Job ID = 10224057 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: 01:19:42 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: 01:19:42 Overall time: 01:19:42 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:44:05: # 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 @ Fri, 16 Oct 2020 10:44:05: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:44:05: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:44:09: 1000000 INFO @ Fri, 16 Oct 2020 10:44:13: 2000000 INFO @ Fri, 16 Oct 2020 10:44:17: 3000000 INFO @ Fri, 16 Oct 2020 10:44:21: 4000000 INFO @ Fri, 16 Oct 2020 10:44:25: 5000000 INFO @ Fri, 16 Oct 2020 10:44:30: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:44:34: # 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 @ Fri, 16 Oct 2020 10:44:34: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:44:34: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:44:34: 7000000 INFO @ Fri, 16 Oct 2020 10:44:39: 1000000 INFO @ Fri, 16 Oct 2020 10:44:39: 8000000 INFO @ Fri, 16 Oct 2020 10:44:43: 2000000 INFO @ Fri, 16 Oct 2020 10:44:44: 9000000 INFO @ Fri, 16 Oct 2020 10:44:48: 3000000 INFO @ Fri, 16 Oct 2020 10:44:48: 10000000 INFO @ Fri, 16 Oct 2020 10:44:52: 4000000 INFO @ Fri, 16 Oct 2020 10:44:53: 11000000 INFO @ Fri, 16 Oct 2020 10:44:57: 5000000 INFO @ Fri, 16 Oct 2020 10:44:57: 12000000 INFO @ Fri, 16 Oct 2020 10:45:01: 13000000 INFO @ Fri, 16 Oct 2020 10:45:02: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 16 Oct 2020 10:45:04: # 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 @ Fri, 16 Oct 2020 10:45:04: #1 read tag files... INFO @ Fri, 16 Oct 2020 10:45:04: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 10:45:06: 14000000 INFO @ Fri, 16 Oct 2020 10:45:07: 7000000 INFO @ Fri, 16 Oct 2020 10:45:09: 1000000 INFO @ Fri, 16 Oct 2020 10:45:11: 15000000 INFO @ Fri, 16 Oct 2020 10:45:13: 8000000 INFO @ Fri, 16 Oct 2020 10:45:15: 2000000 INFO @ Fri, 16 Oct 2020 10:45:16: 16000000 INFO @ Fri, 16 Oct 2020 10:45:18: 9000000 INFO @ Fri, 16 Oct 2020 10:45:20: 3000000 INFO @ Fri, 16 Oct 2020 10:45:21: 17000000 INFO @ Fri, 16 Oct 2020 10:45:22: 10000000 INFO @ Fri, 16 Oct 2020 10:45:25: 4000000 INFO @ Fri, 16 Oct 2020 10:45:25: 18000000 INFO @ Fri, 16 Oct 2020 10:45:27: 11000000 INFO @ Fri, 16 Oct 2020 10:45:30: 19000000 INFO @ Fri, 16 Oct 2020 10:45:30: 5000000 INFO @ Fri, 16 Oct 2020 10:45:32: 12000000 INFO @ Fri, 16 Oct 2020 10:45:35: 20000000 INFO @ Fri, 16 Oct 2020 10:45:37: 6000000 INFO @ Fri, 16 Oct 2020 10:45:37: 13000000 INFO @ Fri, 16 Oct 2020 10:45:40: 21000000 INFO @ Fri, 16 Oct 2020 10:45:42: 14000000 INFO @ Fri, 16 Oct 2020 10:45:43: 7000000 INFO @ Fri, 16 Oct 2020 10:45:43: #1 tag size is determined as 10 bps INFO @ Fri, 16 Oct 2020 10:45:43: #1 tag size = 10 INFO @ Fri, 16 Oct 2020 10:45:43: #1 total tags in treatment: 1440604 INFO @ Fri, 16 Oct 2020 10:45:43: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:45:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:45:43: #1 tags after filtering in treatment: 890983 INFO @ Fri, 16 Oct 2020 10:45:43: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 16 Oct 2020 10:45:43: #1 finished! INFO @ Fri, 16 Oct 2020 10:45:43: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:45:43: #2 number of paired peaks: 219 WARNING @ Fri, 16 Oct 2020 10:45:43: 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 @ Fri, 16 Oct 2020 10:45:43: start model_add_line... INFO @ Fri, 16 Oct 2020 10:45:43: start X-correlation... INFO @ Fri, 16 Oct 2020 10:45:43: end of X-cor INFO @ Fri, 16 Oct 2020 10:45:43: #2 finished! INFO @ Fri, 16 Oct 2020 10:45:43: #2 predicted fragment length is 182 bps INFO @ Fri, 16 Oct 2020 10:45:43: #2 alternative fragment length(s) may be 4,182 bps INFO @ Fri, 16 Oct 2020 10:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_model.r INFO @ Fri, 16 Oct 2020 10:45:43: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:45:46: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:45:47: 15000000 INFO @ Fri, 16 Oct 2020 10:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_peaks.xls INFO @ Fri, 16 Oct 2020 10:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.05_summits.bed INFO @ Fri, 16 Oct 2020 10:45:47: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (507 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:45:49: 