Job ID = 14520868 SRX = SRX8245547 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9481612 spots for SRR11684758/SRR11684758.sra Written 9481612 spots for SRR11684758/SRR11684758.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: 00:10:01 9481612 reads; of these: 9481612 (100.00%) were paired; of these: 6274340 (66.17%) aligned concordantly 0 times 2890112 (30.48%) aligned concordantly exactly 1 time 317160 (3.35%) aligned concordantly >1 times ---- 6274340 pairs aligned concordantly 0 times; of these: 4357 (0.07%) aligned discordantly 1 time ---- 6269983 pairs aligned 0 times concordantly or discordantly; of these: 12539966 mates make up the pairs; of these: 9387852 (74.86%) aligned 0 times 2794702 (22.29%) aligned exactly 1 time 357412 (2.85%) aligned >1 times 50.49% overall alignment rate Time searching: 00:10:01 Overall time: 00:10:01 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] 358519 / 3211064 = 0.1117 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 20:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.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 20:18:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:18:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:18:58: 1000000 INFO @ Sat, 15 Jan 2022 20:19:02: 2000000 INFO @ Sat, 15 Jan 2022 20:19:06: 3000000 INFO @ Sat, 15 Jan 2022 20:19:11: 4000000 INFO @ Sat, 15 Jan 2022 20:19:15: 5000000 INFO @ Sat, 15 Jan 2022 20:19:19: 6000000 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 20:19:23: 7000000 INFO @ Sat, 15 Jan 2022 20:19:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.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 20:19:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:19:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:19:27: 8000000 INFO @ Sat, 15 Jan 2022 20:19:29: 1000000 INFO @ Sat, 15 Jan 2022 20:19:31: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:19:31: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:19:31: #1 total tags in treatment: 2848923 INFO @ Sat, 15 Jan 2022 20:19:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:19:31: #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 20:19:31: #1 tags after filtering in treatment: 1849380 INFO @ Sat, 15 Jan 2022 20:19:31: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:19:31: #1 finished! INFO @ Sat, 15 Jan 2022 20:19:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:19:31: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:19:31: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:19:31: start model_add_line... INFO @ Sat, 15 Jan 2022 20:19:31: start X-correlation... INFO @ Sat, 15 Jan 2022 20:19:31: end of X-cor INFO @ Sat, 15 Jan 2022 20:19:31: #2 finished! INFO @ Sat, 15 Jan 2022 20:19:31: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Jan 2022 20:19:31: #2 alternative fragment length(s) may be 59,74,106,148,170,185,227,250,515,556,559,587 bps INFO @ Sat, 15 Jan 2022 20:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.05_model.r INFO @ Sat, 15 Jan 2022 20:19:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:19:34: 2000000 INFO @ Sat, 15 Jan 2022 20:19:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.05_summits.bed INFO @ Sat, 15 Jan 2022 20:19:37: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:19:39: 3000000 INFO @ Sat, 15 Jan 2022 20:19:44: 4000000 INFO @ Sat, 15 Jan 2022 20:19:49: 5000000 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 20:19:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.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 20:19:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:19:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:19:54: 6000000 INFO @ Sat, 15 Jan 2022 20:19:59: 1000000 INFO @ Sat, 15 Jan 2022 20:19:59: 7000000 INFO @ Sat, 15 Jan 2022 20:20:04: 2000000 INFO @ Sat, 15 Jan 2022 20:20:05: 8000000 INFO @ Sat, 15 Jan 2022 20:20:09: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:20:09: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:20:09: #1 total tags in treatment: 2848923 INFO @ Sat, 15 Jan 2022 20:20:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:20:09: #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 20:20:09: #1 tags after filtering in treatment: 1849380 INFO @ Sat, 15 Jan 2022 20:20:09: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:20:09: #1 finished! INFO @ Sat, 15 Jan 2022 20:20:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:20:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:20:09: 3000000 INFO @ Sat, 15 Jan 2022 20:20:09: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:20:09: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:20:09: start model_add_line... INFO @ Sat, 15 Jan 2022 20:20:09: start X-correlation... INFO @ Sat, 15 Jan 2022 20:20:09: end of X-cor INFO @ Sat, 15 Jan 2022 20:20:09: #2 finished! INFO @ Sat, 15 Jan 2022 20:20:09: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Jan 2022 20:20:09: #2 alternative fragment length(s) may be 59,74,106,148,170,185,227,250,515,556,559,587 bps INFO @ Sat, 15 Jan 2022 20:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.10_model.r INFO @ Sat, 15 Jan 2022 20:20:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:20:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:20:14: 4000000 INFO @ Sat, 15 Jan 2022 20:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.10_summits.bed INFO @ Sat, 15 Jan 2022 20:20:15: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:20:19: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:20:25: 6000000 INFO @ Sat, 15 Jan 2022 20:20:30: 7000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:20:35: 8000000 INFO @ Sat, 15 Jan 2022 20:20:39: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:20:39: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:20:39: #1 total tags in treatment: 2848923 INFO @ Sat, 15 Jan 2022 20:20:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:20:39: #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 20:20:40: #1 tags after filtering in treatment: 1849380 INFO @ Sat, 15 Jan 2022 20:20:40: #1 Redundant rate of treatment: 0.35 INFO @ Sat, 15 Jan 2022 20:20:40: #1 finished! INFO @ Sat, 15 Jan 2022 20:20:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:20:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:20:40: #2 number of paired peaks: 180 WARNING @ Sat, 15 Jan 2022 20:20:40: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Sat, 15 Jan 2022 20:20:40: start model_add_line... INFO @ Sat, 15 Jan 2022 20:20:40: start X-correlation... INFO @ Sat, 15 Jan 2022 20:20:40: end of X-cor INFO @ Sat, 15 Jan 2022 20:20:40: #2 finished! INFO @ Sat, 15 Jan 2022 20:20:40: #2 predicted fragment length is 148 bps INFO @ Sat, 15 Jan 2022 20:20:40: #2 alternative fragment length(s) may be 59,74,106,148,170,185,227,250,515,556,559,587 bps INFO @ Sat, 15 Jan 2022 20:20:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.20_model.r INFO @ Sat, 15 Jan 2022 20:20:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:20:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245547/SRX8245547.20_summits.bed INFO @ Sat, 15 Jan 2022 20:20:45: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (6 records, 4 fields): 4 millis CompletedMACS2peakCalling