Job ID = 14520369 SRX = SRX11781114 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:06 prefetch.2.10.7: 1) Downloading 'SRR15481057'... 2022-01-15T10:01:06 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:43 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:44 prefetch.2.10.7: 'SRR15481057' is valid 2022-01-15T10:01:44 prefetch.2.10.7: 1) 'SRR15481057' was downloaded successfully 2022-01-15T10:01:44 prefetch.2.10.7: 'SRR15481057' has 0 unresolved dependencies Read 6956172 spots for SRR15481057/SRR15481057.sra Written 6956172 spots for SRR15481057/SRR15481057.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: 00:05:16 6956172 reads; of these: 6956172 (100.00%) were paired; of these: 4133030 (59.42%) aligned concordantly 0 times 2012829 (28.94%) aligned concordantly exactly 1 time 810313 (11.65%) aligned concordantly >1 times ---- 4133030 pairs aligned concordantly 0 times; of these: 50266 (1.22%) aligned discordantly 1 time ---- 4082764 pairs aligned 0 times concordantly or discordantly; of these: 8165528 mates make up the pairs; of these: 5105892 (62.53%) aligned 0 times 2132304 (26.11%) aligned exactly 1 time 927332 (11.36%) aligned >1 times 63.30% overall alignment rate Time searching: 00:05:16 Overall time: 00:05:16 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] 281809 / 2872862 = 0.0981 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 19:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.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 19:10:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:18: 1000000 INFO @ Sat, 15 Jan 2022 19:10:25: 2000000 INFO @ Sat, 15 Jan 2022 19:10:31: 3000000 INFO @ Sat, 15 Jan 2022 19:10:38: 4000000 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 19:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.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 19:10:42: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:10:42: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:10:45: 5000000 INFO @ Sat, 15 Jan 2022 19:10:48: 1000000 INFO @ Sat, 15 Jan 2022 19:10:52: 6000000 INFO @ Sat, 15 Jan 2022 19:10:54: 2000000 INFO @ Sat, 15 Jan 2022 19:10:59: 7000000 INFO @ Sat, 15 Jan 2022 19:11:00: 3000000 INFO @ Sat, 15 Jan 2022 19:11:07: 8000000 INFO @ Sat, 15 Jan 2022 19:11:07: 4000000 INFO @ Sat, 15 Jan 2022 19:11:08: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:11:08: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:11:08: #1 total tags in treatment: 2544653 INFO @ Sat, 15 Jan 2022 19:11:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:08: #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 19:11:08: #1 tags after filtering in treatment: 1873838 INFO @ Sat, 15 Jan 2022 19:11:08: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:11:08: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:11:08: #2 number of paired peaks: 119 WARNING @ Sat, 15 Jan 2022 19:11:08: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 15 Jan 2022 19:11:08: start model_add_line... INFO @ Sat, 15 Jan 2022 19:11:08: start X-correlation... INFO @ Sat, 15 Jan 2022 19:11:08: end of X-cor INFO @ Sat, 15 Jan 2022 19:11:08: #2 finished! INFO @ Sat, 15 Jan 2022 19:11:08: #2 predicted fragment length is 203 bps INFO @ Sat, 15 Jan 2022 19:11:08: #2 alternative fragment length(s) may be 2,203,223,247,251 bps INFO @ Sat, 15 Jan 2022 19:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.05_model.r INFO @ Sat, 15 Jan 2022 19:11:08: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:11:08: #3 Pre-compute pvalue-qvalue table... 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 19:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.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 19:11:12: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:11:12: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:11:13: 5000000 INFO @ Sat, 15 Jan 2022 19:11:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.05_summits.bed INFO @ Sat, 15 Jan 2022 19:11:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:11:18: 1000000 INFO @ Sat, 15 Jan 2022 19:11:19: 6000000 INFO @ Sat, 15 Jan 2022 19:11:24: 2000000 INFO @ Sat, 15 Jan 2022 19:11:25: 7000000 INFO @ Sat, 15 Jan 2022 19:11:30: 3000000 INFO @ Sat, 15 Jan 2022 19:11:31: 8000000 INFO @ Sat, 15 Jan 2022 19:11:33: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:11:33: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:11:33: #1 total tags in treatment: 2544653 INFO @ Sat, 15 Jan 2022 19:11:33: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:33: #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 19:11:33: #1 tags after filtering in treatment: 1873838 INFO @ Sat, 15 Jan 2022 19:11:33: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:11:33: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:11:33: #2 number of paired peaks: 119 WARNING @ Sat, 15 Jan 2022 19:11:33: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 15 Jan 2022 19:11:33: start model_add_line... INFO @ Sat, 15 Jan 2022 19:11:33: start X-correlation... INFO @ Sat, 15 Jan 2022 19:11:33: end of X-cor INFO @ Sat, 15 Jan 2022 19:11:33: #2 finished! INFO @ Sat, 15 Jan 2022 19:11:33: #2 predicted fragment length is 203 bps INFO @ Sat, 15 Jan 2022 19:11:33: #2 alternative fragment length(s) may be 2,203,223,247,251 bps INFO @ Sat, 15 Jan 2022 19:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.10_model.r INFO @ Sat, 15 Jan 2022 19:11:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:11:36: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:11:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.10_summits.bed INFO @ Sat, 15 Jan 2022 19:11:40: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (142 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:11:42: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:11:47: 6000000 INFO @ Sat, 15 Jan 2022 19:11:53: 7000000 INFO @ Sat, 15 Jan 2022 19:11:58: 8000000 INFO @ Sat, 15 Jan 2022 19:11:59: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:11:59: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:11:59: #1 total tags in treatment: 2544653 INFO @ Sat, 15 Jan 2022 19:11:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:11:59: #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 19:11:59: #1 tags after filtering in treatment: 1873838 INFO @ Sat, 15 Jan 2022 19:11:59: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 15 Jan 2022 19:11:59: #1 finished! INFO @ Sat, 15 Jan 2022 19:11:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:11:59: #2 number of paired peaks: 119 WARNING @ Sat, 15 Jan 2022 19:11:59: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Sat, 15 Jan 2022 19:11:59: start model_add_line... INFO @ Sat, 15 Jan 2022 19:11:59: start X-correlation... INFO @ Sat, 15 Jan 2022 19:11:59: end of X-cor INFO @ Sat, 15 Jan 2022 19:11:59: #2 finished! INFO @ Sat, 15 Jan 2022 19:11:59: #2 predicted fragment length is 203 bps INFO @ Sat, 15 Jan 2022 19:11:59: #2 alternative fragment length(s) may be 2,203,223,247,251 bps INFO @ Sat, 15 Jan 2022 19:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.20_model.r INFO @ Sat, 15 Jan 2022 19:11:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:12:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781114/SRX11781114.20_summits.bed INFO @ Sat, 15 Jan 2022 19:12:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 29 millis CompletedMACS2peakCalling