Job ID = 14521282 SRX = SRX8952614 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23471501 spots for SRR12458272/SRR12458272.sra Written 23471501 spots for SRR12458272/SRR12458272.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: 01:54:47 23471501 reads; of these: 23471501 (100.00%) were paired; of these: 12946031 (55.16%) aligned concordantly 0 times 4006732 (17.07%) aligned concordantly exactly 1 time 6518738 (27.77%) aligned concordantly >1 times ---- 12946031 pairs aligned concordantly 0 times; of these: 0 (0.00%) aligned discordantly 1 time ---- 12946031 pairs aligned 0 times concordantly or discordantly; of these: 25892062 mates make up the pairs; of these: 7062918 (27.28%) aligned 0 times 8203326 (31.68%) aligned exactly 1 time 10625818 (41.04%) aligned >1 times 84.95% overall alignment rate Time searching: 01:54:47 Overall time: 01:54:47 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 16 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] 9084866 / 10521848 = 0.8634 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 22:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.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 22:55:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:55:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:55:15: 1000000 INFO @ Sat, 15 Jan 2022 22:55:23: 2000000 INFO @ Sat, 15 Jan 2022 22:55:31: 3000000 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 22:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.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 22:55:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:55:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:55:39: 4000000 INFO @ Sat, 15 Jan 2022 22:55:45: 1000000 INFO @ Sat, 15 Jan 2022 22:55:47: 5000000 INFO @ Sat, 15 Jan 2022 22:55:53: 2000000 INFO @ Sat, 15 Jan 2022 22:55:55: 6000000 INFO @ Sat, 15 Jan 2022 22:56:01: 3000000 INFO @ Sat, 15 Jan 2022 22:56:03: 7000000 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 22:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.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 22:56:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:56:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:56:09: 4000000 INFO @ Sat, 15 Jan 2022 22:56:12: 8000000 INFO @ Sat, 15 Jan 2022 22:56:15: 1000000 INFO @ Sat, 15 Jan 2022 22:56:17: 5000000 INFO @ Sat, 15 Jan 2022 22:56:19: 9000000 INFO @ Sat, 15 Jan 2022 22:56:23: 2000000 INFO @ Sat, 15 Jan 2022 22:56:26: 10000000 INFO @ Sat, 15 Jan 2022 22:56:26: 6000000 INFO @ Sat, 15 Jan 2022 22:56:30: 3000000 INFO @ Sat, 15 Jan 2022 22:56:33: 11000000 INFO @ Sat, 15 Jan 2022 22:56:34: 7000000 INFO @ Sat, 15 Jan 2022 22:56:37: 4000000 INFO @ Sat, 15 Jan 2022 22:56:40: 12000000 INFO @ Sat, 15 Jan 2022 22:56:42: 8000000 INFO @ Sat, 15 Jan 2022 22:56:44: 5000000 INFO @ Sat, 15 Jan 2022 22:56:47: 13000000 INFO @ Sat, 15 Jan 2022 22:56:49: 9000000 INFO @ Sat, 15 Jan 2022 22:56:54: 6000000 INFO @ Sat, 15 Jan 2022 22:56:54: 14000000 INFO @ Sat, 15 Jan 2022 22:56:56: 10000000 INFO @ Sat, 15 Jan 2022 22:57:02: 15000000 INFO @ Sat, 15 Jan 2022 22:57:04: 11000000 INFO @ Sat, 15 Jan 2022 22:57:04: 7000000 INFO @ Sat, 15 Jan 2022 22:57:09: 16000000 INFO @ Sat, 15 Jan 2022 22:57:11: 12000000 INFO @ Sat, 15 Jan 2022 22:57:14: 8000000 INFO @ Sat, 15 Jan 2022 22:57:17: 17000000 INFO @ Sat, 15 Jan 2022 22:57:18: 13000000 INFO @ Sat, 15 Jan 2022 22:57:23: 9000000 INFO @ Sat, 15 Jan 2022 22:57:24: 18000000 INFO @ Sat, 15 Jan 2022 22:57:25: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 22:57:31: 10000000 INFO @ Sat, 15 Jan 2022 22:57:32: 19000000 INFO @ Sat, 15 Jan 2022 22:57:33: 15000000 INFO @ Sat, 15 Jan 2022 22:57:40: 20000000 INFO @ Sat, 15 Jan 2022 22:57:40: 11000000 INFO @ Sat, 15 Jan 2022 22:57:42: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 22:57:48: 21000000 INFO @ Sat, 15 Jan 2022 22:57:49: 12000000 INFO @ Sat, 15 Jan 2022 22:57:50: 17000000 INFO @ Sat, 15 Jan 2022 22:57:53: #1 tag size is determined as 10 bps INFO @ Sat, 15 Jan 2022 22:57:53: #1 tag size = 10 INFO @ Sat, 15 Jan 2022 22:57:53: #1 total tags in treatment: 1440604 INFO @ Sat, 15 Jan 2022 22:57:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:57:53: #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 22:57:53: #1 tags after filtering in treatment: 890983 INFO @ Sat, 15 Jan 2022 22:57:53: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 22:57:53: #1 finished! INFO @ Sat, 15 Jan 2022 22:57:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:57:53: #2 number of paired peaks: 219 WARNING @ Sat, 15 Jan 2022 22:57:53: 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 22:57:53: start model_add_line... INFO @ Sat, 15 Jan 2022 22:57:53: start X-correlation... INFO @ Sat, 15 Jan 2022 22:57:53: end of X-cor INFO @ Sat, 15 Jan 2022 22:57:53: #2 finished! INFO @ Sat, 15 Jan 2022 22:57:53: #2 predicted fragment length is 182 bps INFO @ Sat, 15 Jan 2022 22:57:53: #2 alternative fragment length(s) may be 4,182 bps INFO @ Sat, 15 Jan 2022 22:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_model.r INFO @ Sat, 15 Jan 2022 22:57:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:57:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:57:57: 13000000 INFO @ Sat, 15 Jan 2022 22:57:57: 18000000 INFO @ Sat, 15 Jan 2022 22:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_summits.bed INFO @ Sat, 15 Jan 2022 22:57:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (507 records, 4 fields): 751 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:58:04: 19000000 INFO @ Sat, 15 Jan 2022 22:58:05: 14000000 INFO @ Sat, 15 Jan 2022 22:58:12: 20000000 INFO @ Sat, 15 Jan 2022 22:58:14: 15000000 INFO @ Sat, 15 Jan 2022 22:58:19: 21000000 INFO @ Sat, 15 Jan 2022 22:58:23: 16000000 INFO @ Sat, 15 Jan 2022 22:58:24: #1 tag size is determined as 10 bps INFO @ Sat, 15 Jan 2022 22:58:24: #1 tag size = 10 INFO @ Sat, 15 Jan 2022 22:58:24: #1 total tags in treatment: 1440604 INFO @ Sat, 15 Jan 2022 22:58:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:58:24: #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 22:58:24: #1 tags after filtering in treatment: 890983 INFO @ Sat, 15 Jan 2022 22:58:24: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 22:58:24: #1 finished! INFO @ Sat, 15 Jan 2022 22:58:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:58:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:58:24: #2 number of paired peaks: 219 WARNING @ Sat, 15 Jan 2022 22:58:24: 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 22:58:24: start model_add_line... INFO @ Sat, 15 Jan 2022 22:58:24: start X-correlation... INFO @ Sat, 15 Jan 2022 22:58:24: end of X-cor INFO @ Sat, 15 Jan 2022 22:58:24: #2 finished! INFO @ Sat, 15 Jan 2022 22:58:24: #2 predicted fragment length is 182 bps INFO @ Sat, 15 Jan 2022 22:58:24: #2 alternative fragment length(s) may be 4,182 bps INFO @ Sat, 15 Jan 2022 22:58:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_model.r INFO @ Sat, 15 Jan 2022 22:58:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:58:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:58:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_summits.bed INFO @ Sat, 15 Jan 2022 22:58:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (305 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 22:58:31: 17000000 INFO @ Sat, 15 Jan 2022 22:58:39: 18000000 INFO @ Sat, 15 Jan 2022 22:58:47: 19000000 INFO @ Sat, 15 Jan 2022 22:58:56: 20000000 INFO @ Sat, 15 Jan 2022 22:59:04: 21000000 INFO @ Sat, 15 Jan 2022 22:59:09: #1 tag size is determined as 10 bps INFO @ Sat, 15 Jan 2022 22:59:09: #1 tag size = 10 INFO @ Sat, 15 Jan 2022 22:59:09: #1 total tags in treatment: 1440604 INFO @ Sat, 15 Jan 2022 22:59:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:59:09: #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 22:59:09: #1 tags after filtering in treatment: 890983 INFO @ Sat, 15 Jan 2022 22:59:09: #1 Redundant rate of treatment: 0.38 INFO @ Sat, 15 Jan 2022 22:59:09: #1 finished! INFO @ Sat, 15 Jan 2022 22:59:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:59:10: #2 number of paired peaks: 219 WARNING @ Sat, 15 Jan 2022 22:59:10: 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 22:59:10: start model_add_line... INFO @ Sat, 15 Jan 2022 22:59:10: start X-correlation... INFO @ Sat, 15 Jan 2022 22:59:10: end of X-cor INFO @ Sat, 15 Jan 2022 22:59:10: #2 finished! INFO @ Sat, 15 Jan 2022 22:59:10: #2 predicted fragment length is 182 bps INFO @ Sat, 15 Jan 2022 22:59:10: #2 alternative fragment length(s) may be 4,182 bps INFO @ Sat, 15 Jan 2022 22:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_model.r INFO @ Sat, 15 Jan 2022 22:59:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:59:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:59:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:59:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:59:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_summits.bed INFO @ Sat, 15 Jan 2022 22:59:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (143 records, 4 fields): 20 millis CompletedMACS2peakCalling