Job ID = 14521168 SRX = SRX10468509 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4715898 spots for SRR14094820/SRR14094820.sra Written 4715898 spots for SRR14094820/SRR14094820.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: 00:03:46 4715898 reads; of these: 4715898 (100.00%) were paired; of these: 1077928 (22.86%) aligned concordantly 0 times 3288087 (69.72%) aligned concordantly exactly 1 time 349883 (7.42%) aligned concordantly >1 times ---- 1077928 pairs aligned concordantly 0 times; of these: 49208 (4.57%) aligned discordantly 1 time ---- 1028720 pairs aligned 0 times concordantly or discordantly; of these: 2057440 mates make up the pairs; of these: 1951930 (94.87%) aligned 0 times 84790 (4.12%) aligned exactly 1 time 20720 (1.01%) aligned >1 times 79.30% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 156077 / 3653363 = 0.0427 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 20:39:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.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 20:39:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:39:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:39:26: 1000000 INFO @ Sat, 15 Jan 2022 20:39:33: 2000000 INFO @ Sat, 15 Jan 2022 20:39:41: 3000000 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 20:39:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.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 20:39:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:39:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:39:48: 4000000 INFO @ Sat, 15 Jan 2022 20:39:56: 5000000 INFO @ Sat, 15 Jan 2022 20:39:56: 1000000 INFO @ Sat, 15 Jan 2022 20:40:03: 6000000 INFO @ Sat, 15 Jan 2022 20:40:04: 2000000 INFO @ Sat, 15 Jan 2022 20:40:11: 7000000 INFO @ Sat, 15 Jan 2022 20:40:12: 3000000 INFO @ Sat, 15 Jan 2022 20:40:12: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:40:12: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:40:12: #1 total tags in treatment: 3482325 INFO @ Sat, 15 Jan 2022 20:40:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:40:12: #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 20:40:12: #1 tags after filtering in treatment: 2853219 INFO @ Sat, 15 Jan 2022 20:40:12: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 20:40:12: #1 finished! INFO @ Sat, 15 Jan 2022 20:40:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:40:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:40:13: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 20:40:13: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 20:40:13: start model_add_line... INFO @ Sat, 15 Jan 2022 20:40:13: start X-correlation... INFO @ Sat, 15 Jan 2022 20:40:13: end of X-cor INFO @ Sat, 15 Jan 2022 20:40:13: #2 finished! INFO @ Sat, 15 Jan 2022 20:40:13: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:40:13: #2 alternative fragment length(s) may be 3,31 bps INFO @ Sat, 15 Jan 2022 20:40:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.05_model.r WARNING @ Sat, 15 Jan 2022 20:40:13: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:40:13: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Sat, 15 Jan 2022 20:40:13: #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 20:40:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:40:13: #3 Pre-compute pvalue-qvalue table... 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 20:40:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.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 20:40:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:40:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.05_summits.bed INFO @ Sat, 15 Jan 2022 20:40:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:40:20: 4000000 INFO @ Sat, 15 Jan 2022 20:40:26: 1000000 INFO @ Sat, 15 Jan 2022 20:40:28: 5000000 INFO @ Sat, 15 Jan 2022 20:40:34: 2000000 INFO @ Sat, 15 Jan 2022 20:40:35: 6000000 INFO @ Sat, 15 Jan 2022 20:40:42: 3000000 INFO @ Sat, 15 Jan 2022 20:40:43: 7000000 INFO @ Sat, 15 Jan 2022 20:40:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:40:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:40:44: #1 total tags in treatment: 3482325 INFO @ Sat, 15 Jan 2022 20:40:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:40:44: #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 20:40:44: #1 tags after filtering in treatment: 2853219 INFO @ Sat, 15 Jan 2022 20:40:44: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 20:40:44: #1 finished! INFO @ Sat, 15 Jan 2022 20:40:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:40:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:40:44: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 20:40:44: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 20:40:44: start model_add_line... INFO @ Sat, 15 Jan 2022 20:40:44: start X-correlation... INFO @ Sat, 15 Jan 2022 20:40:44: end of X-cor INFO @ Sat, 15 Jan 2022 20:40:44: #2 finished! INFO @ Sat, 15 Jan 2022 20:40:44: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:40:44: #2 alternative fragment length(s) may be 3,31 bps INFO @ Sat, 15 Jan 2022 20:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.10_model.r WARNING @ Sat, 15 Jan 2022 20:40:44: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:40:44: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Sat, 15 Jan 2022 20:40:44: #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 20:40:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:40:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:40:50: 4000000 INFO @ Sat, 15 Jan 2022 20:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.10_summits.bed INFO @ Sat, 15 Jan 2022 20:40:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:40:57: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:41:04: 6000000 INFO @ Sat, 15 Jan 2022 20:41:12: 7000000 INFO @ Sat, 15 Jan 2022 20:41:13: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:41:13: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:41:13: #1 total tags in treatment: 3482325 INFO @ Sat, 15 Jan 2022 20:41:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:41:13: #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 20:41:13: #1 tags after filtering in treatment: 2853219 INFO @ Sat, 15 Jan 2022 20:41:13: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 15 Jan 2022 20:41:13: #1 finished! INFO @ Sat, 15 Jan 2022 20:41:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:41:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:41:13: #2 number of paired peaks: 158 WARNING @ Sat, 15 Jan 2022 20:41:13: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Sat, 15 Jan 2022 20:41:13: start model_add_line... INFO @ Sat, 15 Jan 2022 20:41:13: start X-correlation... INFO @ Sat, 15 Jan 2022 20:41:13: end of X-cor INFO @ Sat, 15 Jan 2022 20:41:13: #2 finished! INFO @ Sat, 15 Jan 2022 20:41:13: #2 predicted fragment length is 3 bps INFO @ Sat, 15 Jan 2022 20:41:13: #2 alternative fragment length(s) may be 3,31 bps INFO @ Sat, 15 Jan 2022 20:41:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.20_model.r WARNING @ Sat, 15 Jan 2022 20:41:13: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:41:13: #2 You may need to consider one of the other alternative d(s): 3,31 WARNING @ Sat, 15 Jan 2022 20:41:13: #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 20:41:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:41:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:41:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:41:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:41:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:41:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10468509/SRX10468509.20_summits.bed INFO @ Sat, 15 Jan 2022 20:41:19: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling