Job ID = 14521954 SRX = SRX10459797 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 791763 spots for SRR14085596/SRR14085596.sra Written 791763 spots for SRR14085596/SRR14085596.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: 00:00:42 791763 reads; of these: 791763 (100.00%) were paired; of these: 169236 (21.37%) aligned concordantly 0 times 554812 (70.07%) aligned concordantly exactly 1 time 67715 (8.55%) aligned concordantly >1 times ---- 169236 pairs aligned concordantly 0 times; of these: 14856 (8.78%) aligned discordantly 1 time ---- 154380 pairs aligned 0 times concordantly or discordantly; of these: 308760 mates make up the pairs; of these: 263903 (85.47%) aligned 0 times 34620 (11.21%) aligned exactly 1 time 10237 (3.32%) aligned >1 times 83.33% overall alignment rate Time searching: 00:00:42 Overall time: 00:00:42 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] 7919 / 633297 = 0.0125 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 21:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.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 21:54:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:54:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:54:50: 1000000 INFO @ Sat, 15 Jan 2022 21:54:52: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:54:52: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:54:52: #1 total tags in treatment: 614729 INFO @ Sat, 15 Jan 2022 21:54:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:54:52: #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 21:54:52: #1 tags after filtering in treatment: 571182 INFO @ Sat, 15 Jan 2022 21:54:52: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 15 Jan 2022 21:54:52: #1 finished! INFO @ Sat, 15 Jan 2022 21:54:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:54:52: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 21:54:52: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 21:54:52: start model_add_line... INFO @ Sat, 15 Jan 2022 21:54:52: start X-correlation... INFO @ Sat, 15 Jan 2022 21:54:52: end of X-cor INFO @ Sat, 15 Jan 2022 21:54:52: #2 finished! INFO @ Sat, 15 Jan 2022 21:54:52: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 21:54:52: #2 alternative fragment length(s) may be 4,213,242,267 bps INFO @ Sat, 15 Jan 2022 21:54:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.05_model.r INFO @ Sat, 15 Jan 2022 21:54:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:54:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:54:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.05_summits.bed INFO @ Sat, 15 Jan 2022 21:54:55: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (42 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 21:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.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 21:55:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:20: 1000000 INFO @ Sat, 15 Jan 2022 21:55:22: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:55:22: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:55:22: #1 total tags in treatment: 614729 INFO @ Sat, 15 Jan 2022 21:55:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:55:22: #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 21:55:22: #1 tags after filtering in treatment: 571182 INFO @ Sat, 15 Jan 2022 21:55:22: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 15 Jan 2022 21:55:22: #1 finished! INFO @ Sat, 15 Jan 2022 21:55:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:55:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:55:22: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 21:55:22: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 21:55:22: start model_add_line... INFO @ Sat, 15 Jan 2022 21:55:22: start X-correlation... INFO @ Sat, 15 Jan 2022 21:55:22: end of X-cor INFO @ Sat, 15 Jan 2022 21:55:22: #2 finished! INFO @ Sat, 15 Jan 2022 21:55:22: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 21:55:22: #2 alternative fragment length(s) may be 4,213,242,267 bps INFO @ Sat, 15 Jan 2022 21:55:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.10_model.r INFO @ Sat, 15 Jan 2022 21:55:22: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:55:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:55:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.10_summits.bed INFO @ Sat, 15 Jan 2022 21:55:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (27 records, 4 fields): 2 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 21:55:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.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 21:55:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:55:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:55:50: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:55:52: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 21:55:52: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 21:55:52: #1 total tags in treatment: 614729 INFO @ Sat, 15 Jan 2022 21:55:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:55:52: #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 21:55:52: #1 tags after filtering in treatment: 571182 INFO @ Sat, 15 Jan 2022 21:55:52: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 15 Jan 2022 21:55:52: #1 finished! INFO @ Sat, 15 Jan 2022 21:55:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:55:52: #2 number of paired peaks: 129 WARNING @ Sat, 15 Jan 2022 21:55:52: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 15 Jan 2022 21:55:52: start model_add_line... INFO @ Sat, 15 Jan 2022 21:55:52: start X-correlation... INFO @ Sat, 15 Jan 2022 21:55:52: end of X-cor INFO @ Sat, 15 Jan 2022 21:55:52: #2 finished! INFO @ Sat, 15 Jan 2022 21:55:52: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Jan 2022 21:55:52: #2 alternative fragment length(s) may be 4,213,242,267 bps INFO @ Sat, 15 Jan 2022 21:55:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.20_model.r INFO @ Sat, 15 Jan 2022 21:55:52: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:55:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:55:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:55:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:55:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:55:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10459797/SRX10459797.20_summits.bed INFO @ Sat, 15 Jan 2022 21:55:55: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (18 records, 4 fields): 1 millis CompletedMACS2peakCalling