Job ID = 14518180 SRX = SRX9430848 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 3691903 spots for SRR12979021/SRR12979021.sra Written 3691903 spots for SRR12979021/SRR12979021.sra Read 5416746 spots for SRR12979022/SRR12979022.sra Written 5416746 spots for SRR12979022/SRR12979022.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:27:03 9108649 reads; of these: 9108649 (100.00%) were unpaired; of these: 1106064 (12.14%) aligned 0 times 5284539 (58.02%) aligned exactly 1 time 2718046 (29.84%) aligned >1 times 87.86% overall alignment rate Time searching: 00:27:09 Overall time: 00:27:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 2139331 / 8002585 = 0.2673 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 11:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.bam'] # control file = None # effective genome size = 2.15e+09 # 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 11:16:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:16:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:17:07: 1000000 INFO @ Sat, 15 Jan 2022 11:17:16: 2000000 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 11:17:25: 3000000 INFO @ Sat, 15 Jan 2022 11:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.bam'] # control file = None # effective genome size = 2.15e+09 # 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 11:17:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:17:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:17:35: 4000000 INFO @ Sat, 15 Jan 2022 11:17:37: 1000000 INFO @ Sat, 15 Jan 2022 11:17:44: 5000000 INFO @ Sat, 15 Jan 2022 11:17:46: 2000000 INFO @ Sat, 15 Jan 2022 11:17:52: #1 tag size is determined as 59 bps INFO @ Sat, 15 Jan 2022 11:17:52: #1 tag size = 59 INFO @ Sat, 15 Jan 2022 11:17:52: #1 total tags in treatment: 5863254 INFO @ Sat, 15 Jan 2022 11:17:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:17:52: #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 11:17:53: #1 tags after filtering in treatment: 5863032 INFO @ Sat, 15 Jan 2022 11:17:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:17:53: #1 finished! INFO @ Sat, 15 Jan 2022 11:17:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:17:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:17:55: #2 number of paired peaks: 36304 INFO @ Sat, 15 Jan 2022 11:17:55: start model_add_line... INFO @ Sat, 15 Jan 2022 11:17:55: start X-correlation... INFO @ Sat, 15 Jan 2022 11:17:55: end of X-cor INFO @ Sat, 15 Jan 2022 11:17:55: #2 finished! INFO @ Sat, 15 Jan 2022 11:17:55: #2 predicted fragment length is 125 bps INFO @ Sat, 15 Jan 2022 11:17:55: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 15 Jan 2022 11:17:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.05_model.r 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 11:17:55: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:17:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:17:55: 3000000 INFO @ Sat, 15 Jan 2022 11:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.bam'] # control file = None # effective genome size = 2.15e+09 # 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 11:17:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:17:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:18:05: 4000000 INFO @ Sat, 15 Jan 2022 11:18:07: 1000000 INFO @ Sat, 15 Jan 2022 11:18:07: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:18:14: 5000000 INFO @ Sat, 15 Jan 2022 11:18:15: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:18:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:18:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.05_summits.bed INFO @ Sat, 15 Jan 2022 11:18:15: Done! pass1 - making usageList (68 chroms): 2 millis pass2 - checking and writing primary data (4624 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:18:16: 2000000 INFO @ Sat, 15 Jan 2022 11:18:23: #1 tag size is determined as 59 bps INFO @ Sat, 15 Jan 2022 11:18:23: #1 tag size = 59 INFO @ Sat, 15 Jan 2022 11:18:23: #1 total tags in treatment: 5863254 INFO @ Sat, 15 Jan 2022 11:18:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:18:23: #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 11:18:23: #1 tags after filtering in treatment: 5863032 INFO @ Sat, 15 Jan 2022 11:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:18:23: #1 finished! INFO @ Sat, 15 Jan 2022 11:18:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:18:25: #2 number of paired peaks: 36304 INFO @ Sat, 15 Jan 2022 11:18:25: start model_add_line... INFO @ Sat, 15 Jan 2022 11:18:25: start X-correlation... INFO @ Sat, 15 Jan 2022 11:18:25: end of X-cor INFO @ Sat, 15 Jan 2022 11:18:25: #2 finished! INFO @ Sat, 15 Jan 2022 11:18:25: #2 predicted fragment length is 125 bps INFO @ Sat, 15 Jan 2022 11:18:25: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 15 Jan 2022 11:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.10_model.r INFO @ Sat, 15 Jan 2022 11:18:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:18:25: 3000000 INFO @ Sat, 15 Jan 2022 11:18:35: 4000000 INFO @ Sat, 15 Jan 2022 11:18:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:18:44: 5000000 INFO @ Sat, 15 Jan 2022 11:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.10_summits.bed INFO @ Sat, 15 Jan 2022 11:18:45: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (1101 records, 4 fields): 2268 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:18:52: #1 tag size is determined as 59 bps INFO @ Sat, 15 Jan 2022 11:18:52: #1 tag size = 59 INFO @ Sat, 15 Jan 2022 11:18:52: #1 total tags in treatment: 5863254 INFO @ Sat, 15 Jan 2022 11:18:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:18:52: #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 11:18:52: #1 tags after filtering in treatment: 5863032 INFO @ Sat, 15 Jan 2022 11:18:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:18:52: #1 finished! INFO @ Sat, 15 Jan 2022 11:18:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:18:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:18:54: #2 number of paired peaks: 36304 INFO @ Sat, 15 Jan 2022 11:18:54: start model_add_line... INFO @ Sat, 15 Jan 2022 11:18:54: start X-correlation... INFO @ Sat, 15 Jan 2022 11:18:54: end of X-cor INFO @ Sat, 15 Jan 2022 11:18:54: #2 finished! INFO @ Sat, 15 Jan 2022 11:18:54: #2 predicted fragment length is 125 bps INFO @ Sat, 15 Jan 2022 11:18:54: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 15 Jan 2022 11:18:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.20_model.r INFO @ Sat, 15 Jan 2022 11:18:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:18:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:19:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:19:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:19:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:19:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430848/SRX9430848.20_summits.bed INFO @ Sat, 15 Jan 2022 11:19:14: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (322 records, 4 fields): 8 millis CompletedMACS2peakCalling