Job ID = 14520329 SRX = SRX8398385 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1714034 spots for SRR11848079/SRR11848079.sra Written 1714034 spots for SRR11848079/SRR11848079.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: 00:00:54 1714034 reads; of these: 1714034 (100.00%) were paired; of these: 273244 (15.94%) aligned concordantly 0 times 1302516 (75.99%) aligned concordantly exactly 1 time 138274 (8.07%) aligned concordantly >1 times ---- 273244 pairs aligned concordantly 0 times; of these: 21303 (7.80%) aligned discordantly 1 time ---- 251941 pairs aligned 0 times concordantly or discordantly; of these: 503882 mates make up the pairs; of these: 490109 (97.27%) aligned 0 times 8668 (1.72%) aligned exactly 1 time 5105 (1.01%) aligned >1 times 85.70% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 155853 / 1455100 = 0.1071 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 18:59:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.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 18:59:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:59:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:59:33: 1000000 INFO @ Sat, 15 Jan 2022 18:59:37: 2000000 INFO @ Sat, 15 Jan 2022 18:59:40: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:59:40: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:59:40: #1 total tags in treatment: 1285653 INFO @ Sat, 15 Jan 2022 18:59:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:59:40: #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 18:59:40: #1 tags after filtering in treatment: 995249 INFO @ Sat, 15 Jan 2022 18:59:40: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 18:59:40: #1 finished! INFO @ Sat, 15 Jan 2022 18:59:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:59:41: #2 number of paired peaks: 414 WARNING @ Sat, 15 Jan 2022 18:59:41: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Sat, 15 Jan 2022 18:59:41: start model_add_line... INFO @ Sat, 15 Jan 2022 18:59:41: start X-correlation... INFO @ Sat, 15 Jan 2022 18:59:41: end of X-cor INFO @ Sat, 15 Jan 2022 18:59:41: #2 finished! INFO @ Sat, 15 Jan 2022 18:59:41: #2 predicted fragment length is 4 bps INFO @ Sat, 15 Jan 2022 18:59:41: #2 alternative fragment length(s) may be 4,8,61,83,131,182,235,331,441,473,501,564 bps INFO @ Sat, 15 Jan 2022 18:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.05_model.r WARNING @ Sat, 15 Jan 2022 18:59:41: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:59:41: #2 You may need to consider one of the other alternative d(s): 4,8,61,83,131,182,235,331,441,473,501,564 WARNING @ Sat, 15 Jan 2022 18:59:41: #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 18:59:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:59:42: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.05_summits.bed INFO @ Sat, 15 Jan 2022 18:59:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 18:59:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.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 18:59:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:59:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:00:04: 1000000 INFO @ Sat, 15 Jan 2022 19:00:10: 2000000 INFO @ Sat, 15 Jan 2022 19:00:13: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:00:13: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:00:13: #1 total tags in treatment: 1285653 INFO @ Sat, 15 Jan 2022 19:00:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:00:13: #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 19:00:13: #1 tags after filtering in treatment: 995249 INFO @ Sat, 15 Jan 2022 19:00:13: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:00:13: #1 finished! INFO @ Sat, 15 Jan 2022 19:00:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:00:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:00:13: #2 number of paired peaks: 414 WARNING @ Sat, 15 Jan 2022 19:00:13: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Sat, 15 Jan 2022 19:00:13: start model_add_line... INFO @ Sat, 15 Jan 2022 19:00:13: start X-correlation... INFO @ Sat, 15 Jan 2022 19:00:13: end of X-cor INFO @ Sat, 15 Jan 2022 19:00:13: #2 finished! INFO @ Sat, 15 Jan 2022 19:00:13: #2 predicted fragment length is 4 bps INFO @ Sat, 15 Jan 2022 19:00:13: #2 alternative fragment length(s) may be 4,8,61,83,131,182,235,331,441,473,501,564 bps INFO @ Sat, 15 Jan 2022 19:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.10_model.r WARNING @ Sat, 15 Jan 2022 19:00:13: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:00:13: #2 You may need to consider one of the other alternative d(s): 4,8,61,83,131,182,235,331,441,473,501,564 WARNING @ Sat, 15 Jan 2022 19:00:13: #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 19:00:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:00:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:00:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.10_summits.bed INFO @ Sat, 15 Jan 2022 19:00:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 19:00:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.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 19:00:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:00:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:00:34: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:00:40: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:00:43: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:00:43: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:00:43: #1 total tags in treatment: 1285653 INFO @ Sat, 15 Jan 2022 19:00:43: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:00:43: #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 19:00:43: #1 tags after filtering in treatment: 995249 INFO @ Sat, 15 Jan 2022 19:00:43: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 15 Jan 2022 19:00:43: #1 finished! INFO @ Sat, 15 Jan 2022 19:00:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:00:43: #2 number of paired peaks: 414 WARNING @ Sat, 15 Jan 2022 19:00:43: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Sat, 15 Jan 2022 19:00:43: start model_add_line... INFO @ Sat, 15 Jan 2022 19:00:43: start X-correlation... INFO @ Sat, 15 Jan 2022 19:00:43: end of X-cor INFO @ Sat, 15 Jan 2022 19:00:43: #2 finished! INFO @ Sat, 15 Jan 2022 19:00:43: #2 predicted fragment length is 4 bps INFO @ Sat, 15 Jan 2022 19:00:43: #2 alternative fragment length(s) may be 4,8,61,83,131,182,235,331,441,473,501,564 bps INFO @ Sat, 15 Jan 2022 19:00:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.20_model.r WARNING @ Sat, 15 Jan 2022 19:00:43: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:00:43: #2 You may need to consider one of the other alternative d(s): 4,8,61,83,131,182,235,331,441,473,501,564 WARNING @ Sat, 15 Jan 2022 19:00:43: #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 19:00:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:00:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:00:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398385/SRX8398385.20_summits.bed INFO @ Sat, 15 Jan 2022 19:00:46: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling