Job ID = 14520648 SRX = SRX7847365 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21330406 spots for SRR11235547/SRR11235547.sra Written 21330406 spots for SRR11235547/SRR11235547.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: 00:09:46 21330406 reads; of these: 21330406 (100.00%) were paired; of these: 4005001 (18.78%) aligned concordantly 0 times 13673890 (64.11%) aligned concordantly exactly 1 time 3651515 (17.12%) aligned concordantly >1 times ---- 4005001 pairs aligned concordantly 0 times; of these: 36995 (0.92%) aligned discordantly 1 time ---- 3968006 pairs aligned 0 times concordantly or discordantly; of these: 7936012 mates make up the pairs; of these: 6840513 (86.20%) aligned 0 times 664387 (8.37%) aligned exactly 1 time 431112 (5.43%) aligned >1 times 83.97% overall alignment rate Time searching: 00:09:46 Overall time: 00:09:46 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 12 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] 16910517 / 17329850 = 0.9758 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 20:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.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 20:03:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:03:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:03:30: 1000000 INFO @ Sat, 15 Jan 2022 20:03:34: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:03:34: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:03:34: #1 total tags in treatment: 444568 INFO @ Sat, 15 Jan 2022 20:03:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:03:34: #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 20:03:34: #1 tags after filtering in treatment: 199848 INFO @ Sat, 15 Jan 2022 20:03:34: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 20:03:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:03:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:03:34: #2 number of paired peaks: 707 WARNING @ Sat, 15 Jan 2022 20:03:34: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Sat, 15 Jan 2022 20:03:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:03:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:03:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:03:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:03:34: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 20:03:34: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 20:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.05_model.r INFO @ Sat, 15 Jan 2022 20:03:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:03:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:03:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:03:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:03:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.05_summits.bed INFO @ Sat, 15 Jan 2022 20:03:35: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (624 records, 4 fields): 3 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 20:03:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.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 20:03:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:03:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:04:00: 1000000 INFO @ Sat, 15 Jan 2022 20:04:05: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:04:05: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:04:05: #1 total tags in treatment: 444568 INFO @ Sat, 15 Jan 2022 20:04:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:04:05: #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 20:04:05: #1 tags after filtering in treatment: 199848 INFO @ Sat, 15 Jan 2022 20:04:05: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 20:04:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:04:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:04:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:04:05: #2 number of paired peaks: 707 WARNING @ Sat, 15 Jan 2022 20:04:05: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Sat, 15 Jan 2022 20:04:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:04:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:04:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:04:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:04:05: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 20:04:05: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 20:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.10_model.r INFO @ Sat, 15 Jan 2022 20:04:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:04:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:04:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.10_summits.bed INFO @ Sat, 15 Jan 2022 20:04:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (466 records, 4 fields): 5 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 20:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.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 20:04:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:04:25: #1 read treatment tags... 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 20:04:29: 1000000 INFO @ Sat, 15 Jan 2022 20:04:34: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 20:04:34: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 20:04:34: #1 total tags in treatment: 444568 INFO @ Sat, 15 Jan 2022 20:04:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:04:34: #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 20:04:34: #1 tags after filtering in treatment: 199848 INFO @ Sat, 15 Jan 2022 20:04:34: #1 Redundant rate of treatment: 0.55 INFO @ Sat, 15 Jan 2022 20:04:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:04:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:04:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:04:34: #2 number of paired peaks: 707 WARNING @ Sat, 15 Jan 2022 20:04:34: Fewer paired peaks (707) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 707 pairs to build model! INFO @ Sat, 15 Jan 2022 20:04:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:04:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:04:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:04:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:04:34: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 20:04:34: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 20:04:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.20_model.r INFO @ Sat, 15 Jan 2022 20:04:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:04:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7847365/SRX7847365.20_summits.bed INFO @ Sat, 15 Jan 2022 20:04:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 4 millis CompletedMACS2peakCalling