Job ID = 6368700 SRX = SRX5402725 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:00 prefetch.2.10.7: 1) Downloading 'SRR8602959'... 2020-06-16T00:30:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:34:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:34:53 prefetch.2.10.7: 1) 'SRR8602959' was downloaded successfully Read 31177070 spots for SRR8602959/SRR8602959.sra Written 31177070 spots for SRR8602959/SRR8602959.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: 00:06:18 31177070 reads; of these: 31177070 (100.00%) were unpaired; of these: 4841757 (15.53%) aligned 0 times 22643901 (72.63%) aligned exactly 1 time 3691412 (11.84%) aligned >1 times 84.47% overall alignment rate Time searching: 00:06:18 Overall time: 00:06:18 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] 11119727 / 26335313 = 0.4222 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 09:48:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.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 09:48:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:48: 1000000 INFO @ Tue, 16 Jun 2020 09:48:54: 2000000 INFO @ Tue, 16 Jun 2020 09:49:00: 3000000 INFO @ Tue, 16 Jun 2020 09:49:06: 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 09:49:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.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 09:49:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:13: 5000000 INFO @ Tue, 16 Jun 2020 09:49:19: 1000000 INFO @ Tue, 16 Jun 2020 09:49:20: 6000000 INFO @ Tue, 16 Jun 2020 09:49:26: 2000000 INFO @ Tue, 16 Jun 2020 09:49:27: 7000000 INFO @ Tue, 16 Jun 2020 09:49:33: 3000000 INFO @ Tue, 16 Jun 2020 09:49:34: 8000000 INFO @ Tue, 16 Jun 2020 09:49:40: 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 09:49:41: 9000000 INFO @ Tue, 16 Jun 2020 09:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.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 09:49:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:47: 5000000 INFO @ Tue, 16 Jun 2020 09:49:49: 10000000 INFO @ Tue, 16 Jun 2020 09:49:51: 1000000 INFO @ Tue, 16 Jun 2020 09:49:55: 6000000 INFO @ Tue, 16 Jun 2020 09:49:57: 11000000 INFO @ Tue, 16 Jun 2020 09:50:00: 2000000 INFO @ Tue, 16 Jun 2020 09:50:03: 7000000 INFO @ Tue, 16 Jun 2020 09:50:05: 12000000 INFO @ Tue, 16 Jun 2020 09:50:08: 3000000 INFO @ Tue, 16 Jun 2020 09:50:11: 8000000 INFO @ Tue, 16 Jun 2020 09:50:13: 13000000 INFO @ Tue, 16 Jun 2020 09:50:17: 4000000 INFO @ Tue, 16 Jun 2020 09:50:19: 9000000 INFO @ Tue, 16 Jun 2020 09:50:21: 14000000 INFO @ Tue, 16 Jun 2020 09:50:26: 5000000 INFO @ Tue, 16 Jun 2020 09:50:27: 10000000 INFO @ Tue, 16 Jun 2020 09:50:29: 15000000 INFO @ Tue, 16 Jun 2020 09:50:31: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:31: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:31: #1 total tags in treatment: 15215586 INFO @ Tue, 16 Jun 2020 09:50:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:31: #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 09:50:31: #1 tags after filtering in treatment: 15215586 INFO @ Tue, 16 Jun 2020 09:50:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:33: #2 number of paired peaks: 2484 INFO @ Tue, 16 Jun 2020 09:50:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:33: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 09:50:33: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 16 Jun 2020 09:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.05_model.r INFO @ Tue, 16 Jun 2020 09:50:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:34: 6000000 INFO @ Tue, 16 Jun 2020 09:50:35: 11000000 INFO @ Tue, 16 Jun 2020 09:50:43: 7000000 INFO @ Tue, 16 Jun 2020 09:50:43: 12000000 INFO @ Tue, 16 Jun 2020 09:50:52: 13000000 INFO @ Tue, 16 Jun 2020 09:50:52: 8000000 INFO @ Tue, 16 Jun 2020 09:51:00: 14000000 INFO @ Tue, 16 Jun 2020 09:51:00: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:08: 15000000 INFO @ Tue, 16 Jun 2020 09:51:09: 10000000 INFO @ Tue, 16 Jun 2020 09:51:09: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:09: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:09: #1 total tags in treatment: 15215586 INFO @ Tue, 16 Jun 2020 09:51:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:09: #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 09:51:10: #1 tags after filtering in treatment: 15215586 INFO @ Tue, 16 Jun 2020 09:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:11: #2 number of paired peaks: 2484 INFO @ Tue, 16 Jun 2020 09:51:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:11: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 09:51:11: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 16 Jun 2020 09:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.10_model.r INFO @ Tue, 16 Jun 2020 09:51:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:17: 11000000 INFO @ Tue, 16 Jun 2020 09:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6874 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:25: 12000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:51:33: 13000000 INFO @ Tue, 16 Jun 2020 09:51:41: 14000000 INFO @ Tue, 16 Jun 2020 09:51:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:48: 15000000 INFO @ Tue, 16 Jun 2020 09:51:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:50: #1 total tags in treatment: 15215586 INFO @ Tue, 16 Jun 2020 09:51:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:50: #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 09:51:50: #1 tags after filtering in treatment: 15215586 INFO @ Tue, 16 Jun 2020 09:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:52: #2 number of paired peaks: 2484 INFO @ Tue, 16 Jun 2020 09:51:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:52: #2 predicted fragment length is 130 bps INFO @ Tue, 16 Jun 2020 09:51:52: #2 alternative fragment length(s) may be 130 bps INFO @ Tue, 16 Jun 2020 09:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.20_model.r INFO @ Tue, 16 Jun 2020 09:51:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.10_summits.bed INFO @ Tue, 16 Jun 2020 09:52:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5556 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402725/SRX5402725.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4491 records, 4 fields): 7 millis CompletedMACS2peakCalling