Job ID = 14521481 SRX = SRX10468481 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2724000 spots for SRR14094792/SRR14094792.sra Written 2724000 spots for SRR14094792/SRR14094792.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: 00:00:39 2724000 reads; of these: 2724000 (100.00%) were paired; of these: 1077727 (39.56%) aligned concordantly 0 times 1189749 (43.68%) aligned concordantly exactly 1 time 456524 (16.76%) aligned concordantly >1 times ---- 1077727 pairs aligned concordantly 0 times; of these: 16880 (1.57%) aligned discordantly 1 time ---- 1060847 pairs aligned 0 times concordantly or discordantly; of these: 2121694 mates make up the pairs; of these: 2077506 (97.92%) aligned 0 times 19855 (0.94%) aligned exactly 1 time 24333 (1.15%) aligned >1 times 61.87% overall alignment rate Time searching: 00:00:39 Overall time: 00:00:39 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] 190874 / 1661242 = 0.1149 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 21:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.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 21:05:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:05:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:05:15: 1000000 INFO @ Sat, 15 Jan 2022 21:05:19: 2000000 INFO @ Sat, 15 Jan 2022 21:05:24: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:05:24: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:05:24: #1 total tags in treatment: 1456477 INFO @ Sat, 15 Jan 2022 21:05:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:05:24: #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 21:05:24: #1 tags after filtering in treatment: 1116007 INFO @ Sat, 15 Jan 2022 21:05:24: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 21:05:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:05:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:05:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:05:24: #2 number of paired peaks: 149 WARNING @ Sat, 15 Jan 2022 21:05:24: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sat, 15 Jan 2022 21:05:24: start model_add_line... INFO @ Sat, 15 Jan 2022 21:05:24: start X-correlation... INFO @ Sat, 15 Jan 2022 21:05:24: end of X-cor INFO @ Sat, 15 Jan 2022 21:05:24: #2 finished! INFO @ Sat, 15 Jan 2022 21:05:24: #2 predicted fragment length is 88 bps INFO @ Sat, 15 Jan 2022 21:05:24: #2 alternative fragment length(s) may be 3,58,88 bps INFO @ Sat, 15 Jan 2022 21:05:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.05_model.r INFO @ Sat, 15 Jan 2022 21:05:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:05:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:05:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:05:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:05:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.05_summits.bed INFO @ Sat, 15 Jan 2022 21:05:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (551 records, 4 fields): 2 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 21:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.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 21:05:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:05:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:05:46: 1000000 INFO @ Sat, 15 Jan 2022 21:05:52: 2000000 INFO @ Sat, 15 Jan 2022 21:05:57: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:05:57: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:05:57: #1 total tags in treatment: 1456477 INFO @ Sat, 15 Jan 2022 21:05:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:05:57: #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 21:05:57: #1 tags after filtering in treatment: 1116007 INFO @ Sat, 15 Jan 2022 21:05:57: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 21:05:57: #1 finished! INFO @ Sat, 15 Jan 2022 21:05:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:05:57: #2 number of paired peaks: 149 WARNING @ Sat, 15 Jan 2022 21:05:57: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sat, 15 Jan 2022 21:05:57: start model_add_line... INFO @ Sat, 15 Jan 2022 21:05:57: start X-correlation... INFO @ Sat, 15 Jan 2022 21:05:57: end of X-cor INFO @ Sat, 15 Jan 2022 21:05:57: #2 finished! INFO @ Sat, 15 Jan 2022 21:05:57: #2 predicted fragment length is 88 bps INFO @ Sat, 15 Jan 2022 21:05:57: #2 alternative fragment length(s) may be 3,58,88 bps INFO @ Sat, 15 Jan 2022 21:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.10_model.r INFO @ Sat, 15 Jan 2022 21:05:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:05:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:06:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:06:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:06:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.10_summits.bed INFO @ Sat, 15 Jan 2022 21:06:00: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (235 records, 4 fields): 460 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 21:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.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 21:06:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:06:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:06:15: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:06:20: 2000000 INFO @ Sat, 15 Jan 2022 21:06:24: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 21:06:24: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 21:06:24: #1 total tags in treatment: 1456477 INFO @ Sat, 15 Jan 2022 21:06:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:06:24: #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 21:06:24: #1 tags after filtering in treatment: 1116007 INFO @ Sat, 15 Jan 2022 21:06:24: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 21:06:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:06:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:06:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:06:24: #2 number of paired peaks: 149 WARNING @ Sat, 15 Jan 2022 21:06:24: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Sat, 15 Jan 2022 21:06:24: start model_add_line... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:06:24: start X-correlation... INFO @ Sat, 15 Jan 2022 21:06:24: end of X-cor INFO @ Sat, 15 Jan 2022 21:06:24: #2 finished! INFO @ Sat, 15 Jan 2022 21:06:24: #2 predicted fragment length is 88 bps INFO @ Sat, 15 Jan 2022 21:06:24: #2 alternative fragment length(s) may be 3,58,88 bps INFO @ Sat, 15 Jan 2022 21:06:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.20_model.r INFO @ Sat, 15 Jan 2022 21:06:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:06:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:06:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:06:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:06:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:06:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468481/SRX10468481.20_summits.bed INFO @ Sat, 15 Jan 2022 21:06:27: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 2 millis CompletedMACS2peakCalling