Job ID = 14521286 SRX = SRX8952618 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3812916 spots for SRR12458268/SRR12458268.sra Written 3812916 spots for SRR12458268/SRR12458268.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: 00:01:24 3812916 reads; of these: 3812916 (100.00%) were paired; of these: 2701385 (70.85%) aligned concordantly 0 times 974411 (25.56%) aligned concordantly exactly 1 time 137120 (3.60%) aligned concordantly >1 times ---- 2701385 pairs aligned concordantly 0 times; of these: 222329 (8.23%) aligned discordantly 1 time ---- 2479056 pairs aligned 0 times concordantly or discordantly; of these: 4958112 mates make up the pairs; of these: 3758588 (75.81%) aligned 0 times 1042628 (21.03%) aligned exactly 1 time 156896 (3.16%) aligned >1 times 50.71% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 243364 / 1315689 = 0.1850 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 20:48:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.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 20:48:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:48:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:48:55: 1000000 INFO @ Sat, 15 Jan 2022 20:49:00: 2000000 INFO @ Sat, 15 Jan 2022 20:49:05: 3000000 INFO @ Sat, 15 Jan 2022 20:49:07: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 20:49:07: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 20:49:07: #1 total tags in treatment: 932743 INFO @ Sat, 15 Jan 2022 20:49:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:07: #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 20:49:07: #1 tags after filtering in treatment: 851643 INFO @ Sat, 15 Jan 2022 20:49:07: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 20:49:07: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:07: #2 number of paired peaks: 219 WARNING @ Sat, 15 Jan 2022 20:49:07: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:07: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:07: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:07: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:07: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:07: #2 predicted fragment length is 228 bps INFO @ Sat, 15 Jan 2022 20:49:07: #2 alternative fragment length(s) may be 212,228,262 bps INFO @ Sat, 15 Jan 2022 20:49:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.05_model.r INFO @ Sat, 15 Jan 2022 20:49:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.05_summits.bed INFO @ Sat, 15 Jan 2022 20:49:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 170 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 20:49:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.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 20:49:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:25: 1000000 INFO @ Sat, 15 Jan 2022 20:49:30: 2000000 INFO @ Sat, 15 Jan 2022 20:49:35: 3000000 INFO @ Sat, 15 Jan 2022 20:49:37: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 20:49:37: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 20:49:37: #1 total tags in treatment: 932743 INFO @ Sat, 15 Jan 2022 20:49:37: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:49:37: #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 20:49:37: #1 tags after filtering in treatment: 851643 INFO @ Sat, 15 Jan 2022 20:49:37: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 20:49:37: #1 finished! INFO @ Sat, 15 Jan 2022 20:49:37: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:49:37: #2 number of paired peaks: 219 WARNING @ Sat, 15 Jan 2022 20:49:37: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 15 Jan 2022 20:49:37: start model_add_line... INFO @ Sat, 15 Jan 2022 20:49:37: start X-correlation... INFO @ Sat, 15 Jan 2022 20:49:37: end of X-cor INFO @ Sat, 15 Jan 2022 20:49:37: #2 finished! INFO @ Sat, 15 Jan 2022 20:49:37: #2 predicted fragment length is 228 bps INFO @ Sat, 15 Jan 2022 20:49:37: #2 alternative fragment length(s) may be 212,228,262 bps INFO @ Sat, 15 Jan 2022 20:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.10_model.r INFO @ Sat, 15 Jan 2022 20:49:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:49:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:49:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:49:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:49:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.10_summits.bed INFO @ Sat, 15 Jan 2022 20:49:41: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 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 20:49:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.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 20:49:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:49:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:49:55: 1000000 INFO @ Sat, 15 Jan 2022 20:50:00: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:50:05: 3000000 INFO @ Sat, 15 Jan 2022 20:50:07: #1 tag size is determined as 43 bps INFO @ Sat, 15 Jan 2022 20:50:07: #1 tag size = 43 INFO @ Sat, 15 Jan 2022 20:50:07: #1 total tags in treatment: 932743 INFO @ Sat, 15 Jan 2022 20:50:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:50:07: #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 20:50:07: #1 tags after filtering in treatment: 851643 INFO @ Sat, 15 Jan 2022 20:50:07: #1 Redundant rate of treatment: 0.09 INFO @ Sat, 15 Jan 2022 20:50:07: #1 finished! INFO @ Sat, 15 Jan 2022 20:50:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:50:07: #2 number of paired peaks: 219 WARNING @ Sat, 15 Jan 2022 20:50:07: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 15 Jan 2022 20:50:07: start model_add_line... INFO @ Sat, 15 Jan 2022 20:50:07: start X-correlation... INFO @ Sat, 15 Jan 2022 20:50:07: end of X-cor INFO @ Sat, 15 Jan 2022 20:50:07: #2 finished! INFO @ Sat, 15 Jan 2022 20:50:07: #2 predicted fragment length is 228 bps INFO @ Sat, 15 Jan 2022 20:50:07: #2 alternative fragment length(s) may be 212,228,262 bps INFO @ Sat, 15 Jan 2022 20:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.20_model.r INFO @ Sat, 15 Jan 2022 20:50:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:50:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:50:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952618/SRX8952618.20_summits.bed INFO @ Sat, 15 Jan 2022 20:50:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 1 millis CompletedMACS2peakCalling