Job ID = 14521498 SRX = SRX10754396 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6406422 spots for SRR14402200/SRR14402200.sra Written 6406422 spots for SRR14402200/SRR14402200.sra Read 6079294 spots for SRR14402201/SRR14402201.sra Written 6079294 spots for SRR14402201/SRR14402201.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: 00:06:41 12485716 reads; of these: 12485716 (100.00%) were paired; of these: 525729 (4.21%) aligned concordantly 0 times 10462091 (83.79%) aligned concordantly exactly 1 time 1497896 (12.00%) aligned concordantly >1 times ---- 525729 pairs aligned concordantly 0 times; of these: 114316 (21.74%) aligned discordantly 1 time ---- 411413 pairs aligned 0 times concordantly or discordantly; of these: 822826 mates make up the pairs; of these: 655638 (79.68%) aligned 0 times 110841 (13.47%) aligned exactly 1 time 56347 (6.85%) aligned >1 times 97.37% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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 12 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] 2745901 / 12041085 = 0.2280 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 21:21:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.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 21:21:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:21:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:21:43: 1000000 INFO @ Sat, 15 Jan 2022 21:21:48: 2000000 INFO @ Sat, 15 Jan 2022 21:21:54: 3000000 INFO @ Sat, 15 Jan 2022 21:21:59: 4000000 INFO @ Sat, 15 Jan 2022 21:22:04: 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 21:22:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.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 21:22:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:22:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:22:09: 6000000 INFO @ Sat, 15 Jan 2022 21:22:14: 1000000 INFO @ Sat, 15 Jan 2022 21:22:15: 7000000 INFO @ Sat, 15 Jan 2022 21:22:20: 2000000 INFO @ Sat, 15 Jan 2022 21:22:22: 8000000 INFO @ Sat, 15 Jan 2022 21:22:27: 3000000 INFO @ Sat, 15 Jan 2022 21:22:28: 9000000 INFO @ Sat, 15 Jan 2022 21:22:34: 4000000 INFO @ Sat, 15 Jan 2022 21:22:34: 10000000 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 21:22:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.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 21:22:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:22:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:22:41: 11000000 INFO @ Sat, 15 Jan 2022 21:22:41: 5000000 INFO @ Sat, 15 Jan 2022 21:22:44: 1000000 INFO @ Sat, 15 Jan 2022 21:22:47: 12000000 INFO @ Sat, 15 Jan 2022 21:22:48: 6000000 INFO @ Sat, 15 Jan 2022 21:22:50: 2000000 INFO @ Sat, 15 Jan 2022 21:22:54: 13000000 INFO @ Sat, 15 Jan 2022 21:22:56: 7000000 INFO @ Sat, 15 Jan 2022 21:22:57: 3000000 INFO @ Sat, 15 Jan 2022 21:23:00: 14000000 INFO @ Sat, 15 Jan 2022 21:23:03: 8000000 INFO @ Sat, 15 Jan 2022 21:23:04: 4000000 INFO @ Sat, 15 Jan 2022 21:23:06: 15000000 INFO @ Sat, 15 Jan 2022 21:23:10: 9000000 INFO @ Sat, 15 Jan 2022 21:23:11: 5000000 INFO @ Sat, 15 Jan 2022 21:23:13: 16000000 INFO @ Sat, 15 Jan 2022 21:23:18: 10000000 INFO @ Sat, 15 Jan 2022 21:23:18: 6000000 INFO @ Sat, 15 Jan 2022 21:23:19: 17000000 INFO @ Sat, 15 Jan 2022 21:23:25: 11000000 INFO @ Sat, 15 Jan 2022 21:23:25: 7000000 INFO @ Sat, 15 Jan 2022 21:23:26: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:23:31: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 21:23:31: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 21:23:31: #1 total tags in treatment: 9235175 INFO @ Sat, 15 Jan 2022 21:23:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:23:31: #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 21:23:31: #1 tags after filtering in treatment: 4191691 INFO @ Sat, 15 Jan 2022 21:23:31: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 21:23:31: #1 finished! INFO @ Sat, 15 Jan 2022 21:23:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:23:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:23:32: #2 number of paired peaks: 203 WARNING @ Sat, 15 Jan 2022 21:23:32: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 15 Jan 2022 21:23:32: start model_add_line... INFO @ Sat, 15 Jan 2022 21:23:32: start X-correlation... INFO @ Sat, 15 Jan 2022 21:23:32: end of X-cor INFO @ Sat, 15 Jan 2022 21:23:32: #2 finished! INFO @ Sat, 15 Jan 2022 21:23:32: #2 predicted fragment length is 151 bps INFO @ Sat, 15 Jan 2022 21:23:32: #2 alternative fragment length(s) may be 4,151,170 bps INFO @ Sat, 15 Jan 2022 21:23:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.05_model.r