8000000 INFO @ Fri, 16 Oct 2020 10:45:52: 16000000 INFO @ Fri, 16 Oct 2020 10:45:54: 9000000 INFO @ Fri, 16 Oct 2020 10:45:57: 17000000 INFO @ Fri, 16 Oct 2020 10:45:59: 10000000 INFO @ Fri, 16 Oct 2020 10:46:02: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 10:46:05: 11000000 INFO @ Fri, 16 Oct 2020 10:46:06: 19000000 INFO @ Fri, 16 Oct 2020 10:46:10: 12000000 INFO @ Fri, 16 Oct 2020 10:46:11: 20000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 10:46:15: 13000000 INFO @ Fri, 16 Oct 2020 10:46:16: 21000000 INFO @ Fri, 16 Oct 2020 10:46:20: #1 tag size is determined as 10 bps INFO @ Fri, 16 Oct 2020 10:46:20: #1 tag size = 10 INFO @ Fri, 16 Oct 2020 10:46:20: #1 total tags in treatment: 1440604 INFO @ Fri, 16 Oct 2020 10:46:20: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:46:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:46:20: #1 tags after filtering in treatment: 890983 INFO @ Fri, 16 Oct 2020 10:46:20: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 16 Oct 2020 10:46:20: #1 finished! INFO @ Fri, 16 Oct 2020 10:46:20: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:46:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:46:20: #2 number of paired peaks: 219 WARNING @ Fri, 16 Oct 2020 10:46:20: 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 @ Fri, 16 Oct 2020 10:46:20: start model_add_line... INFO @ Fri, 16 Oct 2020 10:46:20: start X-correlation... INFO @ Fri, 16 Oct 2020 10:46:20: end of X-cor INFO @ Fri, 16 Oct 2020 10:46:20: #2 finished! INFO @ Fri, 16 Oct 2020 10:46:20: #2 predicted fragment length is 182 bps INFO @ Fri, 16 Oct 2020 10:46:20: #2 alternative fragment length(s) may be 4,182 bps INFO @ Fri, 16 Oct 2020 10:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_model.r INFO @ Fri, 16 Oct 2020 10:46:20: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:46:20: 14000000 INFO @ Fri, 16 Oct 2020 10:46:22: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_peaks.xls INFO @ Fri, 16 Oct 2020 10:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.10_summits.bed INFO @ Fri, 16 Oct 2020 10:46:23: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (305 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 10:46:25: 15000000 INFO @ Fri, 16 Oct 2020 10:46:31: 16000000 INFO @ Fri, 16 Oct 2020 10:46:36: 17000000 INFO @ Fri, 16 Oct 2020 10:46:40: 18000000 INFO @ Fri, 16 Oct 2020 10:46:45: 19000000 INFO @ Fri, 16 Oct 2020 10:46:50: 20000000 INFO @ Fri, 16 Oct 2020 10:46:55: 21000000 INFO @ Fri, 16 Oct 2020 10:46:58: #1 tag size is determined as 10 bps INFO @ Fri, 16 Oct 2020 10:46:58: #1 tag size = 10 INFO @ Fri, 16 Oct 2020 10:46:58: #1 total tags in treatment: 1440604 INFO @ Fri, 16 Oct 2020 10:46:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 10:46:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 10:46:58: #1 tags after filtering in treatment: 890983 INFO @ Fri, 16 Oct 2020 10:46:58: #1 Redundant rate of treatment: 0.38 INFO @ Fri, 16 Oct 2020 10:46:58: #1 finished! INFO @ Fri, 16 Oct 2020 10:46:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 10:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 10:46:58: #2 number of paired peaks: 219 WARNING @ Fri, 16 Oct 2020 10:46:58: 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 @ Fri, 16 Oct 2020 10:46:58: start model_add_line... INFO @ Fri, 16 Oct 2020 10:46:58: start X-correlation... INFO @ Fri, 16 Oct 2020 10:46:58: end of X-cor INFO @ Fri, 16 Oct 2020 10:46:58: #2 finished! INFO @ Fri, 16 Oct 2020 10:46:58: #2 predicted fragment length is 182 bps INFO @ Fri, 16 Oct 2020 10:46:58: #2 alternative fragment length(s) may be 4,182 bps INFO @ Fri, 16 Oct 2020 10:46:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_model.r INFO @ Fri, 16 Oct 2020 10:46:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 10:46:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 10:47:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 10:47:02: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_peaks.xls INFO @ Fri, 16 Oct 2020 10:47:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 10:47:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952614/SRX8952614.20_summits.bed INFO @ Fri, 16 Oct 2020 10:47:02: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (143 records, 4 fields): 2 millis CompletedMACS2peakCalling