Job ID = 14521974 SRX = SRX7637543 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 329645 spots for SRR10972023/SRR10972023.sra Written 329645 spots for SRR10972023/SRR10972023.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: 00:00:13 329645 reads; of these: 329645 (100.00%) were paired; of these: 154250 (46.79%) aligned concordantly 0 times 124735 (37.84%) aligned concordantly exactly 1 time 50660 (15.37%) aligned concordantly >1 times ---- 154250 pairs aligned concordantly 0 times; of these: 72 (0.05%) aligned discordantly 1 time ---- 154178 pairs aligned 0 times concordantly or discordantly; of these: 308356 mates make up the pairs; of these: 306040 (99.25%) aligned 0 times 1229 (0.40%) aligned exactly 1 time 1087 (0.35%) aligned >1 times 53.58% overall alignment rate Time searching: 00:00:13 Overall time: 00:00:13 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] 5473 / 175078 = 0.0313 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 21:55:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.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 21:55:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:49: #1 tag size is determined as 74 bps INFO @ Sat, 15 Jan 2022 21:55:49: #1 tag size = 74 INFO @ Sat, 15 Jan 2022 21:55:49: #1 total tags in treatment: 169929 INFO @ Sat, 15 Jan 2022 21:55:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:55:49: #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 21:55:49: #1 tags after filtering in treatment: 156387 INFO @ Sat, 15 Jan 2022 21:55:49: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 21:55:49: #1 finished! INFO @ Sat, 15 Jan 2022 21:55:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:55:49: #2 number of paired peaks: 311 WARNING @ Sat, 15 Jan 2022 21:55:49: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 15 Jan 2022 21:55:49: start model_add_line... INFO @ Sat, 15 Jan 2022 21:55:49: start X-correlation... INFO @ Sat, 15 Jan 2022 21:55:49: end of X-cor INFO @ Sat, 15 Jan 2022 21:55:49: #2 finished! INFO @ Sat, 15 Jan 2022 21:55:49: #2 predicted fragment length is 256 bps INFO @ Sat, 15 Jan 2022 21:55:49: #2 alternative fragment length(s) may be 21,52,102,256,271,306,389 bps INFO @ Sat, 15 Jan 2022 21:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.05_model.r INFO @ Sat, 15 Jan 2022 21:55:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:55:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:55:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:55:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:55:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.05_summits.bed INFO @ Sat, 15 Jan 2022 21:55:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (112 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 21:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.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 21:56:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:56:19: #1 tag size is determined as 74 bps INFO @ Sat, 15 Jan 2022 21:56:19: #1 tag size = 74 INFO @ Sat, 15 Jan 2022 21:56:19: #1 total tags in treatment: 169929 INFO @ Sat, 15 Jan 2022 21:56:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:19: #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 21:56:19: #1 tags after filtering in treatment: 156387 INFO @ Sat, 15 Jan 2022 21:56:19: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 21:56:19: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:19: #2 number of paired peaks: 311 WARNING @ Sat, 15 Jan 2022 21:56:19: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:19: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:19: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:19: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:19: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:19: #2 predicted fragment length is 256 bps INFO @ Sat, 15 Jan 2022 21:56:19: #2 alternative fragment length(s) may be 21,52,102,256,271,306,389 bps INFO @ Sat, 15 Jan 2022 21:56:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.10_model.r INFO @ Sat, 15 Jan 2022 21:56:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.10_summits.bed INFO @ Sat, 15 Jan 2022 21:56:20: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (32 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 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:56:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.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 21:56:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:47: #1 read treatment tags... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:56:49: #1 tag size is determined as 74 bps INFO @ Sat, 15 Jan 2022 21:56:49: #1 tag size = 74 INFO @ Sat, 15 Jan 2022 21:56:49: #1 total tags in treatment: 169929 INFO @ Sat, 15 Jan 2022 21:56:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:56:49: #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 21:56:49: #1 tags after filtering in treatment: 156387 INFO @ Sat, 15 Jan 2022 21:56:49: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 21:56:49: #1 finished! INFO @ Sat, 15 Jan 2022 21:56:49: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:56:49: #2 number of paired peaks: 311 WARNING @ Sat, 15 Jan 2022 21:56:49: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Sat, 15 Jan 2022 21:56:49: start model_add_line... INFO @ Sat, 15 Jan 2022 21:56:49: start X-correlation... INFO @ Sat, 15 Jan 2022 21:56:49: end of X-cor INFO @ Sat, 15 Jan 2022 21:56:49: #2 finished! INFO @ Sat, 15 Jan 2022 21:56:49: #2 predicted fragment length is 256 bps INFO @ Sat, 15 Jan 2022 21:56:49: #2 alternative fragment length(s) may be 21,52,102,256,271,306,389 bps INFO @ Sat, 15 Jan 2022 21:56:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.20_model.r INFO @ Sat, 15 Jan 2022 21:56:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:56:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:56:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7637543/SRX7637543.20_summits.bed INFO @ Sat, 15 Jan 2022 21:56:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (16 records, 4 fields): 1 millis CompletedMACS2peakCalling