Job ID = 14520385 SRX = SRX11781120 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:21 prefetch.2.10.7: 1) Downloading 'SRR15481063'... 2022-01-15T10:01:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:35 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:35 prefetch.2.10.7: 'SRR15481063' is valid 2022-01-15T10:01:35 prefetch.2.10.7: 1) 'SRR15481063' was downloaded successfully 2022-01-15T10:01:35 prefetch.2.10.7: 'SRR15481063' has 0 unresolved dependencies Read 6627657 spots for SRR15481063/SRR15481063.sra Written 6627657 spots for SRR15481063/SRR15481063.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: 00:04:15 6627657 reads; of these: 6627657 (100.00%) were paired; of these: 4463246 (67.34%) aligned concordantly 0 times 1623355 (24.49%) aligned concordantly exactly 1 time 541056 (8.16%) aligned concordantly >1 times ---- 4463246 pairs aligned concordantly 0 times; of these: 42338 (0.95%) aligned discordantly 1 time ---- 4420908 pairs aligned 0 times concordantly or discordantly; of these: 8841816 mates make up the pairs; of these: 5404858 (61.13%) aligned 0 times 2581108 (29.19%) aligned exactly 1 time 855850 (9.68%) aligned >1 times 59.22% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 216820 / 2205408 = 0.0983 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 19:08:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.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 19:08:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:36: 1000000 INFO @ Sat, 15 Jan 2022 19:08:41: 2000000 INFO @ Sat, 15 Jan 2022 19:08:47: 3000000 INFO @ Sat, 15 Jan 2022 19:08:52: 4000000 INFO @ Sat, 15 Jan 2022 19:08:58: 5000000 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 19:09:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.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 19:09:00: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:00: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:04: 6000000 INFO @ Sat, 15 Jan 2022 19:09:06: 1000000 INFO @ Sat, 15 Jan 2022 19:09:10: 7000000 INFO @ Sat, 15 Jan 2022 19:09:12: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:12: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:12: #1 total tags in treatment: 1950195 INFO @ Sat, 15 Jan 2022 19:09:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:12: #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 19:09:12: #1 tags after filtering in treatment: 1513655 INFO @ Sat, 15 Jan 2022 19:09:12: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:09:12: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:12: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 19:09:12: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 19:09:12: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:12: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:12: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:12: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:12: #2 predicted fragment length is 223 bps INFO @ Sat, 15 Jan 2022 19:09:12: #2 alternative fragment length(s) may be 2,223,244,263 bps INFO @ Sat, 15 Jan 2022 19:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.05_model.r INFO @ Sat, 15 Jan 2022 19:09:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:12: 2000000 INFO @ Sat, 15 Jan 2022 19:09:17: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:18: 3000000 INFO @ Sat, 15 Jan 2022 19:09:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.05_summits.bed INFO @ Sat, 15 Jan 2022 19:09:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (525 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:09:24: 4000000 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 19:09:30: 5000000 INFO @ Sat, 15 Jan 2022 19:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.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 19:09:30: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:09:30: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:09:36: 6000000 INFO @ Sat, 15 Jan 2022 19:09:36: 1000000 INFO @ Sat, 15 Jan 2022 19:09:42: 7000000 INFO @ Sat, 15 Jan 2022 19:09:43: 2000000 INFO @ Sat, 15 Jan 2022 19:09:45: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:45: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:45: #1 total tags in treatment: 1950195 INFO @ Sat, 15 Jan 2022 19:09:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:45: #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 19:09:45: #1 tags after filtering in treatment: 1513655 INFO @ Sat, 15 Jan 2022 19:09:45: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:09:45: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:45: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 19:09:45: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 19:09:45: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:45: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:45: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:45: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:45: #2 predicted fragment length is 223 bps INFO @ Sat, 15 Jan 2022 19:09:45: #2 alternative fragment length(s) may be 2,223,244,263 bps INFO @ Sat, 15 Jan 2022 19:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.10_model.r INFO @ Sat, 15 Jan 2022 19:09:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:49: 3000000 INFO @ Sat, 15 Jan 2022 19:09:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.10_summits.bed INFO @ Sat, 15 Jan 2022 19:09:52: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (270 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:09:54: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:10:00: 5000000 INFO @ Sat, 15 Jan 2022 19:10:06: 6000000 INFO @ Sat, 15 Jan 2022 19:10:12: 7000000 INFO @ Sat, 15 Jan 2022 19:10:14: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:10:14: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:10:14: #1 total tags in treatment: 1950195 INFO @ Sat, 15 Jan 2022 19:10:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:10:14: #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 19:10:14: #1 tags after filtering in treatment: 1513655 INFO @ Sat, 15 Jan 2022 19:10:14: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 15 Jan 2022 19:10:14: #1 finished! INFO @ Sat, 15 Jan 2022 19:10:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:10:14: #2 number of paired peaks: 191 WARNING @ Sat, 15 Jan 2022 19:10:14: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Sat, 15 Jan 2022 19:10:14: start model_add_line... INFO @ Sat, 15 Jan 2022 19:10:14: start X-correlation... INFO @ Sat, 15 Jan 2022 19:10:14: end of X-cor INFO @ Sat, 15 Jan 2022 19:10:14: #2 finished! INFO @ Sat, 15 Jan 2022 19:10:14: #2 predicted fragment length is 223 bps INFO @ Sat, 15 Jan 2022 19:10:14: #2 alternative fragment length(s) may be 2,223,244,263 bps INFO @ Sat, 15 Jan 2022 19:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.20_model.r INFO @ Sat, 15 Jan 2022 19:10:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:10:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:10:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:10:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:10:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781120/SRX11781120.20_summits.bed INFO @ Sat, 15 Jan 2022 19:10:20: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (101 records, 4 fields): 1 millis CompletedMACS2peakCalling