Job ID = 14520635 SRX = SRX11781092 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:29:04 prefetch.2.10.7: 1) Downloading 'SRR15481035'... 2022-01-15T10:29:04 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:30:07 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:30:07 prefetch.2.10.7: 1) 'SRR15481035' was downloaded successfully 2022-01-15T10:30:07 prefetch.2.10.7: 'SRR15481035' has 0 unresolved dependencies Read 13032599 spots for SRR15481035/SRR15481035.sra Written 13032599 spots for SRR15481035/SRR15481035.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: 01:04:28 13032599 reads; of these: 13032599 (100.00%) were paired; of these: 2107716 (16.17%) aligned concordantly 0 times 3520383 (27.01%) aligned concordantly exactly 1 time 7404500 (56.82%) aligned concordantly >1 times ---- 2107716 pairs aligned concordantly 0 times; of these: 36151 (1.72%) aligned discordantly 1 time ---- 2071565 pairs aligned 0 times concordantly or discordantly; of these: 4143130 mates make up the pairs; of these: 2901107 (70.02%) aligned 0 times 403564 (9.74%) aligned exactly 1 time 838459 (20.24%) aligned >1 times 88.87% overall alignment rate Time searching: 01:04:28 Overall time: 01:04:28 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] 1712960 / 10958543 = 0.1563 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 20:46:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.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 20:46:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:46: 1000000 INFO @ Sat, 15 Jan 2022 20:46:52: 2000000 INFO @ Sat, 15 Jan 2022 20:46:58: 3000000 INFO @ Sat, 15 Jan 2022 20:47:04: 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 20:47:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.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 20:47:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:11: 5000000 INFO @ Sat, 15 Jan 2022 20:47:16: 1000000 INFO @ Sat, 15 Jan 2022 20:47:18: 6000000 INFO @ Sat, 15 Jan 2022 20:47:23: 2000000 INFO @ Sat, 15 Jan 2022 20:47:25: 7000000 INFO @ Sat, 15 Jan 2022 20:47:29: 3000000 INFO @ Sat, 15 Jan 2022 20:47:32: 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 20:47:36: 4000000 INFO @ Sat, 15 Jan 2022 20:47:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.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 20:47:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:39: 9000000 INFO @ Sat, 15 Jan 2022 20:47:43: 5000000 INFO @ Sat, 15 Jan 2022 20:47:46: 1000000 INFO @ Sat, 15 Jan 2022 20:47:46: 10000000 INFO @ Sat, 15 Jan 2022 20:47:50: 6000000 INFO @ Sat, 15 Jan 2022 20:47:53: 11000000 INFO @ Sat, 15 Jan 2022 20:47:53: 2000000 INFO @ Sat, 15 Jan 2022 20:47:57: 7000000 INFO @ Sat, 15 Jan 2022 20:48:00: 12000000 INFO @ Sat, 15 Jan 2022 20:48:01: 3000000 INFO @ Sat, 15 Jan 2022 20:48:04: 8000000 INFO @ Sat, 15 Jan 2022 20:48:08: 13000000 INFO @ Sat, 15 Jan 2022 20:48:08: 4000000 INFO @ Sat, 15 Jan 2022 20:48:12: 9000000 INFO @ Sat, 15 Jan 2022 20:48:15: 14000000 INFO @ Sat, 15 Jan 2022 20:48:16: 5000000 INFO @ Sat, 15 Jan 2022 20:48:19: 10000000 INFO @ Sat, 15 Jan 2022 20:48:22: 15000000 INFO @ Sat, 15 Jan 2022 20:48:23: 6000000 INFO @ Sat, 15 Jan 2022 20:48:26: 11000000 INFO @ Sat, 15 Jan 2022 20:48:29: 16000000 INFO @ Sat, 15 Jan 2022 20:48:31: 7000000 INFO @ Sat, 15 Jan 2022 20:48:33: 12000000 INFO @ Sat, 15 Jan 2022 20:48:36: 17000000 INFO @ Sat, 15 Jan 2022 20:48:39: 8000000 INFO @ Sat, 15 Jan 2022 20:48:40: 13000000 INFO @ Sat, 15 Jan 2022 20:48:43: 18000000 INFO @ Sat, 15 Jan 2022 20:48:46: 9000000 INFO @ Sat, 15 Jan 2022 20:48:47: 14000000 INFO @ Sat, 15 Jan 2022 20:48:50: 19000000 INFO @ Sat, 15 Jan 2022 20:48:54: 10000000 INFO @ Sat, 15 Jan 2022 20:48:54: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:48:56: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:48:56: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:48:56: #1 total tags in treatment: 9214466 INFO @ Sat, 15 Jan 2022 20:48:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:56: #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 20:48:56: #1 tags after filtering in treatment: 3030161 INFO @ Sat, 15 Jan 2022 20:48:56: #1 Redundant rate of treatment: 0.67 INFO @ Sat, 15 Jan 2022 20:48:56: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:56: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:48:56: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:56: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:56: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:56: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:56: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:56: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:48:56: #2 alternative fragment length(s) may be 78,84,90,129,178,209,223,236,257,285,317,342,355,363,424,464,525,531,550,566,586 bps INFO @ Sat, 15 Jan 2022 20:48:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.05_model.r INFO @ Sat, 15 Jan 2022 20:48:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:01: 16000000 INFO @ Sat, 15 Jan 2022 20:49:02: 11000000 INFO @ Sat, 15 Jan 2022 20:49:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:49:08: 17000000 INFO @ Sat, 15 Jan 2022 20:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.05_summits.bed INFO @ Sat, 15 Jan 2022 20:49:08: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (380 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:49:09: 12000000 INFO @ Sat, 15 Jan 2022 20:49:15: 18000000 INFO @ Sat, 15 Jan 2022 20:49:17: 13000000 INFO @ Sat, 15 Jan 2022 20:49:23: 19000000 INFO @ Sat, 15 Jan 2022 20:49:25: 14000000 INFO @ Sat, 15 Jan 2022 20:49:29: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:49:29: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:49:29: #1 total tags in treatment: 9214466 INFO @ Sat, 15 Jan 2022 20:49:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:29: #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 20:49:29: #1 tags after filtering in treatment: 3030161 INFO @ Sat, 15 Jan 2022 20:49:29: #1 Redundant rate of treatment: 0.67 INFO @ Sat, 15 Jan 2022 20:49:29: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:29: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:49:29: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:29: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:29: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:29: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:29: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:29: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:49:29: #2 alternative fragment length(s) may be 78,84,90,129,178,209,223,236,257,285,317,342,355,363,424,464,525,531,550,566,586 bps INFO @ Sat, 15 Jan 2022 20:49:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.10_model.r INFO @ Sat, 15 Jan 2022 20:49:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:32: 15000000 INFO @ Sat, 15 Jan 2022 20:49:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:40: 16000000 INFO @ Sat, 15 Jan 2022 20:49:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.10_summits.bed INFO @ Sat, 15 Jan 2022 20:49:41: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:49:47: 17000000 INFO @ Sat, 15 Jan 2022 20:49:55: 18000000 INFO @ Sat, 15 Jan 2022 20:50:03: 19000000 INFO @ Sat, 15 Jan 2022 20:50:09: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:50:09: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:50:09: #1 total tags in treatment: 9214466 INFO @ Sat, 15 Jan 2022 20:50:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:09: #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 20:50:09: #1 tags after filtering in treatment: 3030161 INFO @ Sat, 15 Jan 2022 20:50:09: #1 Redundant rate of treatment: 0.67 INFO @ Sat, 15 Jan 2022 20:50:09: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:09: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 20:50:09: Fewer paired peaks (172) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 172 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:09: #2 predicted fragment length is 178 bps INFO @ Sat, 15 Jan 2022 20:50:09: #2 alternative fragment length(s) may be 78,84,90,129,178,209,223,236,257,285,317,342,355,363,424,464,525,531,550,566,586 bps INFO @ Sat, 15 Jan 2022 20:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.20_model.r INFO @ Sat, 15 Jan 2022 20:50:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:50:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781092/SRX11781092.20_summits.bed INFO @ Sat, 15 Jan 2022 20:50:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (50 records, 4 fields): 2 millis CompletedMACS2peakCalling