Job ID = 10224105 SRX = SRX8952658 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7364947 spots for SRR12458228/SRR12458228.sra Written 7364947 spots for SRR12458228/SRR12458228.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: 00:01:47 7364947 reads; of these: 7364947 (100.00%) were paired; of these: 6044282 (82.07%) aligned concordantly 0 times 1172466 (15.92%) aligned concordantly exactly 1 time 148199 (2.01%) aligned concordantly >1 times ---- 6044282 pairs aligned concordantly 0 times; of these: 300511 (4.97%) aligned discordantly 1 time ---- 5743771 pairs aligned 0 times concordantly or discordantly; of these: 11487542 mates make up the pairs; of these: 9616104 (83.71%) aligned 0 times 1640281 (14.28%) aligned exactly 1 time 231157 (2.01%) aligned >1 times 34.72% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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_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] 438771 / 1613129 = 0.2720 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 09:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.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 09:29:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:29:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:29:12: 1000000 INFO @ Fri, 16 Oct 2020 09:29:17: 2000000 INFO @ Fri, 16 Oct 2020 09:29:23: 3000000 INFO @ Fri, 16 Oct 2020 09:29:29: 4000000 INFO @ Fri, 16 Oct 2020 09:29:31: #1 tag size is determined as 39 bps INFO @ Fri, 16 Oct 2020 09:29:31: #1 tag size = 39 INFO @ Fri, 16 Oct 2020 09:29:31: #1 total tags in treatment: 1039092 INFO @ Fri, 16 Oct 2020 09:29:31: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:29:31: #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 09:29:31: #1 tags after filtering in treatment: 967289 INFO @ Fri, 16 Oct 2020 09:29:31: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:29:31: #1 finished! INFO @ Fri, 16 Oct 2020 09:29:31: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:29:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:29:31: #2 number of paired peaks: 183 WARNING @ Fri, 16 Oct 2020 09:29:31: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Oct 2020 09:29:31: start model_add_line... INFO @ Fri, 16 Oct 2020 09:29:31: start X-correlation... INFO @ Fri, 16 Oct 2020 09:29:31: end of X-cor INFO @ Fri, 16 Oct 2020 09:29:31: #2 finished! INFO @ Fri, 16 Oct 2020 09:29:31: #2 predicted fragment length is 281 bps INFO @ Fri, 16 Oct 2020 09:29:31: #2 alternative fragment length(s) may be 3,238,281 bps INFO @ Fri, 16 Oct 2020 09:29:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.05_model.r INFO @ Fri, 16 Oct 2020 09:29:31: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:29:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:29:33: #3 Call peaks for each chromosome... 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 09:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.05_summits.bed INFO @ Fri, 16 Oct 2020 09:29:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.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 09:29:36: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:29:36: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:29:42: 1000000 INFO @ Fri, 16 Oct 2020 09:29:48: 2000000 INFO @ Fri, 16 Oct 2020 09:29:54: 3000000 INFO @ Fri, 16 Oct 2020 09:30:00: 4000000 INFO @ Fri, 16 Oct 2020 09:30:02: #1 tag size is determined as 39 bps INFO @ Fri, 16 Oct 2020 09:30:02: #1 tag size = 39 INFO @ Fri, 16 Oct 2020 09:30:02: #1 total tags in treatment: 1039092 INFO @ Fri, 16 Oct 2020 09:30:02: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:30:02: #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 09:30:02: #1 tags after filtering in treatment: 967289 INFO @ Fri, 16 Oct 2020 09:30:02: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:30:02: #1 finished! INFO @ Fri, 16 Oct 2020 09:30:02: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:30:02: #2 number of paired peaks: 183 WARNING @ Fri, 16 Oct 2020 09:30:02: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Oct 2020 09:30:02: start model_add_line... INFO @ Fri, 16 Oct 2020 09:30:02: start X-correlation... INFO @ Fri, 16 Oct 2020 09:30:02: end of X-cor INFO @ Fri, 16 Oct 2020 09:30:02: #2 finished! INFO @ Fri, 16 Oct 2020 09:30:02: #2 predicted fragment length is 281 bps INFO @ Fri, 16 Oct 2020 09:30:02: #2 alternative fragment length(s) may be 3,238,281 bps INFO @ Fri, 16 Oct 2020 09:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.10_model.r INFO @ Fri, 16 Oct 2020 09:30:02: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:30:02: #3 Pre-compute pvalue-qvalue table... 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 09:30:04: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:30:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:30:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:30:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.10_summits.bed INFO @ Fri, 16 Oct 2020 09:30:05: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 16 Oct 2020 09:30:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.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 09:30:06: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:30:06: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:30:12: 1000000 INFO @ Fri, 16 Oct 2020 09:30:18: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:30:24: 3000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:30:29: 4000000 INFO @ Fri, 16 Oct 2020 09:30:30: #1 tag size is determined as 39 bps INFO @ Fri, 16 Oct 2020 09:30:30: #1 tag size = 39 INFO @ Fri, 16 Oct 2020 09:30:30: #1 total tags in treatment: 1039092 INFO @ Fri, 16 Oct 2020 09:30:30: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:30:30: #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 09:30:30: #1 tags after filtering in treatment: 967289 INFO @ Fri, 16 Oct 2020 09:30:30: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 16 Oct 2020 09:30:30: #1 finished! INFO @ Fri, 16 Oct 2020 09:30:30: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:30:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:30:30: #2 number of paired peaks: 183 WARNING @ Fri, 16 Oct 2020 09:30:30: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Fri, 16 Oct 2020 09:30:30: start model_add_line... INFO @ Fri, 16 Oct 2020 09:30:30: start X-correlation... INFO @ Fri, 16 Oct 2020 09:30:30: end of X-cor INFO @ Fri, 16 Oct 2020 09:30:30: #2 finished! INFO @ Fri, 16 Oct 2020 09:30:30: #2 predicted fragment length is 281 bps INFO @ Fri, 16 Oct 2020 09:30:30: #2 alternative fragment length(s) may be 3,238,281 bps INFO @ Fri, 16 Oct 2020 09:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.20_model.r INFO @ Fri, 16 Oct 2020 09:30:30: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:30:33: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:30:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:30:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:30:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952658/SRX8952658.20_summits.bed INFO @ Fri, 16 Oct 2020 09:30:34: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (98 records, 4 fields): 2 millis CompletedMACS2peakCalling