Job ID = 14520649 SRX = SRX7847366 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 49606467 spots for SRR11235548/SRR11235548.sra Written 49606467 spots for SRR11235548/SRR11235548.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: 00:29:59 49606467 reads; of these: 49606467 (100.00%) were paired; of these: 6425784 (12.95%) aligned concordantly 0 times 30185072 (60.85%) aligned concordantly exactly 1 time 12995611 (26.20%) aligned concordantly >1 times ---- 6425784 pairs aligned concordantly 0 times; of these: 36123 (0.56%) aligned discordantly 1 time ---- 6389661 pairs aligned 0 times concordantly or discordantly; of these: 12779322 mates make up the pairs; of these: 10383107 (81.25%) aligned 0 times 1331193 (10.42%) aligned exactly 1 time 1065022 (8.33%) aligned >1 times 89.53% overall alignment rate Time searching: 00:29:59 Overall time: 00:29:59 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 24 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] 42641758 / 43179266 = 0.9876 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 20:21:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.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 20:21:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:21:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:21:57: 1000000 INFO @ Sat, 15 Jan 2022 20:22:02: 2000000 INFO @ Sat, 15 Jan 2022 20:22:07: 3000000 INFO @ Sat, 15 Jan 2022 20:22:09: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:22:09: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:22:09: #1 total tags in treatment: 566990 INFO @ Sat, 15 Jan 2022 20:22:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:22:09: #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 20:22:09: #1 tags after filtering in treatment: 271411 INFO @ Sat, 15 Jan 2022 20:22:09: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 20:22:09: #1 finished! INFO @ Sat, 15 Jan 2022 20:22:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:22:09: #2 number of paired peaks: 690 WARNING @ Sat, 15 Jan 2022 20:22:09: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sat, 15 Jan 2022 20:22:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:22:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:22:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:22:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:22:09: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 20:22:09: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 20:22:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.05_model.r INFO @ Sat, 15 Jan 2022 20:22:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:22:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.05_summits.bed INFO @ Sat, 15 Jan 2022 20:22:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (667 records, 4 fields): 4 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 20:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.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 20:22:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:22:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:22:27: 1000000 INFO @ Sat, 15 Jan 2022 20:22:32: 2000000 INFO @ Sat, 15 Jan 2022 20:22:37: 3000000 INFO @ Sat, 15 Jan 2022 20:22:39: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:22:39: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:22:39: #1 total tags in treatment: 566990 INFO @ Sat, 15 Jan 2022 20:22:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:22:39: #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 20:22:39: #1 tags after filtering in treatment: 271411 INFO @ Sat, 15 Jan 2022 20:22:39: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 20:22:39: #1 finished! INFO @ Sat, 15 Jan 2022 20:22:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:22:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:22:39: #2 number of paired peaks: 690 WARNING @ Sat, 15 Jan 2022 20:22:39: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sat, 15 Jan 2022 20:22:39: start model_add_line... INFO @ Sat, 15 Jan 2022 20:22:39: start X-correlation... INFO @ Sat, 15 Jan 2022 20:22:39: end of X-cor INFO @ Sat, 15 Jan 2022 20:22:39: #2 finished! INFO @ Sat, 15 Jan 2022 20:22:39: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 20:22:39: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 20:22:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.10_model.r INFO @ Sat, 15 Jan 2022 20:22:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:22:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:22:40: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:22:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:22:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:22:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.10_summits.bed INFO @ Sat, 15 Jan 2022 20:22:41: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (468 records, 4 fields): 3 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 20:22:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.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 20:22:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:22:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:22:57: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:23:02: 2000000 INFO @ Sat, 15 Jan 2022 20:23:07: 3000000 INFO @ Sat, 15 Jan 2022 20:23:09: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:23:10: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:23:10: #1 total tags in treatment: 566990 INFO @ Sat, 15 Jan 2022 20:23:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:23:10: #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 20:23:10: #1 tags after filtering in treatment: 271411 INFO @ Sat, 15 Jan 2022 20:23:10: #1 Redundant rate of treatment: 0.52 INFO @ Sat, 15 Jan 2022 20:23:10: #1 finished! INFO @ Sat, 15 Jan 2022 20:23:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:23:10: #2 number of paired peaks: 690 WARNING @ Sat, 15 Jan 2022 20:23:10: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Sat, 15 Jan 2022 20:23:10: start model_add_line... INFO @ Sat, 15 Jan 2022 20:23:10: start X-correlation... INFO @ Sat, 15 Jan 2022 20:23:10: end of X-cor INFO @ Sat, 15 Jan 2022 20:23:10: #2 finished! INFO @ Sat, 15 Jan 2022 20:23:10: #2 predicted fragment length is 167 bps INFO @ Sat, 15 Jan 2022 20:23:10: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 15 Jan 2022 20:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.20_model.r INFO @ Sat, 15 Jan 2022 20:23:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:23:11: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:23:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:23:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:23:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847366/SRX7847366.20_summits.bed INFO @ Sat, 15 Jan 2022 20:23:11: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 165 millis CompletedMACS2peakCalling