Job ID = 6368909 SRX = SRX6720175 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:40:29 prefetch.2.10.7: 1) Downloading 'SRR9972855'... 2020-06-16T00:40:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:43:11 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:43:11 prefetch.2.10.7: 1) 'SRR9972855' was downloaded successfully Read 18438971 spots for SRR9972855/SRR9972855.sra Written 18438971 spots for SRR9972855/SRR9972855.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: 00:04:11 18438971 reads; of these: 18438971 (100.00%) were unpaired; of these: 308528 (1.67%) aligned 0 times 15444721 (83.76%) aligned exactly 1 time 2685722 (14.57%) aligned >1 times 98.33% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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 8 files... [bam_rmdupse_core] 4955279 / 18130443 = 0.2733 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 09:52:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.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 09:52:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:57: 1000000 INFO @ Tue, 16 Jun 2020 09:53:03: 2000000 INFO @ Tue, 16 Jun 2020 09:53:10: 3000000 INFO @ Tue, 16 Jun 2020 09:53:17: 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 09:53:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.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 09:53:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:23: 5000000 INFO @ Tue, 16 Jun 2020 09:53:26: 1000000 INFO @ Tue, 16 Jun 2020 09:53:30: 6000000 INFO @ Tue, 16 Jun 2020 09:53:32: 2000000 INFO @ Tue, 16 Jun 2020 09:53:37: 7000000 INFO @ Tue, 16 Jun 2020 09:53:38: 3000000 INFO @ Tue, 16 Jun 2020 09:53:44: 8000000 INFO @ Tue, 16 Jun 2020 09:53:45: 4000000 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 09:53:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.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 09:53:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:51: 5000000 INFO @ Tue, 16 Jun 2020 09:53:51: 9000000 INFO @ Tue, 16 Jun 2020 09:53:56: 1000000 INFO @ Tue, 16 Jun 2020 09:53:57: 6000000 INFO @ Tue, 16 Jun 2020 09:53:59: 10000000 INFO @ Tue, 16 Jun 2020 09:54:02: 2000000 INFO @ Tue, 16 Jun 2020 09:54:04: 7000000 INFO @ Tue, 16 Jun 2020 09:54:06: 11000000 INFO @ Tue, 16 Jun 2020 09:54:08: 3000000 INFO @ Tue, 16 Jun 2020 09:54:10: 8000000 INFO @ Tue, 16 Jun 2020 09:54:13: 12000000 INFO @ Tue, 16 Jun 2020 09:54:15: 4000000 INFO @ Tue, 16 Jun 2020 09:54:16: 9000000 INFO @ Tue, 16 Jun 2020 09:54:20: 13000000 INFO @ Tue, 16 Jun 2020 09:54:21: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:21: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:21: #1 total tags in treatment: 13175164 INFO @ Tue, 16 Jun 2020 09:54:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:21: #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 09:54:21: 5000000 INFO @ Tue, 16 Jun 2020 09:54:21: #1 tags after filtering in treatment: 13175164 INFO @ Tue, 16 Jun 2020 09:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:22: #2 number of paired peaks: 1793 INFO @ Tue, 16 Jun 2020 09:54:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:22: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 09:54:22: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 09:54:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.05_model.r INFO @ Tue, 16 Jun 2020 09:54:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:23: 10000000 INFO @ Tue, 16 Jun 2020 09:54:27: 6000000 INFO @ Tue, 16 Jun 2020 09:54:29: 11000000 INFO @ Tue, 16 Jun 2020 09:54:33: 7000000 INFO @ Tue, 16 Jun 2020 09:54:35: 12000000 INFO @ Tue, 16 Jun 2020 09:54:40: 8000000 INFO @ Tue, 16 Jun 2020 09:54:41: 13000000 INFO @ Tue, 16 Jun 2020 09:54:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:54:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:54:42: #1 total tags in treatment: 13175164 INFO @ Tue, 16 Jun 2020 09:54:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:42: #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 09:54:42: #1 tags after filtering in treatment: 13175164 INFO @ Tue, 16 Jun 2020 09:54:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:43: #2 number of paired peaks: 1793 INFO @ Tue, 16 Jun 2020 09:54:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:44: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 09:54:44: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 09:54:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.10_model.r INFO @ Tue, 16 Jun 2020 09:54:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:46: 9000000 INFO @ Tue, 16 Jun 2020 09:54:51: 10000000 INFO @ Tue, 16 Jun 2020 09:54:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:57: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:55:03: 12000000 INFO @ Tue, 16 Jun 2020 09:55:08: 13000000 INFO @ Tue, 16 Jun 2020 09:55:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:55:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:55:09: #1 total tags in treatment: 13175164 INFO @ Tue, 16 Jun 2020 09:55:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:09: #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 09:55:10: #1 tags after filtering in treatment: 13175164 INFO @ Tue, 16 Jun 2020 09:55:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:11: #2 number of paired peaks: 1793 INFO @ Tue, 16 Jun 2020 09:55:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:11: #2 predicted fragment length is 169 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2 alternative fragment length(s) may be 169 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.20_model.r INFO @ Tue, 16 Jun 2020 09:55:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.05_summits.bed INFO @ Tue, 16 Jun 2020 09:55:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5914 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:55:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4003 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720175/SRX6720175.20_summits.bed INFO @ Tue, 16 Jun 2020 09:56:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2207 records, 4 fields): 3 millis CompletedMACS2peakCalling