Job ID = 14522017 SRX = SRX1829041 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19375043 spots for SRR3644964/SRR3644964.sra Written 19375043 spots for SRR3644964/SRR3644964.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: 00:01:55 19375043 reads; of these: 19375043 (100.00%) were unpaired; of these: 4310558 (22.25%) aligned 0 times 12761771 (65.87%) aligned exactly 1 time 2302714 (11.88%) aligned >1 times 77.75% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 13981216 / 15064485 = 0.9281 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 22:04:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.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 22:04:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:12: 1000000 INFO @ Sat, 15 Jan 2022 22:04:13: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 22:04:13: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 22:04:13: #1 total tags in treatment: 1083269 INFO @ Sat, 15 Jan 2022 22:04:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:04:13: #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 22:04:13: #1 tags after filtering in treatment: 1083269 INFO @ Sat, 15 Jan 2022 22:04:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 22:04:13: #1 finished! INFO @ Sat, 15 Jan 2022 22:04:13: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:04:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:04:13: #2 number of paired peaks: 494 WARNING @ Sat, 15 Jan 2022 22:04:13: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sat, 15 Jan 2022 22:04:13: start model_add_line... INFO @ Sat, 15 Jan 2022 22:04:13: start X-correlation... INFO @ Sat, 15 Jan 2022 22:04:13: end of X-cor INFO @ Sat, 15 Jan 2022 22:04:13: #2 finished! INFO @ Sat, 15 Jan 2022 22:04:13: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 22:04:13: #2 alternative fragment length(s) may be 1,41,61,147,166,187,217,576 bps INFO @ Sat, 15 Jan 2022 22:04:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.05_model.r INFO @ Sat, 15 Jan 2022 22:04:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:04:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:04:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:04:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.05_peaks.xls INFO @ Sat, 15 Jan 2022 22:04:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:04:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.05_summits.bed INFO @ Sat, 15 Jan 2022 22:04:17: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (374 records, 4 fields): 17 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 22:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.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 22:04:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:04:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 22:04:42: 1000000 INFO @ Sat, 15 Jan 2022 22:04:42: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 22:04:42: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 22:04:42: #1 total tags in treatment: 1083269 INFO @ Sat, 15 Jan 2022 22:04:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:04:42: #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 22:04:42: #1 tags after filtering in treatment: 1083269 INFO @ Sat, 15 Jan 2022 22:04:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 22:04:42: #1 finished! INFO @ Sat, 15 Jan 2022 22:04:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:04:42: #2 number of paired peaks: 494 WARNING @ Sat, 15 Jan 2022 22:04:42: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sat, 15 Jan 2022 22:04:42: start model_add_line... INFO @ Sat, 15 Jan 2022 22:04:42: start X-correlation... INFO @ Sat, 15 Jan 2022 22:04:42: end of X-cor INFO @ Sat, 15 Jan 2022 22:04:42: #2 finished! INFO @ Sat, 15 Jan 2022 22:04:42: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 22:04:42: #2 alternative fragment length(s) may be 1,41,61,147,166,187,217,576 bps INFO @ Sat, 15 Jan 2022 22:04:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.10_model.r INFO @ Sat, 15 Jan 2022 22:04:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:04:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.10_peaks.xls INFO @ Sat, 15 Jan 2022 22:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:04:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.10_summits.bed INFO @ Sat, 15 Jan 2022 22:04:46: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 2 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 22:05:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.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 22:05:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 22:05:06: #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 22:05:11: 1000000 INFO @ Sat, 15 Jan 2022 22:05:11: #1 tag size is determined as 36 bps INFO @ Sat, 15 Jan 2022 22:05:11: #1 tag size = 36 INFO @ Sat, 15 Jan 2022 22:05:11: #1 total tags in treatment: 1083269 INFO @ Sat, 15 Jan 2022 22:05:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 22:05:11: #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 22:05:11: #1 tags after filtering in treatment: 1083269 INFO @ Sat, 15 Jan 2022 22:05:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 22:05:11: #1 finished! INFO @ Sat, 15 Jan 2022 22:05:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 22:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 22:05:12: #2 number of paired peaks: 494 WARNING @ Sat, 15 Jan 2022 22:05:12: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Sat, 15 Jan 2022 22:05:12: start model_add_line... INFO @ Sat, 15 Jan 2022 22:05:12: start X-correlation... INFO @ Sat, 15 Jan 2022 22:05:12: end of X-cor INFO @ Sat, 15 Jan 2022 22:05:12: #2 finished! INFO @ Sat, 15 Jan 2022 22:05:12: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 22:05:12: #2 alternative fragment length(s) may be 1,41,61,147,166,187,217,576 bps INFO @ Sat, 15 Jan 2022 22:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.20_model.r INFO @ Sat, 15 Jan 2022 22:05:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 22:05:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 22:05:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 22:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.20_peaks.xls INFO @ Sat, 15 Jan 2022 22:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 22:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX1829041/SRX1829041.20_summits.bed INFO @ Sat, 15 Jan 2022 22:05:16: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 1 millis CompletedMACS2peakCalling