Job ID = 14521123 SRX = SRX9431281 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4675557 spots for SRR12979575/SRR12979575.sra Written 4675557 spots for SRR12979575/SRR12979575.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: 00:00:55 4675557 reads; of these: 4675557 (100.00%) were unpaired; of these: 497536 (10.64%) aligned 0 times 3683464 (78.78%) aligned exactly 1 time 494557 (10.58%) aligned >1 times 89.36% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 1513514 / 4178021 = 0.3623 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 20:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.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 20:30:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:30:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:30:45: 1000000 INFO @ Sat, 15 Jan 2022 20:30:51: 2000000 INFO @ Sat, 15 Jan 2022 20:30:55: #1 tag size is determined as 65 bps INFO @ Sat, 15 Jan 2022 20:30:55: #1 tag size = 65 INFO @ Sat, 15 Jan 2022 20:30:55: #1 total tags in treatment: 2664507 INFO @ Sat, 15 Jan 2022 20:30:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:30:55: #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 20:30:55: #1 tags after filtering in treatment: 2664507 INFO @ Sat, 15 Jan 2022 20:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:30:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:30:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:30:55: #2 number of paired peaks: 106 WARNING @ Sat, 15 Jan 2022 20:30:55: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Jan 2022 20:30:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:30:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:30:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:30:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:30:55: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Jan 2022 20:30:55: #2 alternative fragment length(s) may be 4,227,230,257 bps INFO @ Sat, 15 Jan 2022 20:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.05_model.r INFO @ Sat, 15 Jan 2022 20:30:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:31:05: #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 20:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.05_summits.bed INFO @ Sat, 15 Jan 2022 20:31:08: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (756 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.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 20:31:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:31:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:31:15: 1000000 INFO @ Sat, 15 Jan 2022 20:31:21: 2000000 INFO @ Sat, 15 Jan 2022 20:31:25: #1 tag size is determined as 65 bps INFO @ Sat, 15 Jan 2022 20:31:25: #1 tag size = 65 INFO @ Sat, 15 Jan 2022 20:31:25: #1 total tags in treatment: 2664507 INFO @ Sat, 15 Jan 2022 20:31:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:31:25: #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 20:31:25: #1 tags after filtering in treatment: 2664507 INFO @ Sat, 15 Jan 2022 20:31:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:31:25: #1 finished! INFO @ Sat, 15 Jan 2022 20:31:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:31:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:31:25: #2 number of paired peaks: 106 WARNING @ Sat, 15 Jan 2022 20:31:25: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Jan 2022 20:31:25: start model_add_line... INFO @ Sat, 15 Jan 2022 20:31:26: start X-correlation... INFO @ Sat, 15 Jan 2022 20:31:26: end of X-cor INFO @ Sat, 15 Jan 2022 20:31:26: #2 finished! INFO @ Sat, 15 Jan 2022 20:31:26: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Jan 2022 20:31:26: #2 alternative fragment length(s) may be 4,227,230,257 bps INFO @ Sat, 15 Jan 2022 20:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.10_model.r INFO @ Sat, 15 Jan 2022 20:31:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:31:35: #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 20:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.10_summits.bed INFO @ Sat, 15 Jan 2022 20:31:38: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.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 20:31:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:31:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:31:45: 1000000 INFO @ Sat, 15 Jan 2022 20:31:51: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:31:55: #1 tag size is determined as 65 bps INFO @ Sat, 15 Jan 2022 20:31:55: #1 tag size = 65 INFO @ Sat, 15 Jan 2022 20:31:55: #1 total tags in treatment: 2664507 INFO @ Sat, 15 Jan 2022 20:31:55: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:31:55: #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 20:31:55: #1 tags after filtering in treatment: 2664507 INFO @ Sat, 15 Jan 2022 20:31:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 20:31:55: #1 finished! INFO @ Sat, 15 Jan 2022 20:31:55: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:31:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:31:55: #2 number of paired peaks: 106 WARNING @ Sat, 15 Jan 2022 20:31:55: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Jan 2022 20:31:55: start model_add_line... INFO @ Sat, 15 Jan 2022 20:31:55: start X-correlation... INFO @ Sat, 15 Jan 2022 20:31:55: end of X-cor INFO @ Sat, 15 Jan 2022 20:31:55: #2 finished! INFO @ Sat, 15 Jan 2022 20:31:55: #2 predicted fragment length is 257 bps INFO @ Sat, 15 Jan 2022 20:31:55: #2 alternative fragment length(s) may be 4,227,230,257 bps INFO @ Sat, 15 Jan 2022 20:31:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.20_model.r INFO @ Sat, 15 Jan 2022 20:31:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:31:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:32:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:32:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:32:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:32:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9431281/SRX9431281.20_summits.bed INFO @ Sat, 15 Jan 2022 20:32:07: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 3 millis CompletedMACS2peakCalling