Job ID = 14520185 SRX = SRX7496388 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7094288 spots for SRR10822999/SRR10822999.sra Written 7094288 spots for SRR10822999/SRR10822999.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: 00:02:30 7094288 reads; of these: 7094288 (100.00%) were paired; of these: 4606146 (64.93%) aligned concordantly 0 times 1604390 (22.62%) aligned concordantly exactly 1 time 883752 (12.46%) aligned concordantly >1 times ---- 4606146 pairs aligned concordantly 0 times; of these: 8900 (0.19%) aligned discordantly 1 time ---- 4597246 pairs aligned 0 times concordantly or discordantly; of these: 9194492 mates make up the pairs; of these: 7242916 (78.77%) aligned 0 times 1458253 (15.86%) aligned exactly 1 time 493323 (5.37%) aligned >1 times 48.95% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 551591 / 2496668 = 0.2209 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 18:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.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 18:36:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:36:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:36:21: 1000000 INFO @ Sat, 15 Jan 2022 18:36:25: 2000000 INFO @ Sat, 15 Jan 2022 18:36:29: 3000000 INFO @ Sat, 15 Jan 2022 18:36:33: 4000000 INFO @ Sat, 15 Jan 2022 18:36:37: 5000000 INFO @ Sat, 15 Jan 2022 18:36:40: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:36:40: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:36:40: #1 total tags in treatment: 1936654 INFO @ Sat, 15 Jan 2022 18:36:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:36:40: #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 18:36:40: #1 tags after filtering in treatment: 1063120 INFO @ Sat, 15 Jan 2022 18:36:40: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 18:36:40: #1 finished! INFO @ Sat, 15 Jan 2022 18:36:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:36:40: #2 number of paired peaks: 148 WARNING @ Sat, 15 Jan 2022 18:36:40: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 15 Jan 2022 18:36:40: start model_add_line... INFO @ Sat, 15 Jan 2022 18:36:40: start X-correlation... INFO @ Sat, 15 Jan 2022 18:36:40: end of X-cor INFO @ Sat, 15 Jan 2022 18:36:40: #2 finished! INFO @ Sat, 15 Jan 2022 18:36:40: #2 predicted fragment length is 268 bps INFO @ Sat, 15 Jan 2022 18:36:40: #2 alternative fragment length(s) may be 242,268 bps INFO @ Sat, 15 Jan 2022 18:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_model.r INFO @ Sat, 15 Jan 2022 18:36:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:36:44: #3 Call peaks for each chromosome... 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 18:36:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:36:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:36:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.05_summits.bed INFO @ Sat, 15 Jan 2022 18:36:46: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (417 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:36:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.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 18:36:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:36:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:36:51: 1000000 INFO @ Sat, 15 Jan 2022 18:36:55: 2000000 INFO @ Sat, 15 Jan 2022 18:36:59: 3000000 INFO @ Sat, 15 Jan 2022 18:37:03: 4000000 INFO @ Sat, 15 Jan 2022 18:37:07: 5000000 INFO @ Sat, 15 Jan 2022 18:37:10: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:37:10: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:37:10: #1 total tags in treatment: 1936654 INFO @ Sat, 15 Jan 2022 18:37:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:37:10: #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 18:37:10: #1 tags after filtering in treatment: 1063120 INFO @ Sat, 15 Jan 2022 18:37:10: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 18:37:10: #1 finished! INFO @ Sat, 15 Jan 2022 18:37:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:37:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:37:11: #2 number of paired peaks: 148 WARNING @ Sat, 15 Jan 2022 18:37:11: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 15 Jan 2022 18:37:11: start model_add_line... INFO @ Sat, 15 Jan 2022 18:37:11: start X-correlation... INFO @ Sat, 15 Jan 2022 18:37:11: end of X-cor INFO @ Sat, 15 Jan 2022 18:37:11: #2 finished! INFO @ Sat, 15 Jan 2022 18:37:11: #2 predicted fragment length is 268 bps INFO @ Sat, 15 Jan 2022 18:37:11: #2 alternative fragment length(s) may be 242,268 bps INFO @ Sat, 15 Jan 2022 18:37:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_model.r INFO @ Sat, 15 Jan 2022 18:37:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:37:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:37:15: #3 Call peaks for each chromosome... 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 18:37:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:37:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:37:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.10_summits.bed INFO @ Sat, 15 Jan 2022 18:37:16: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (184 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 18:37:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.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 18:37:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:37:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:37:22: 1000000 INFO @ Sat, 15 Jan 2022 18:37:27: 2000000 INFO @ Sat, 15 Jan 2022 18:37:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:37:37: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:37:41: 5000000 INFO @ Sat, 15 Jan 2022 18:37:46: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:37:46: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:37:46: #1 total tags in treatment: 1936654 INFO @ Sat, 15 Jan 2022 18:37:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:37:46: #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 18:37:46: #1 tags after filtering in treatment: 1063120 INFO @ Sat, 15 Jan 2022 18:37:46: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 18:37:46: #1 finished! INFO @ Sat, 15 Jan 2022 18:37:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:37:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:37:46: #2 number of paired peaks: 148 WARNING @ Sat, 15 Jan 2022 18:37:46: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Sat, 15 Jan 2022 18:37:46: start model_add_line... INFO @ Sat, 15 Jan 2022 18:37:46: start X-correlation... INFO @ Sat, 15 Jan 2022 18:37:46: end of X-cor INFO @ Sat, 15 Jan 2022 18:37:46: #2 finished! INFO @ Sat, 15 Jan 2022 18:37:46: #2 predicted fragment length is 268 bps INFO @ Sat, 15 Jan 2022 18:37:46: #2 alternative fragment length(s) may be 242,268 bps INFO @ Sat, 15 Jan 2022 18:37:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_model.r INFO @ Sat, 15 Jan 2022 18:37:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:37:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:37:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:37:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:37:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:37:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496388/SRX7496388.20_summits.bed INFO @ Sat, 15 Jan 2022 18:37:51: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (68 records, 4 fields): 2 millis CompletedMACS2peakCalling