Job ID = 14521337 SRX = SRX8952633 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3626062 spots for SRR12458253/SRR12458253.sra Written 3626062 spots for SRR12458253/SRR12458253.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: 00:01:23 3626062 reads; of these: 3626062 (100.00%) were paired; of these: 2625313 (72.40%) aligned concordantly 0 times 888573 (24.51%) aligned concordantly exactly 1 time 112176 (3.09%) aligned concordantly >1 times ---- 2625313 pairs aligned concordantly 0 times; of these: 427222 (16.27%) aligned discordantly 1 time ---- 2198091 pairs aligned 0 times concordantly or discordantly; of these: 4396182 mates make up the pairs; of these: 2880572 (65.52%) aligned 0 times 1306605 (29.72%) aligned exactly 1 time 209005 (4.75%) aligned >1 times 60.28% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 427987 / 1287146 = 0.3325 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 20:53:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.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 20:53:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:53:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:53:43: 1000000 INFO @ Sat, 15 Jan 2022 20:53:48: 2000000 INFO @ Sat, 15 Jan 2022 20:53:53: 3000000 INFO @ Sat, 15 Jan 2022 20:53:56: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:53:56: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:53:56: #1 total tags in treatment: 763704 INFO @ Sat, 15 Jan 2022 20:53:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:53:56: #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 20:53:56: #1 tags after filtering in treatment: 700081 INFO @ Sat, 15 Jan 2022 20:53:56: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:53:56: #1 finished! INFO @ Sat, 15 Jan 2022 20:53:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:53:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:53:56: #2 number of paired peaks: 190 WARNING @ Sat, 15 Jan 2022 20:53:56: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sat, 15 Jan 2022 20:53:56: start model_add_line... INFO @ Sat, 15 Jan 2022 20:53:56: start X-correlation... INFO @ Sat, 15 Jan 2022 20:53:56: end of X-cor INFO @ Sat, 15 Jan 2022 20:53:56: #2 finished! INFO @ Sat, 15 Jan 2022 20:53:56: #2 predicted fragment length is 277 bps INFO @ Sat, 15 Jan 2022 20:53:56: #2 alternative fragment length(s) may be 1,23,63,149,240,277,304,344,500,558 bps INFO @ Sat, 15 Jan 2022 20:53:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.05_model.r INFO @ Sat, 15 Jan 2022 20:53:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:53:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:53:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:53:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:53:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:53:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.05_summits.bed INFO @ Sat, 15 Jan 2022 20:53:58: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 20:54:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.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 20:54:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:13: 1000000 INFO @ Sat, 15 Jan 2022 20:54:17: 2000000 INFO @ Sat, 15 Jan 2022 20:54:22: 3000000 INFO @ Sat, 15 Jan 2022 20:54:25: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:54:25: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:54:25: #1 total tags in treatment: 763704 INFO @ Sat, 15 Jan 2022 20:54:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:25: #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 20:54:25: #1 tags after filtering in treatment: 700081 INFO @ Sat, 15 Jan 2022 20:54:25: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:54:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:25: #2 number of paired peaks: 190 WARNING @ Sat, 15 Jan 2022 20:54:25: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sat, 15 Jan 2022 20:54:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:25: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:25: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:25: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:25: #2 predicted fragment length is 277 bps INFO @ Sat, 15 Jan 2022 20:54:25: #2 alternative fragment length(s) may be 1,23,63,149,240,277,304,344,500,558 bps INFO @ Sat, 15 Jan 2022 20:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.10_model.r INFO @ Sat, 15 Jan 2022 20:54:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.10_summits.bed INFO @ Sat, 15 Jan 2022 20:54:27: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 20:54:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.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 20:54:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:54:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:54:43: 1000000 INFO @ Sat, 15 Jan 2022 20:54:48: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:54:53: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:54:55: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 20:54:55: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 20:54:55: #1 total tags in treatment: 763704 INFO @ Sat, 15 Jan 2022 20:54:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:54:55: #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 20:54:55: #1 tags after filtering in treatment: 700081 INFO @ Sat, 15 Jan 2022 20:54:55: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 15 Jan 2022 20:54:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:54:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:54:56: #2 number of paired peaks: 190 WARNING @ Sat, 15 Jan 2022 20:54:56: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Sat, 15 Jan 2022 20:54:56: start model_add_line... INFO @ Sat, 15 Jan 2022 20:54:56: start X-correlation... INFO @ Sat, 15 Jan 2022 20:54:56: end of X-cor INFO @ Sat, 15 Jan 2022 20:54:56: #2 finished! INFO @ Sat, 15 Jan 2022 20:54:56: #2 predicted fragment length is 277 bps INFO @ Sat, 15 Jan 2022 20:54:56: #2 alternative fragment length(s) may be 1,23,63,149,240,277,304,344,500,558 bps INFO @ Sat, 15 Jan 2022 20:54:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.20_model.r INFO @ Sat, 15 Jan 2022 20:54:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:54:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:54:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:54:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:54:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:54:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952633/SRX8952633.20_summits.bed INFO @ Sat, 15 Jan 2022 20:54:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (13 records, 4 fields): 87 millis CompletedMACS2peakCalling