Job ID = 14521922 SRX = SRX11539773 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15810688 spots for SRR15233872/SRR15233872.sra Written 15810688 spots for SRR15233872/SRR15233872.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: 00:07:22 15810688 reads; of these: 15810688 (100.00%) were paired; of these: 15076463 (95.36%) aligned concordantly 0 times 237743 (1.50%) aligned concordantly exactly 1 time 496482 (3.14%) aligned concordantly >1 times ---- 15076463 pairs aligned concordantly 0 times; of these: 203826 (1.35%) aligned discordantly 1 time ---- 14872637 pairs aligned 0 times concordantly or discordantly; of these: 29745274 mates make up the pairs; of these: 29158589 (98.03%) aligned 0 times 428074 (1.44%) aligned exactly 1 time 158611 (0.53%) aligned >1 times 7.79% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 769735 / 931029 = 0.8268 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 21:59:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.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 21:59:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:59:40: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:59:47: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 21:59:47: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 21:59:47: #1 total tags in treatment: 100025 INFO @ Sat, 15 Jan 2022 21:59:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:59:47: #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 21:59:47: #1 tags after filtering in treatment: 90368 INFO @ Sat, 15 Jan 2022 21:59:47: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:59:47: #1 finished! INFO @ Sat, 15 Jan 2022 21:59:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:59:47: #2 number of paired peaks: 110 WARNING @ Sat, 15 Jan 2022 21:59:47: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 15 Jan 2022 21:59:47: start model_add_line... INFO @ Sat, 15 Jan 2022 21:59:47: start X-correlation... INFO @ Sat, 15 Jan 2022 21:59:47: end of X-cor INFO @ Sat, 15 Jan 2022 21:59:47: #2 finished! INFO @ Sat, 15 Jan 2022 21:59:47: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 21:59:47: #2 alternative fragment length(s) may be 1,55,116,146,161,193,229,248,299,349,407,461,508,529 bps INFO @ Sat, 15 Jan 2022 21:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.05_model.r WARNING @ Sat, 15 Jan 2022 21:59:47: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:59:47: #2 You may need to consider one of the other alternative d(s): 1,55,116,146,161,193,229,248,299,349,407,461,508,529 WARNING @ Sat, 15 Jan 2022 21:59:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:59:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:59:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:59:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:59:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:59:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.05_summits.bed INFO @ Sat, 15 Jan 2022 21:59:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 38 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 22:00:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.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 22:00:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:00:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:00:17: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 22:00:17: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 22:00:17: #1 total tags in treatment: 100025 INFO @ Sat, 15 Jan 2022 22:00:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:00:17: #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 22:00:17: #1 tags after filtering in treatment: 90368 INFO @ Sat, 15 Jan 2022 22:00:17: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 22:00:17: #1 finished! INFO @ Sat, 15 Jan 2022 22:00:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:00:17: #2 number of paired peaks: 110 WARNING @ Sat, 15 Jan 2022 22:00:17: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 15 Jan 2022 22:00:17: start model_add_line... INFO @ Sat, 15 Jan 2022 22:00:17: start X-correlation... INFO @ Sat, 15 Jan 2022 22:00:17: end of X-cor INFO @ Sat, 15 Jan 2022 22:00:17: #2 finished! INFO @ Sat, 15 Jan 2022 22:00:17: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 22:00:17: #2 alternative fragment length(s) may be 1,55,116,146,161,193,229,248,299,349,407,461,508,529 bps INFO @ Sat, 15 Jan 2022 22:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.10_model.r WARNING @ Sat, 15 Jan 2022 22:00:17: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:00:17: #2 You may need to consider one of the other alternative d(s): 1,55,116,146,161,193,229,248,299,349,407,461,508,529 WARNING @ Sat, 15 Jan 2022 22:00:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:00:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:00:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:00:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:00:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.10_summits.bed INFO @ Sat, 15 Jan 2022 22:00:18: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 3 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 22:00:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.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 22:00:40: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:00:40: #1 read treatment tags... 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 22:00:46: #1 tag size is determined as 45 bps INFO @ Sat, 15 Jan 2022 22:00:46: #1 tag size = 45 INFO @ Sat, 15 Jan 2022 22:00:46: #1 total tags in treatment: 100025 INFO @ Sat, 15 Jan 2022 22:00:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:00:46: #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 22:00:46: #1 tags after filtering in treatment: 90368 INFO @ Sat, 15 Jan 2022 22:00:46: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 22:00:46: #1 finished! INFO @ Sat, 15 Jan 2022 22:00:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:00:46: #2 number of paired peaks: 110 WARNING @ Sat, 15 Jan 2022 22:00:46: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 15 Jan 2022 22:00:46: start model_add_line... INFO @ Sat, 15 Jan 2022 22:00:46: start X-correlation... INFO @ Sat, 15 Jan 2022 22:00:46: end of X-cor INFO @ Sat, 15 Jan 2022 22:00:46: #2 finished! INFO @ Sat, 15 Jan 2022 22:00:46: #2 predicted fragment length is 55 bps INFO @ Sat, 15 Jan 2022 22:00:46: #2 alternative fragment length(s) may be 1,55,116,146,161,193,229,248,299,349,407,461,508,529 bps INFO @ Sat, 15 Jan 2022 22:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.20_model.r WARNING @ Sat, 15 Jan 2022 22:00:46: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 22:00:46: #2 You may need to consider one of the other alternative d(s): 1,55,116,146,161,193,229,248,299,349,407,461,508,529 WARNING @ Sat, 15 Jan 2022 22:00:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 22:00:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:00:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:00:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:00:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11539773/SRX11539773.20_summits.bed INFO @ Sat, 15 Jan 2022 22:00:47: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 12 millis CompletedMACS2peakCalling