Job ID = 14520391 SRX = SRX11781123 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:01:36 prefetch.2.10.7: 1) Downloading 'SRR15481066'... 2022-01-15T10:01:36 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:01:54 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:01:54 prefetch.2.10.7: 'SRR15481066' is valid 2022-01-15T10:01:54 prefetch.2.10.7: 1) 'SRR15481066' was downloaded successfully 2022-01-15T10:01:54 prefetch.2.10.7: 'SRR15481066' has 0 unresolved dependencies Read 7573090 spots for SRR15481066/SRR15481066.sra Written 7573090 spots for SRR15481066/SRR15481066.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: 00:02:53 7573090 reads; of these: 7573090 (100.00%) were paired; of these: 5234883 (69.12%) aligned concordantly 0 times 2131937 (28.15%) aligned concordantly exactly 1 time 206270 (2.72%) aligned concordantly >1 times ---- 5234883 pairs aligned concordantly 0 times; of these: 46229 (0.88%) aligned discordantly 1 time ---- 5188654 pairs aligned 0 times concordantly or discordantly; of these: 10377308 mates make up the pairs; of these: 5655120 (54.50%) aligned 0 times 4224748 (40.71%) aligned exactly 1 time 497440 (4.79%) aligned >1 times 62.66% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 275667 / 2383479 = 0.1157 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 19:07:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.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 19:07:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:07:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:07:41: 1000000 INFO @ Sat, 15 Jan 2022 19:07:45: 2000000 INFO @ Sat, 15 Jan 2022 19:07:49: 3000000 INFO @ Sat, 15 Jan 2022 19:07:54: 4000000 INFO @ Sat, 15 Jan 2022 19:07:58: 5000000 INFO @ Sat, 15 Jan 2022 19:08:02: 6000000 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 19:08:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.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 19:08:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:07: 7000000 INFO @ Sat, 15 Jan 2022 19:08:12: 8000000 INFO @ Sat, 15 Jan 2022 19:08:13: 1000000 INFO @ Sat, 15 Jan 2022 19:08:17: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:08:17: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:08:17: #1 total tags in treatment: 2065638 INFO @ Sat, 15 Jan 2022 19:08:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:08:17: #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 19:08:17: #1 tags after filtering in treatment: 1548630 INFO @ Sat, 15 Jan 2022 19:08:17: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:08:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:08:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:08:17: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:08:17: 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 19:08:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:08:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:08:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:08:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:08:17: #2 predicted fragment length is 293 bps INFO @ Sat, 15 Jan 2022 19:08:17: #2 alternative fragment length(s) may be 0,249,293 bps INFO @ Sat, 15 Jan 2022 19:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.05_model.r INFO @ Sat, 15 Jan 2022 19:08:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:08:19: 2000000 INFO @ Sat, 15 Jan 2022 19:08:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:08:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:08:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:08:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.05_summits.bed INFO @ Sat, 15 Jan 2022 19:08:23: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (23 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:08:25: 3000000 INFO @ Sat, 15 Jan 2022 19:08:30: 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 19:08:36: 5000000 INFO @ Sat, 15 Jan 2022 19:08:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.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 19:08:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:08:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:08:42: 1000000 INFO @ Sat, 15 Jan 2022 19:08:42: 6000000 INFO @ Sat, 15 Jan 2022 19:08:47: 2000000 INFO @ Sat, 15 Jan 2022 19:08:49: 7000000 INFO @ Sat, 15 Jan 2022 19:08:53: 3000000 INFO @ Sat, 15 Jan 2022 19:08:55: 8000000 INFO @ Sat, 15 Jan 2022 19:08:58: 4000000 INFO @ Sat, 15 Jan 2022 19:09:01: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:01: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:01: #1 total tags in treatment: 2065638 INFO @ Sat, 15 Jan 2022 19:09:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:01: #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 19:09:01: #1 tags after filtering in treatment: 1548630 INFO @ Sat, 15 Jan 2022 19:09:01: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:09:01: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:01: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:09:01: 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 19:09:01: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:01: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:01: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:01: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:01: #2 predicted fragment length is 293 bps INFO @ Sat, 15 Jan 2022 19:09:01: #2 alternative fragment length(s) may be 0,249,293 bps INFO @ Sat, 15 Jan 2022 19:09:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.10_model.r INFO @ Sat, 15 Jan 2022 19:09:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:01: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:09:03: 5000000 INFO @ Sat, 15 Jan 2022 19:09:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.10_summits.bed INFO @ Sat, 15 Jan 2022 19:09:06: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:09:08: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:09:13: 7000000 INFO @ Sat, 15 Jan 2022 19:09:18: 8000000 INFO @ Sat, 15 Jan 2022 19:09:22: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:09:22: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:09:22: #1 total tags in treatment: 2065638 INFO @ Sat, 15 Jan 2022 19:09:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:09:22: #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 19:09:22: #1 tags after filtering in treatment: 1548630 INFO @ Sat, 15 Jan 2022 19:09:22: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:09:22: #1 finished! INFO @ Sat, 15 Jan 2022 19:09:22: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:09:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:09:23: #2 number of paired peaks: 172 WARNING @ Sat, 15 Jan 2022 19:09:23: 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 19:09:23: start model_add_line... INFO @ Sat, 15 Jan 2022 19:09:23: start X-correlation... INFO @ Sat, 15 Jan 2022 19:09:23: end of X-cor INFO @ Sat, 15 Jan 2022 19:09:23: #2 finished! INFO @ Sat, 15 Jan 2022 19:09:23: #2 predicted fragment length is 293 bps INFO @ Sat, 15 Jan 2022 19:09:23: #2 alternative fragment length(s) may be 0,249,293 bps INFO @ Sat, 15 Jan 2022 19:09:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.20_model.r INFO @ Sat, 15 Jan 2022 19:09:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:09:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:09:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:09:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781123/SRX11781123.20_summits.bed INFO @ Sat, 15 Jan 2022 19:09:28: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 9 millis CompletedMACS2peakCalling