO @ Sat, 15 Jan 2022 17:34:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:34:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:34:24: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 17:34:24: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 17:34:24: start model_add_line... INFO @ Sat, 15 Jan 2022 17:34:24: start X-correlation... INFO @ Sat, 15 Jan 2022 17:34:24: end of X-cor INFO @ Sat, 15 Jan 2022 17:34:24: #2 finished! INFO @ Sat, 15 Jan 2022 17:34:24: #2 predicted fragment length is 120 bps INFO @ Sat, 15 Jan 2022 17:34:24: #2 alternative fragment length(s) may be 3,120,564 bps INFO @ Sat, 15 Jan 2022 17:34:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.05_model.r INFO @ Sat, 15 Jan 2022 17:34:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:34:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:34:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.05_summits.bed INFO @ Sat, 15 Jan 2022 17:34:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (126 records, 4 fields): 21 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 17:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.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 17:34:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:34:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:34:48: 1000000 INFO @ Sat, 15 Jan 2022 17:34:52: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:34:52: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:34:52: #1 total tags in treatment: 873133 INFO @ Sat, 15 Jan 2022 17:34:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:34:52: #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 17:34:52: #1 tags after filtering in treatment: 651620 INFO @ Sat, 15 Jan 2022 17:34:52: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 17:34:52: #1 finished! INFO @ Sat, 15 Jan 2022 17:34:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:34:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:34:52: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 17:34:52: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 17:34:52: start model_add_line... INFO @ Sat, 15 Jan 2022 17:34:52: start X-correlation... INFO @ Sat, 15 Jan 2022 17:34:52: end of X-cor INFO @ Sat, 15 Jan 2022 17:34:52: #2 finished! INFO @ Sat, 15 Jan 2022 17:34:52: #2 predicted fragment length is 120 bps INFO @ Sat, 15 Jan 2022 17:34:52: #2 alternative fragment length(s) may be 3,120,564 bps INFO @ Sat, 15 Jan 2022 17:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.10_model.r INFO @ Sat, 15 Jan 2022 17:34:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:34:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:34:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:34:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:34:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.10_summits.bed INFO @ Sat, 15 Jan 2022 17:34:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (75 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 17:35:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.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 17:35:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:35:12: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:35:18: 1000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:35:22: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 17:35:22: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 17:35:22: #1 total tags in treatment: 873133 INFO @ Sat, 15 Jan 2022 17:35:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:35:22: #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 17:35:22: #1 tags after filtering in treatment: 651620 INFO @ Sat, 15 Jan 2022 17:35:22: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 17:35:22: #1 finished! INFO @ Sat, 15 Jan 2022 17:35:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:35:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:35:22: #2 number of paired peaks: 185 WARNING @ Sat, 15 Jan 2022 17:35:22: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Sat, 15 Jan 2022 17:35:22: start model_add_line... INFO @ Sat, 15 Jan 2022 17:35:22: start X-correlation... INFO @ Sat, 15 Jan 2022 17:35:22: end of X-cor INFO @ Sat, 15 Jan 2022 17:35:22: #2 finished! INFO @ Sat, 15 Jan 2022 17:35:22: #2 predicted fragment length is 120 bps INFO @ Sat, 15 Jan 2022 17:35:22: #2 alternative fragment length(s) may be 3,120,564 bps INFO @ Sat, 15 Jan 2022 17:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.20_model.r INFO @ Sat, 15 Jan 2022 17:35:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:35:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:35:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:35:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:35:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8754202/SRX8754202.20_summits.bed INFO @ Sat, 15 Jan 2022 17:35:25: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling