Job ID = 14521255 SRX = SRX10468524 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2677599 spots for SRR14094835/SRR14094835.sra Written 2677599 spots for SRR14094835/SRR14094835.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: 00:01:13 2677599 reads; of these: 2677599 (100.00%) were paired; of these: 663738 (24.79%) aligned concordantly 0 times 1822912 (68.08%) aligned concordantly exactly 1 time 190949 (7.13%) aligned concordantly >1 times ---- 663738 pairs aligned concordantly 0 times; of these: 19182 (2.89%) aligned discordantly 1 time ---- 644556 pairs aligned 0 times concordantly or discordantly; of these: 1289112 mates make up the pairs; of these: 1246151 (96.67%) aligned 0 times 33210 (2.58%) aligned exactly 1 time 9751 (0.76%) aligned >1 times 76.73% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 37263 / 2016044 = 0.0185 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 20:45:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.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 20:45:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:45:28: 1000000 INFO @ Sat, 15 Jan 2022 20:45:35: 2000000 INFO @ Sat, 15 Jan 2022 20:45:42: 3000000 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 20:45:49: 4000000 INFO @ Sat, 15 Jan 2022 20:45:50: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:45:50: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:45:50: #1 total tags in treatment: 1976628 INFO @ Sat, 15 Jan 2022 20:45:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:45:50: #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 20:45:50: #1 tags after filtering in treatment: 1745671 INFO @ Sat, 15 Jan 2022 20:45:50: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Jan 2022 20:45:50: #1 finished! INFO @ Sat, 15 Jan 2022 20:45:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:45:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:45:50: #2 number of paired peaks: 269 WARNING @ Sat, 15 Jan 2022 20:45:50: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 15 Jan 2022 20:45:50: start model_add_line... INFO @ Sat, 15 Jan 2022 20:45:50: start X-correlation... INFO @ Sat, 15 Jan 2022 20:45:50: end of X-cor INFO @ Sat, 15 Jan 2022 20:45:50: #2 finished! INFO @ Sat, 15 Jan 2022 20:45:50: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 20:45:50: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sat, 15 Jan 2022 20:45:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.05_model.r INFO @ Sat, 15 Jan 2022 20:45:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:45:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.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 20:45:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:45:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:45:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.05_summits.bed INFO @ Sat, 15 Jan 2022 20:45:56: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (763 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:45:57: 1000000 INFO @ Sat, 15 Jan 2022 20:46:04: 2000000 INFO @ Sat, 15 Jan 2022 20:46:11: 3000000 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 20:46:18: 4000000 INFO @ Sat, 15 Jan 2022 20:46:18: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:46:18: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:46:18: #1 total tags in treatment: 1976628 INFO @ Sat, 15 Jan 2022 20:46:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:18: #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 20:46:18: #1 tags after filtering in treatment: 1745671 INFO @ Sat, 15 Jan 2022 20:46:18: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Jan 2022 20:46:18: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:18: #2 number of paired peaks: 269 WARNING @ Sat, 15 Jan 2022 20:46:18: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 15 Jan 2022 20:46:18: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:18: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:18: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:18: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:18: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 20:46:18: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sat, 15 Jan 2022 20:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.10_model.r INFO @ Sat, 15 Jan 2022 20:46:18: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:46:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.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 20:46:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:46:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:46:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:46:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.10_summits.bed INFO @ Sat, 15 Jan 2022 20:46:24: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:46:27: 1000000 INFO @ Sat, 15 Jan 2022 20:46:35: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:46:42: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:46:48: 4000000 INFO @ Sat, 15 Jan 2022 20:46:49: #1 tag size is determined as 25 bps INFO @ Sat, 15 Jan 2022 20:46:49: #1 tag size = 25 INFO @ Sat, 15 Jan 2022 20:46:49: #1 total tags in treatment: 1976628 INFO @ Sat, 15 Jan 2022 20:46:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:49: #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 20:46:49: #1 tags after filtering in treatment: 1745671 INFO @ Sat, 15 Jan 2022 20:46:49: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Jan 2022 20:46:49: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:49: #2 number of paired peaks: 269 WARNING @ Sat, 15 Jan 2022 20:46:49: Fewer paired peaks (269) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 269 pairs to build model! INFO @ Sat, 15 Jan 2022 20:46:49: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:49: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:49: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:49: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:49: #2 predicted fragment length is 79 bps INFO @ Sat, 15 Jan 2022 20:46:49: #2 alternative fragment length(s) may be 4,79 bps INFO @ Sat, 15 Jan 2022 20:46:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.20_model.r INFO @ Sat, 15 Jan 2022 20:46:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:46:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:46:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:46:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:46:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468524/SRX10468524.20_summits.bed INFO @ Sat, 15 Jan 2022 20:46:55: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (264 records, 4 fields): 22 millis CompletedMACS2peakCalling