Job ID = 6366950 SRX = SRX2576650 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:07:53 prefetch.2.10.7: 1) Downloading 'SRR5272607'... 2020-06-15T23:07:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:10:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:10:15 prefetch.2.10.7: 1) 'SRR5272607' was downloaded successfully Read 22612410 spots for SRR5272607/SRR5272607.sra Written 22612410 spots for SRR5272607/SRR5272607.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: 00:05:05 22612410 reads; of these: 22612410 (100.00%) were unpaired; of these: 2461181 (10.88%) aligned 0 times 16782815 (74.22%) aligned exactly 1 time 3368414 (14.90%) aligned >1 times 89.12% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 10338668 / 20151229 = 0.5131 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:20:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:20:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:56: 1000000 INFO @ Tue, 16 Jun 2020 08:21:02: 2000000 INFO @ Tue, 16 Jun 2020 08:21:07: 3000000 INFO @ Tue, 16 Jun 2020 08:21:13: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:21:19: 5000000 INFO @ Tue, 16 Jun 2020 08:21:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:21:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:25: 6000000 INFO @ Tue, 16 Jun 2020 08:21:27: 1000000 INFO @ Tue, 16 Jun 2020 08:21:31: 7000000 INFO @ Tue, 16 Jun 2020 08:21:33: 2000000 INFO @ Tue, 16 Jun 2020 08:21:37: 8000000 INFO @ Tue, 16 Jun 2020 08:21:39: 3000000 INFO @ Tue, 16 Jun 2020 08:21:43: 9000000 INFO @ Tue, 16 Jun 2020 08:21:45: 4000000 INFO @ Tue, 16 Jun 2020 08:21:48: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:21:48: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:21:48: #1 total tags in treatment: 9812561 INFO @ Tue, 16 Jun 2020 08:21:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:21:48: #1 tags after filtering in treatment: 9812561 INFO @ Tue, 16 Jun 2020 08:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:48: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:48: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:21:49: #2 number of paired peaks: 1288 INFO @ Tue, 16 Jun 2020 08:21:49: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:49: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:49: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:49: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:49: #2 predicted fragment length is 174 bps INFO @ Tue, 16 Jun 2020 08:21:49: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 16 Jun 2020 08:21:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.05_model.r INFO @ Tue, 16 Jun 2020 08:21:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 08:21:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:21:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:21:51: 5000000 INFO @ Tue, 16 Jun 2020 08:21:57: 1000000 INFO @ Tue, 16 Jun 2020 08:21:57: 6000000 INFO @ Tue, 16 Jun 2020 08:22:03: 2000000 INFO @ Tue, 16 Jun 2020 08:22:04: 7000000 INFO @ Tue, 16 Jun 2020 08:22:09: 3000000 INFO @ Tue, 16 Jun 2020 08:22:10: 8000000 INFO @ Tue, 16 Jun 2020 08:22:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:16: 4000000 INFO @ Tue, 16 Jun 2020 08:22:17: 9000000 INFO @ Tue, 16 Jun 2020 08:22:22: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:22: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:22: #1 total tags in treatment: 9812561 INFO @ Tue, 16 Jun 2020 08:22:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:22:22: #1 tags after filtering in treatment: 9812561 INFO @ Tue, 16 Jun 2020 08:22:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:22: 5000000 INFO @ Tue, 16 Jun 2020 08:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.05_summits.bed INFO @ Tue, 16 Jun 2020 08:22:23: Done! INFO @ Tue, 16 Jun 2020 08:22:23: #2 number of paired peaks: 1288 INFO @ Tue, 16 Jun 2020 08:22:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:23: #2 predicted fragment length is 174 bps INFO @ Tue, 16 Jun 2020 08:22:23: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 16 Jun 2020 08:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.10_model.r INFO @ Tue, 16 Jun 2020 08:22:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:23: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3616 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:22:28: 6000000 INFO @ Tue, 16 Jun 2020 08:22:35: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:22:41: 8000000 INFO @ Tue, 16 Jun 2020 08:22:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:47: 9000000 INFO @ Tue, 16 Jun 2020 08:22:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:22:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:22:51: #1 total tags in treatment: 9812561 INFO @ Tue, 16 Jun 2020 08:22:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:22:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:22:52: #1 tags after filtering in treatment: 9812561 INFO @ Tue, 16 Jun 2020 08:22:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:22:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:22:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:22:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:22:52: #2 number of paired peaks: 1288 INFO @ Tue, 16 Jun 2020 08:22:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:22:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:22:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:22:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:22:53: #2 predicted fragment length is 174 bps INFO @ Tue, 16 Jun 2020 08:22:53: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 16 Jun 2020 08:22:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.20_model.r INFO @ Tue, 16 Jun 2020 08:22:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:22:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2815 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:23:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576650/SRX2576650.20_summits.bed INFO @ Tue, 16 Jun 2020 08:23:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1993 records, 4 fields): 3 millis CompletedMACS2peakCalling