Job ID = 14520364 SRX = SRX11781109 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:00:22 prefetch.2.10.7: 1) Downloading 'SRR15481052'... 2022-01-15T10:00:22 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:02:03 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:02:03 prefetch.2.10.7: 1) 'SRR15481052' was downloaded successfully 2022-01-15T10:02:03 prefetch.2.10.7: 'SRR15481052' has 0 unresolved dependencies Read 17124810 spots for SRR15481052/SRR15481052.sra Written 17124810 spots for SRR15481052/SRR15481052.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: 00:12:34 17124810 reads; of these: 17124810 (100.00%) were paired; of these: 3281165 (19.16%) aligned concordantly 0 times 12717783 (74.27%) aligned concordantly exactly 1 time 1125862 (6.57%) aligned concordantly >1 times ---- 3281165 pairs aligned concordantly 0 times; of these: 383567 (11.69%) aligned discordantly 1 time ---- 2897598 pairs aligned 0 times concordantly or discordantly; of these: 5795196 mates make up the pairs; of these: 3521695 (60.77%) aligned 0 times 1981155 (34.19%) aligned exactly 1 time 292346 (5.04%) aligned >1 times 89.72% overall alignment rate Time searching: 00:12:34 Overall time: 00:12:34 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_sort_core] merging from 16 files... [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] 5696809 / 14226241 = 0.4004 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 19:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.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 19:25:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:31: 1000000 INFO @ Sat, 15 Jan 2022 19:25:37: 2000000 INFO @ Sat, 15 Jan 2022 19:25:44: 3000000 INFO @ Sat, 15 Jan 2022 19:25:51: 4000000 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 19:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.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 19:25:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:25:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:25:57: 5000000 INFO @ Sat, 15 Jan 2022 19:26:01: 1000000 INFO @ Sat, 15 Jan 2022 19:26:04: 6000000 INFO @ Sat, 15 Jan 2022 19:26:09: 2000000 INFO @ Sat, 15 Jan 2022 19:26:11: 7000000 INFO @ Sat, 15 Jan 2022 19:26:16: 3000000 INFO @ Sat, 15 Jan 2022 19:26:18: 8000000 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 19:26:23: 4000000 INFO @ Sat, 15 Jan 2022 19:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.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 19:26:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:26:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:26:25: 9000000 INFO @ Sat, 15 Jan 2022 19:26:30: 5000000 INFO @ Sat, 15 Jan 2022 19:26:30: 1000000 INFO @ Sat, 15 Jan 2022 19:26:32: 10000000 INFO @ Sat, 15 Jan 2022 19:26:37: 2000000 INFO @ Sat, 15 Jan 2022 19:26:37: 6000000 INFO @ Sat, 15 Jan 2022 19:26:39: 11000000 INFO @ Sat, 15 Jan 2022 19:26:43: 3000000 INFO @ Sat, 15 Jan 2022 19:26:45: 7000000 INFO @ Sat, 15 Jan 2022 19:26:47: 12000000 INFO @ Sat, 15 Jan 2022 19:26:49: 4000000 INFO @ Sat, 15 Jan 2022 19:26:52: 8000000 INFO @ Sat, 15 Jan 2022 19:26:54: 13000000 INFO @ Sat, 15 Jan 2022 19:26:55: 5000000 INFO @ Sat, 15 Jan 2022 19:26:59: 9000000 INFO @ Sat, 15 Jan 2022 19:27:00: 6000000 INFO @ Sat, 15 Jan 2022 19:27:01: 14000000 INFO @ Sat, 15 Jan 2022 19:27:06: 10000000 INFO @ Sat, 15 Jan 2022 19:27:06: 7000000 INFO @ Sat, 15 Jan 2022 19:27:08: 15000000 INFO @ Sat, 15 Jan 2022 19:27:12: 8000000 INFO @ Sat, 15 Jan 2022 19:27:13: 11000000 INFO @ Sat, 15 Jan 2022 19:27:15: 16000000 INFO @ Sat, 15 Jan 2022 19:27:18: 9000000 INFO @ Sat, 15 Jan 2022 19:27:21: 12000000 INFO @ Sat, 15 Jan 2022 19:27:23: 17000000 INFO @ Sat, 15 Jan 2022 19:27:24: 10000000 INFO @ Sat, 15 Jan 2022 19:27:28: 13000000 INFO @ Sat, 15 Jan 2022 19:27:30: 18000000 INFO @ Sat, 15 Jan 2022 19:27:30: 11000000 INFO @ Sat, 15 Jan 2022 19:27:35: 14000000 INFO @ Sat, 15 Jan 2022 19:27:36: 12000000 INFO @ Sat, 15 Jan 2022 19:27:37: 19000000 INFO @ Sat, 15 Jan 2022 19:27:40: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:27:40: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:27:40: #1 total tags in treatment: 8247306 INFO @ Sat, 15 Jan 2022 19:27:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:27:40: #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 19:27:40: #1 tags after filtering in treatment: 3964920 INFO @ Sat, 15 Jan 2022 19:27:40: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 19:27:40: #1 finished! INFO @ Sat, 15 Jan 2022 19:27:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:27:40: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 19:27:40: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 19:27:40: start model_add_line... INFO @ Sat, 15 Jan 2022 19:27:40: start X-correlation... INFO @ Sat, 15 Jan 2022 19:27:40: end of X-cor INFO @ Sat, 15 Jan 2022 19:27:40: #2 finished! INFO @ Sat, 15 Jan 2022 19:27:40: #2 predicted fragment length is 69 bps INFO @ Sat, 15 Jan 2022 19:27:40: #2 alternative fragment length(s) may be 13,38,69,97,131,145,159,191,212,261,289,323,355,375,418,467,485,512,578 bps INFO @ Sat, 15 Jan 2022 19:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.05_model.r WARNING @ Sat, 15 Jan 2022 19:27:40: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:27:40: #2 You may need to consider one of the other alternative d(s): 13,38,69,97,131,145,159,191,212,261,289,323,355,375,418,467,485,512,578 WARNING @ Sat, 15 Jan 2022 19:27:40: #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 19:27:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:27:42: 13000000 INFO @ Sat, 15 Jan 2022 19:27:43: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:27:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.05_summits.bed INFO @ Sat, 15 Jan 2022 19:27:48: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:27:48: 14000000 INFO @ Sat, 15 Jan 2022 19:27:50: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:27:54: 15000000 INFO @ Sat, 15 Jan 2022 19:27:57: 17000000 INFO @ Sat, 15 Jan 2022 19:28:00: 16000000 INFO @ Sat, 15 Jan 2022 19:28:05: 18000000 INFO @ Sat, 15 Jan 2022 19:28:06: 17000000 INFO @ Sat, 15 Jan 2022 19:28:12: 19000000 INFO @ Sat, 15 Jan 2022 19:28:12: 18000000 INFO @ Sat, 15 Jan 2022 19:28:14: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:28:14: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:28:14: #1 total tags in treatment: 8247306 INFO @ Sat, 15 Jan 2022 19:28:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:28:14: #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 19:28:14: #1 tags after filtering in treatment: 3964920 INFO @ Sat, 15 Jan 2022 19:28:14: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 19:28:14: #1 finished! INFO @ Sat, 15 Jan 2022 19:28:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:28:15: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 19:28:15: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 19:28:15: start model_add_line... INFO @ Sat, 15 Jan 2022 19:28:15: start X-correlation... INFO @ Sat, 15 Jan 2022 19:28:15: end of X-cor INFO @ Sat, 15 Jan 2022 19:28:15: #2 finished! INFO @ Sat, 15 Jan 2022 19:28:15: #2 predicted fragment length is 69 bps INFO @ Sat, 15 Jan 2022 19:28:15: #2 alternative fragment length(s) may be 13,38,69,97,131,145,159,191,212,261,289,323,355,375,418,467,485,512,578 bps INFO @ Sat, 15 Jan 2022 19:28:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.10_model.r WARNING @ Sat, 15 Jan 2022 19:28:15: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:28:15: #2 You may need to consider one of the other alternative d(s): 13,38,69,97,131,145,159,191,212,261,289,323,355,375,418,467,485,512,578 WARNING @ Sat, 15 Jan 2022 19:28:15: #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 19:28:15: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:28:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:28:18: 19000000 INFO @ Sat, 15 Jan 2022 19:28:20: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 19:28:20: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 19:28:20: #1 total tags in treatment: 8247306 INFO @ Sat, 15 Jan 2022 19:28:20: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:28:20: #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 19:28:20: #1 tags after filtering in treatment: 3964920 INFO @ Sat, 15 Jan 2022 19:28:20: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 19:28:20: #1 finished! INFO @ Sat, 15 Jan 2022 19:28:20: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:28:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:28:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:28:20: #2 number of paired peaks: 164 WARNING @ Sat, 15 Jan 2022 19:28:20: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Sat, 15 Jan 2022 19:28:20: start model_add_line... INFO @ Sat, 15 Jan 2022 19:28:20: start X-correlation... INFO @ Sat, 15 Jan 2022 19:28:20: end of X-cor INFO @ Sat, 15 Jan 2022 19:28:20: #2 finished! INFO @ Sat, 15 Jan 2022 19:28:20: #2 predicted fragment length is 69 bps INFO @ Sat, 15 Jan 2022 19:28:20: #2 alternative fragment length(s) may be 13,38,69,97,131,145,159,191,212,261,289,323,355,375,418,467,485,512,578 bps INFO @ Sat, 15 Jan 2022 19:28:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.20_model.r WARNING @ Sat, 15 Jan 2022 19:28:20: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 19:28:20: #2 You may need to consider one of the other alternative d(s): 13,38,69,97,131,145,159,191,212,261,289,323,355,375,418,467,485,512,578 WARNING @ Sat, 15 Jan 2022 19:28:20: #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 19:28:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:28:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:28:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:28:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.10_summits.bed INFO @ Sat, 15 Jan 2022 19:28:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (8 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:28:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:28:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:28:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781109/SRX11781109.20_summits.bed INFO @ Sat, 15 Jan 2022 19:28:28: Done! pass1 - making usageList (2 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling