Job ID = 14521410 SRX = SRX9385120 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1556050 spots for SRR12920583/SRR12920583.sra Written 1556050 spots for SRR12920583/SRR12920583.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: 00:00:51 1556050 reads; of these: 1556050 (100.00%) were paired; of these: 316267 (20.32%) aligned concordantly 0 times 1087121 (69.86%) aligned concordantly exactly 1 time 152662 (9.81%) aligned concordantly >1 times ---- 316267 pairs aligned concordantly 0 times; of these: 59415 (18.79%) aligned discordantly 1 time ---- 256852 pairs aligned 0 times concordantly or discordantly; of these: 513704 mates make up the pairs; of these: 484374 (94.29%) aligned 0 times 14007 (2.73%) aligned exactly 1 time 15323 (2.98%) aligned >1 times 84.44% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 102389 / 1297551 = 0.0789 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 20:58:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.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 20:58:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:58:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:58:28: 1000000 INFO @ Sat, 15 Jan 2022 20:58:33: 2000000 INFO @ Sat, 15 Jan 2022 20:58:35: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:58:35: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:58:35: #1 total tags in treatment: 1140181 INFO @ Sat, 15 Jan 2022 20:58:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:58:35: #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 20:58:35: #1 tags after filtering in treatment: 927841 INFO @ Sat, 15 Jan 2022 20:58:35: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 20:58:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:58:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:58:35: #2 number of paired peaks: 159 WARNING @ Sat, 15 Jan 2022 20:58:35: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Jan 2022 20:58:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:58:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:58:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:58:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:58:35: #2 predicted fragment length is 114 bps INFO @ Sat, 15 Jan 2022 20:58:35: #2 alternative fragment length(s) may be 10,73,114,148,171,190,524,558 bps INFO @ Sat, 15 Jan 2022 20:58:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.05_model.r INFO @ Sat, 15 Jan 2022 20:58:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:58:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:58:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:58:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:58:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:58:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.05_summits.bed INFO @ Sat, 15 Jan 2022 20:58:38: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (162 records, 4 fields): 2 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 20:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.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 20:58:53: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:58:53: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:58:58: 1000000 INFO @ Sat, 15 Jan 2022 20:59:03: 2000000 INFO @ Sat, 15 Jan 2022 20:59:05: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:59:05: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:59:05: #1 total tags in treatment: 1140181 INFO @ Sat, 15 Jan 2022 20:59:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:59:05: #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 20:59:05: #1 tags after filtering in treatment: 927841 INFO @ Sat, 15 Jan 2022 20:59:05: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 20:59:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:59:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:59:05: #2 number of paired peaks: 159 WARNING @ Sat, 15 Jan 2022 20:59:05: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Jan 2022 20:59:05: start model_add_line... INFO @ Sat, 15 Jan 2022 20:59:05: start X-correlation... INFO @ Sat, 15 Jan 2022 20:59:05: end of X-cor INFO @ Sat, 15 Jan 2022 20:59:05: #2 finished! INFO @ Sat, 15 Jan 2022 20:59:05: #2 predicted fragment length is 114 bps INFO @ Sat, 15 Jan 2022 20:59:05: #2 alternative fragment length(s) may be 10,73,114,148,171,190,524,558 bps INFO @ Sat, 15 Jan 2022 20:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.10_model.r INFO @ Sat, 15 Jan 2022 20:59:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:59:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.10_summits.bed INFO @ Sat, 15 Jan 2022 20:59:08: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 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 20:59:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.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 20:59:23: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:59:23: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:59:28: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:59:33: 2000000 INFO @ Sat, 15 Jan 2022 20:59:35: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 20:59:35: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 20:59:35: #1 total tags in treatment: 1140181 INFO @ Sat, 15 Jan 2022 20:59:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:59:35: #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 20:59:35: #1 tags after filtering in treatment: 927841 INFO @ Sat, 15 Jan 2022 20:59:35: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 15 Jan 2022 20:59:35: #1 finished! INFO @ Sat, 15 Jan 2022 20:59:35: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:59:35: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:59:35: #2 number of paired peaks: 159 WARNING @ Sat, 15 Jan 2022 20:59:35: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Sat, 15 Jan 2022 20:59:35: start model_add_line... INFO @ Sat, 15 Jan 2022 20:59:35: start X-correlation... INFO @ Sat, 15 Jan 2022 20:59:35: end of X-cor INFO @ Sat, 15 Jan 2022 20:59:35: #2 finished! INFO @ Sat, 15 Jan 2022 20:59:35: #2 predicted fragment length is 114 bps INFO @ Sat, 15 Jan 2022 20:59:35: #2 alternative fragment length(s) may be 10,73,114,148,171,190,524,558 bps INFO @ Sat, 15 Jan 2022 20:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.20_model.r INFO @ Sat, 15 Jan 2022 20:59:35: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:59:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9385120/SRX9385120.20_summits.bed INFO @ Sat, 15 Jan 2022 20:59:38: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 0 millis CompletedMACS2peakCalling