Job ID = 14520689 SRX = SRX8866057 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 1066802 spots for SRR12366840/SRR12366840.sra Written 1066802 spots for SRR12366840/SRR12366840.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: 00:00:09 1066802 reads; of these: 1066802 (100.00%) were unpaired; of these: 223225 (20.92%) aligned 0 times 728187 (68.26%) aligned exactly 1 time 115390 (10.82%) aligned >1 times 79.08% overall alignment rate Time searching: 00:00:09 Overall time: 00:00:09 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_rmdupse_core] 155989 / 843577 = 0.1849 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 19:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.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 19:38:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:38:11: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:38:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:38:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:38:16: #1 total tags in treatment: 687588 INFO @ Sat, 15 Jan 2022 19:38:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:38:16: #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 19:38:16: #1 tags after filtering in treatment: 687588 INFO @ Sat, 15 Jan 2022 19:38:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:38:16: #1 finished! INFO @ Sat, 15 Jan 2022 19:38:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:38:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:38:16: #2 number of paired peaks: 541 WARNING @ Sat, 15 Jan 2022 19:38:16: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 15 Jan 2022 19:38:16: start model_add_line... INFO @ Sat, 15 Jan 2022 19:38:16: start X-correlation... INFO @ Sat, 15 Jan 2022 19:38:16: end of X-cor INFO @ Sat, 15 Jan 2022 19:38:16: #2 finished! INFO @ Sat, 15 Jan 2022 19:38:16: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Jan 2022 19:38:16: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 15 Jan 2022 19:38:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.05_model.r INFO @ Sat, 15 Jan 2022 19:38:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:38:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:38:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.05_summits.bed INFO @ Sat, 15 Jan 2022 19:38:20: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1234 records, 4 fields): 23 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 19:38:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.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 19:38:41: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:38:41: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:38:46: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:38:46: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:38:46: #1 total tags in treatment: 687588 INFO @ Sat, 15 Jan 2022 19:38:46: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:38:46: #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 19:38:46: #1 tags after filtering in treatment: 687588 INFO @ Sat, 15 Jan 2022 19:38:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:38:46: #1 finished! INFO @ Sat, 15 Jan 2022 19:38:46: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:38:46: #2 number of paired peaks: 541 WARNING @ Sat, 15 Jan 2022 19:38:46: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 15 Jan 2022 19:38:46: start model_add_line... INFO @ Sat, 15 Jan 2022 19:38:46: start X-correlation... INFO @ Sat, 15 Jan 2022 19:38:46: end of X-cor INFO @ Sat, 15 Jan 2022 19:38:46: #2 finished! INFO @ Sat, 15 Jan 2022 19:38:46: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Jan 2022 19:38:46: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 15 Jan 2022 19:38:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.10_model.r INFO @ Sat, 15 Jan 2022 19:38:46: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:38:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:38:50: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:38:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:38:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.10_summits.bed INFO @ Sat, 15 Jan 2022 19:38:50: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (710 records, 4 fields): 3 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 19:39:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.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 19:39:11: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:39:11: #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 19:39:16: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 19:39:16: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 19:39:16: #1 total tags in treatment: 687588 INFO @ Sat, 15 Jan 2022 19:39:16: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:39:16: #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 19:39:16: #1 tags after filtering in treatment: 687588 INFO @ Sat, 15 Jan 2022 19:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 19:39:16: #1 finished! INFO @ Sat, 15 Jan 2022 19:39:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:39:16: #2 number of paired peaks: 541 WARNING @ Sat, 15 Jan 2022 19:39:16: Fewer paired peaks (541) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 541 pairs to build model! INFO @ Sat, 15 Jan 2022 19:39:16: start model_add_line... INFO @ Sat, 15 Jan 2022 19:39:16: start X-correlation... INFO @ Sat, 15 Jan 2022 19:39:16: end of X-cor INFO @ Sat, 15 Jan 2022 19:39:16: #2 finished! INFO @ Sat, 15 Jan 2022 19:39:16: #2 predicted fragment length is 130 bps INFO @ Sat, 15 Jan 2022 19:39:16: #2 alternative fragment length(s) may be 130 bps INFO @ Sat, 15 Jan 2022 19:39:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.20_model.r INFO @ Sat, 15 Jan 2022 19:39:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:39:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:39:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:39:19: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:39:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:39:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8866057/SRX8866057.20_summits.bed INFO @ Sat, 15 Jan 2022 19:39:19: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (334 records, 4 fields): 8 millis CompletedMACS2peakCalling