Job ID = 14521388 SRX = SRX8952650 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5051142 spots for SRR12458236/SRR12458236.sra Written 5051142 spots for SRR12458236/SRR12458236.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: 00:02:27 5051142 reads; of these: 5051142 (100.00%) were paired; of these: 3791484 (75.06%) aligned concordantly 0 times 1107617 (21.93%) aligned concordantly exactly 1 time 152041 (3.01%) aligned concordantly >1 times ---- 3791484 pairs aligned concordantly 0 times; of these: 434730 (11.47%) aligned discordantly 1 time ---- 3356754 pairs aligned 0 times concordantly or discordantly; of these: 6713508 mates make up the pairs; of these: 5077053 (75.62%) aligned 0 times 1391417 (20.73%) aligned exactly 1 time 245038 (3.65%) aligned >1 times 49.74% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 414167 / 1611562 = 0.2570 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 21:00:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.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 21:00:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:00:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:00:18: 1000000 INFO @ Sat, 15 Jan 2022 21:00:26: 2000000 INFO @ Sat, 15 Jan 2022 21:00:35: 3000000 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 21:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.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 21:00:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:00:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:00:43: 4000000 INFO @ Sat, 15 Jan 2022 21:00:45: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 21:00:45: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 21:00:45: #1 total tags in treatment: 1088485 INFO @ Sat, 15 Jan 2022 21:00:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:00:45: #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 21:00:45: #1 tags after filtering in treatment: 975438 INFO @ Sat, 15 Jan 2022 21:00:45: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:00:45: #1 finished! INFO @ Sat, 15 Jan 2022 21:00:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:00:45: #2 number of paired peaks: 205 WARNING @ Sat, 15 Jan 2022 21:00:45: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sat, 15 Jan 2022 21:00:45: start model_add_line... INFO @ Sat, 15 Jan 2022 21:00:45: start X-correlation... INFO @ Sat, 15 Jan 2022 21:00:45: end of X-cor INFO @ Sat, 15 Jan 2022 21:00:45: #2 finished! INFO @ Sat, 15 Jan 2022 21:00:45: #2 predicted fragment length is 236 bps INFO @ Sat, 15 Jan 2022 21:00:45: #2 alternative fragment length(s) may be 3,236,257 bps INFO @ Sat, 15 Jan 2022 21:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.05_model.r INFO @ Sat, 15 Jan 2022 21:00:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:00:47: 1000000 INFO @ Sat, 15 Jan 2022 21:00:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.05_summits.bed INFO @ Sat, 15 Jan 2022 21:00:49: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:00:56: 2000000 INFO @ Sat, 15 Jan 2022 21:01:04: 3000000 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 21:01:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.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 21:01:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:01:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:01:13: 4000000 INFO @ Sat, 15 Jan 2022 21:01:14: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 21:01:14: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 21:01:14: #1 total tags in treatment: 1088485 INFO @ Sat, 15 Jan 2022 21:01:14: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:14: #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 21:01:14: #1 tags after filtering in treatment: 975438 INFO @ Sat, 15 Jan 2022 21:01:14: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:01:14: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:14: #2 number of paired peaks: 205 WARNING @ Sat, 15 Jan 2022 21:01:14: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sat, 15 Jan 2022 21:01:14: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:14: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:14: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:14: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:14: #2 predicted fragment length is 236 bps INFO @ Sat, 15 Jan 2022 21:01:14: #2 alternative fragment length(s) may be 3,236,257 bps INFO @ Sat, 15 Jan 2022 21:01:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.10_model.r INFO @ Sat, 15 Jan 2022 21:01:14: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:01:17: 1000000 INFO @ Sat, 15 Jan 2022 21:01:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.10_summits.bed INFO @ Sat, 15 Jan 2022 21:01:19: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:01:25: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:01:34: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:01:42: 4000000 INFO @ Sat, 15 Jan 2022 21:01:44: #1 tag size is determined as 41 bps INFO @ Sat, 15 Jan 2022 21:01:44: #1 tag size = 41 INFO @ Sat, 15 Jan 2022 21:01:44: #1 total tags in treatment: 1088485 INFO @ Sat, 15 Jan 2022 21:01:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:01:44: #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 21:01:44: #1 tags after filtering in treatment: 975438 INFO @ Sat, 15 Jan 2022 21:01:44: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 15 Jan 2022 21:01:44: #1 finished! INFO @ Sat, 15 Jan 2022 21:01:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:01:44: #2 number of paired peaks: 205 WARNING @ Sat, 15 Jan 2022 21:01:44: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Sat, 15 Jan 2022 21:01:44: start model_add_line... INFO @ Sat, 15 Jan 2022 21:01:44: start X-correlation... INFO @ Sat, 15 Jan 2022 21:01:44: end of X-cor INFO @ Sat, 15 Jan 2022 21:01:44: #2 finished! INFO @ Sat, 15 Jan 2022 21:01:44: #2 predicted fragment length is 236 bps INFO @ Sat, 15 Jan 2022 21:01:44: #2 alternative fragment length(s) may be 3,236,257 bps INFO @ Sat, 15 Jan 2022 21:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.20_model.r INFO @ Sat, 15 Jan 2022 21:01:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:01:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:01:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:01:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:01:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952650/SRX8952650.20_summits.bed INFO @ Sat, 15 Jan 2022 21:01:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (107 records, 4 fields): 3 millis CompletedMACS2peakCalling