Job ID = 10224040 SRX = SRX8926525 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 4273001 spots for SRR12430726/SRR12430726.sra Written 4273001 spots for SRR12430726/SRR12430726.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:30 4273001 reads; of these: 4273001 (100.00%) were paired; of these: 1893829 (44.32%) aligned concordantly 0 times 2119217 (49.60%) aligned concordantly exactly 1 time 259955 (6.08%) aligned concordantly >1 times ---- 1893829 pairs aligned concordantly 0 times; of these: 2401 (0.13%) aligned discordantly 1 time ---- 1891428 pairs aligned 0 times concordantly or discordantly; of these: 3782856 mates make up the pairs; of these: 3746480 (99.04%) aligned 0 times 28011 (0.74%) aligned exactly 1 time 8365 (0.22%) aligned >1 times 56.16% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 680823 / 2381325 = 0.2859 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 09:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.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 09:13:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:13:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:13:53: 1000000 INFO @ Fri, 16 Oct 2020 09:13:58: 2000000 INFO @ Fri, 16 Oct 2020 09:14:02: 3000000 INFO @ Fri, 16 Oct 2020 09:14:04: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:14:04: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:14:04: #1 total tags in treatment: 1698645 INFO @ Fri, 16 Oct 2020 09:14:04: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:14:04: #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 09:14:04: #1 tags after filtering in treatment: 1536095 INFO @ Fri, 16 Oct 2020 09:14:04: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:14:04: #1 finished! INFO @ Fri, 16 Oct 2020 09:14:04: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:14:04: #2 number of paired peaks: 139 WARNING @ Fri, 16 Oct 2020 09:14:04: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Fri, 16 Oct 2020 09:14:04: start model_add_line... INFO @ Fri, 16 Oct 2020 09:14:04: start X-correlation... INFO @ Fri, 16 Oct 2020 09:14:04: end of X-cor INFO @ Fri, 16 Oct 2020 09:14:04: #2 finished! INFO @ Fri, 16 Oct 2020 09:14:04: #2 predicted fragment length is 224 bps INFO @ Fri, 16 Oct 2020 09:14:04: #2 alternative fragment length(s) may be 224 bps INFO @ Fri, 16 Oct 2020 09:14:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.05_model.r INFO @ Fri, 16 Oct 2020 09:14:04: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:14:08: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:14:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.05_summits.bed INFO @ Fri, 16 Oct 2020 09:14:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:14:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.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 09:14:19: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:14:19: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:14:24: 1000000 INFO @ Fri, 16 Oct 2020 09:14:28: 2000000 INFO @ Fri, 16 Oct 2020 09:14:33: 3000000 INFO @ Fri, 16 Oct 2020 09:14:35: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:14:35: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:14:35: #1 total tags in treatment: 1698645 INFO @ Fri, 16 Oct 2020 09:14:35: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:14:35: #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 09:14:35: #1 tags after filtering in treatment: 1536095 INFO @ Fri, 16 Oct 2020 09:14:35: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:14:35: #1 finished! INFO @ Fri, 16 Oct 2020 09:14:35: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:14:35: #2 number of paired peaks: 139 WARNING @ Fri, 16 Oct 2020 09:14:35: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Fri, 16 Oct 2020 09:14:35: start model_add_line... INFO @ Fri, 16 Oct 2020 09:14:35: start X-correlation... INFO @ Fri, 16 Oct 2020 09:14:35: end of X-cor INFO @ Fri, 16 Oct 2020 09:14:35: #2 finished! INFO @ Fri, 16 Oct 2020 09:14:35: #2 predicted fragment length is 224 bps INFO @ Fri, 16 Oct 2020 09:14:35: #2 alternative fragment length(s) may be 224 bps INFO @ Fri, 16 Oct 2020 09:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.10_model.r INFO @ Fri, 16 Oct 2020 09:14:35: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:14:39: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:14:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:14:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:14:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.10_summits.bed INFO @ Fri, 16 Oct 2020 09:14:40: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:14:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.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 09:14:49: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:14:49: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:14:54: 1000000 INFO @ Fri, 16 Oct 2020 09:14:58: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:15:03: 3000000 INFO @ Fri, 16 Oct 2020 09:15:05: #1 tag size is determined as 51 bps INFO @ Fri, 16 Oct 2020 09:15:05: #1 tag size = 51 INFO @ Fri, 16 Oct 2020 09:15:05: #1 total tags in treatment: 1698645 INFO @ Fri, 16 Oct 2020 09:15:05: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:15:05: #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 09:15:05: #1 tags after filtering in treatment: 1536095 INFO @ Fri, 16 Oct 2020 09:15:05: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 16 Oct 2020 09:15:05: #1 finished! INFO @ Fri, 16 Oct 2020 09:15:05: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:15:05: #2 number of paired peaks: 139 WARNING @ Fri, 16 Oct 2020 09:15:05: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Fri, 16 Oct 2020 09:15:05: start model_add_line... INFO @ Fri, 16 Oct 2020 09:15:05: start X-correlation... INFO @ Fri, 16 Oct 2020 09:15:05: end of X-cor INFO @ Fri, 16 Oct 2020 09:15:05: #2 finished! INFO @ Fri, 16 Oct 2020 09:15:05: #2 predicted fragment length is 224 bps INFO @ Fri, 16 Oct 2020 09:15:05: #2 alternative fragment length(s) may be 224 bps INFO @ Fri, 16 Oct 2020 09:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.20_model.r INFO @ Fri, 16 Oct 2020 09:15:05: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:15:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:15:09: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:15:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:15:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:15:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8926525/SRX8926525.20_summits.bed INFO @ Fri, 16 Oct 2020 09:15:10: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (87 records, 4 fields): 2 millis CompletedMACS2peakCalling