Job ID = 14520115 SRX = SRX7496420 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3888891 spots for SRR10823031/SRR10823031.sra Written 3888891 spots for SRR10823031/SRR10823031.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: 00:01:06 3888891 reads; of these: 3888891 (100.00%) were paired; of these: 2801935 (72.05%) aligned concordantly 0 times 962076 (24.74%) aligned concordantly exactly 1 time 124880 (3.21%) aligned concordantly >1 times ---- 2801935 pairs aligned concordantly 0 times; of these: 5140 (0.18%) aligned discordantly 1 time ---- 2796795 pairs aligned 0 times concordantly or discordantly; of these: 5593590 mates make up the pairs; of these: 4594984 (82.15%) aligned 0 times 880187 (15.74%) aligned exactly 1 time 118419 (2.12%) aligned >1 times 40.92% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 89159 / 1091879 = 0.0817 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 18:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.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 18:23:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:23:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:23:50: 1000000 INFO @ Sat, 15 Jan 2022 18:23:55: 2000000 INFO @ Sat, 15 Jan 2022 18:24:00: 3000000 INFO @ Sat, 15 Jan 2022 18:24:00: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:24:00: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:24:00: #1 total tags in treatment: 997918 INFO @ Sat, 15 Jan 2022 18:24:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:24:00: #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 18:24:00: #1 tags after filtering in treatment: 615180 INFO @ Sat, 15 Jan 2022 18:24:00: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 18:24:00: #1 finished! INFO @ Sat, 15 Jan 2022 18:24:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:24:00: #2 number of paired peaks: 700 WARNING @ Sat, 15 Jan 2022 18:24:00: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Sat, 15 Jan 2022 18:24:00: start model_add_line... INFO @ Sat, 15 Jan 2022 18:24:00: start X-correlation... INFO @ Sat, 15 Jan 2022 18:24:00: end of X-cor INFO @ Sat, 15 Jan 2022 18:24:00: #2 finished! INFO @ Sat, 15 Jan 2022 18:24:00: #2 predicted fragment length is 253 bps INFO @ Sat, 15 Jan 2022 18:24:00: #2 alternative fragment length(s) may be 0,253 bps INFO @ Sat, 15 Jan 2022 18:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.05_model.r INFO @ Sat, 15 Jan 2022 18:24:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:24:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:24:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.05_summits.bed INFO @ Sat, 15 Jan 2022 18:24:04: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (434 records, 4 fields): 18 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 18:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.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 18:24:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:24:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:24:22: 1000000 INFO @ Sat, 15 Jan 2022 18:24:28: 2000000 INFO @ Sat, 15 Jan 2022 18:24:34: 3000000 INFO @ Sat, 15 Jan 2022 18:24:34: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:24:34: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:24:34: #1 total tags in treatment: 997918 INFO @ Sat, 15 Jan 2022 18:24:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:24:34: #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 18:24:34: #1 tags after filtering in treatment: 615180 INFO @ Sat, 15 Jan 2022 18:24:34: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 18:24:34: #1 finished! INFO @ Sat, 15 Jan 2022 18:24:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:24:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:24:34: #2 number of paired peaks: 700 WARNING @ Sat, 15 Jan 2022 18:24:34: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Sat, 15 Jan 2022 18:24:34: start model_add_line... INFO @ Sat, 15 Jan 2022 18:24:34: start X-correlation... INFO @ Sat, 15 Jan 2022 18:24:34: end of X-cor INFO @ Sat, 15 Jan 2022 18:24:34: #2 finished! INFO @ Sat, 15 Jan 2022 18:24:34: #2 predicted fragment length is 253 bps INFO @ Sat, 15 Jan 2022 18:24:34: #2 alternative fragment length(s) may be 0,253 bps INFO @ Sat, 15 Jan 2022 18:24:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.10_model.r INFO @ Sat, 15 Jan 2022 18:24:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:24:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:24:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:24:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:24:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:24:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.10_summits.bed INFO @ Sat, 15 Jan 2022 18:24:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (290 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 18:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.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 18:24:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:24:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:24:51: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:24:57: 2000000 INFO @ Sat, 15 Jan 2022 18:25:03: 3000000 INFO @ Sat, 15 Jan 2022 18:25:03: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:25:03: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:25:03: #1 total tags in treatment: 997918 INFO @ Sat, 15 Jan 2022 18:25:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:25:03: #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 18:25:03: #1 tags after filtering in treatment: 615180 INFO @ Sat, 15 Jan 2022 18:25:03: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 18:25:03: #1 finished! INFO @ Sat, 15 Jan 2022 18:25:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:25:03: #2 number of paired peaks: 700 WARNING @ Sat, 15 Jan 2022 18:25:03: Fewer paired peaks (700) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 700 pairs to build model! INFO @ Sat, 15 Jan 2022 18:25:03: start model_add_line... INFO @ Sat, 15 Jan 2022 18:25:03: start X-correlation... INFO @ Sat, 15 Jan 2022 18:25:03: end of X-cor INFO @ Sat, 15 Jan 2022 18:25:03: #2 finished! INFO @ Sat, 15 Jan 2022 18:25:03: #2 predicted fragment length is 253 bps INFO @ Sat, 15 Jan 2022 18:25:03: #2 alternative fragment length(s) may be 0,253 bps INFO @ Sat, 15 Jan 2022 18:25:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.20_model.r INFO @ Sat, 15 Jan 2022 18:25:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:25:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:25:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:25:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:25:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496420/SRX7496420.20_summits.bed INFO @ Sat, 15 Jan 2022 18:25:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 25 millis CompletedMACS2peakCalling