INFO @ Sat, 15 Jan 2022 21:23:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:23:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:23:32: 8000000 INFO @ Sat, 15 Jan 2022 21:23:32: 12000000 INFO @ Sat, 15 Jan 2022 21:23:40: 9000000 INFO @ Sat, 15 Jan 2022 21:23:40: 13000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:23:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.05_summits.bed INFO @ Sat, 15 Jan 2022 21:23:44: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1242 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:23:47: 10000000 INFO @ Sat, 15 Jan 2022 21:23:47: 14000000 INFO @ Sat, 15 Jan 2022 21:23:54: 11000000 INFO @ Sat, 15 Jan 2022 21:23:54: 15000000 INFO @ Sat, 15 Jan 2022 21:24:02: 12000000 INFO @ Sat, 15 Jan 2022 21:24:02: 16000000 INFO @ Sat, 15 Jan 2022 21:24:09: 13000000 INFO @ Sat, 15 Jan 2022 21:24:09: 17000000 INFO @ Sat, 15 Jan 2022 21:24:16: 14000000 INFO @ Sat, 15 Jan 2022 21:24:16: 18000000 INFO @ Sat, 15 Jan 2022 21:24:22: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 21:24:22: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 21:24:22: #1 total tags in treatment: 9235175 INFO @ Sat, 15 Jan 2022 21:24:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:24:22: #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 21:24:22: #1 tags after filtering in treatment: 4191691 INFO @ Sat, 15 Jan 2022 21:24:22: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 21:24:22: #1 finished! INFO @ Sat, 15 Jan 2022 21:24:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:24:23: #2 number of paired peaks: 203 WARNING @ Sat, 15 Jan 2022 21:24:23: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 15 Jan 2022 21:24:23: start model_add_line... INFO @ Sat, 15 Jan 2022 21:24:23: start X-correlation... INFO @ Sat, 15 Jan 2022 21:24:23: end of X-cor INFO @ Sat, 15 Jan 2022 21:24:23: #2 finished! INFO @ Sat, 15 Jan 2022 21:24:23: #2 predicted fragment length is 151 bps INFO @ Sat, 15 Jan 2022 21:24:23: #2 alternative fragment length(s) may be 4,151,170 bps INFO @ Sat, 15 Jan 2022 21:24:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.10_model.r INFO @ Sat, 15 Jan 2022 21:24:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:24:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:24:23: 15000000 INFO @ Sat, 15 Jan 2022 21:24:30: 16000000 INFO @ Sat, 15 Jan 2022 21:24:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:24:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:24:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:24:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.10_summits.bed INFO @ Sat, 15 Jan 2022 21:24:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1026 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:24:37: 17000000 INFO @ Sat, 15 Jan 2022 21:24:43: 18000000 INFO @ Sat, 15 Jan 2022 21:24:48: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 21:24:48: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 21:24:48: #1 total tags in treatment: 9235175 INFO @ Sat, 15 Jan 2022 21:24:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:24:48: #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 21:24:48: #1 tags after filtering in treatment: 4191691 INFO @ Sat, 15 Jan 2022 21:24:48: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 21:24:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:24:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:24:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:24:49: #2 number of paired peaks: 203 WARNING @ Sat, 15 Jan 2022 21:24:49: Fewer paired peaks (203) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 203 pairs to build model! INFO @ Sat, 15 Jan 2022 21:24:49: start model_add_line... INFO @ Sat, 15 Jan 2022 21:24:49: start X-correlation... INFO @ Sat, 15 Jan 2022 21:24:49: end of X-cor INFO @ Sat, 15 Jan 2022 21:24:49: #2 finished! INFO @ Sat, 15 Jan 2022 21:24:49: #2 predicted fragment length is 151 bps INFO @ Sat, 15 Jan 2022 21:24:49: #2 alternative fragment length(s) may be 4,151,170 bps INFO @ Sat, 15 Jan 2022 21:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.20_model.r INFO @ Sat, 15 Jan 2022 21:24:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:24:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:25:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:25:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:25:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX10754396/SRX10754396.20_summits.bed INFO @ Sat, 15 Jan 2022 21:25:02: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (836 records, 4 fields): 22 millis CompletedMACS2peakCalling