Job ID = 6368902 SRX = SRX6720161 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:16 prefetch.2.10.7: 1) Downloading 'SRR9972869'... 2020-06-16T00:30:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:51 prefetch.2.10.7: 'SRR9972869' is valid 2020-06-16T00:32:51 prefetch.2.10.7: 1) 'SRR9972869' was downloaded successfully Read 13329835 spots for SRR9972869/SRR9972869.sra Written 13329835 spots for SRR9972869/SRR9972869.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: 00:02:32 13329835 reads; of these: 13329835 (100.00%) were unpaired; of these: 2768540 (20.77%) aligned 0 times 9191012 (68.95%) aligned exactly 1 time 1370283 (10.28%) aligned >1 times 79.23% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 2907874 / 10561295 = 0.2753 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 09:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.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 09:39:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:56: 1000000 INFO @ Tue, 16 Jun 2020 09:40:01: 2000000 INFO @ Tue, 16 Jun 2020 09:40:07: 3000000 INFO @ Tue, 16 Jun 2020 09:40:12: 4000000 INFO @ Tue, 16 Jun 2020 09:40:18: 5000000 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 09:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.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 09:40:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:23: 6000000 INFO @ Tue, 16 Jun 2020 09:40:28: 1000000 INFO @ Tue, 16 Jun 2020 09:40:29: 7000000 INFO @ Tue, 16 Jun 2020 09:40:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:33: #1 total tags in treatment: 7653421 INFO @ Tue, 16 Jun 2020 09:40:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:33: #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 09:40:33: #1 tags after filtering in treatment: 7653421 INFO @ Tue, 16 Jun 2020 09:40:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:33: #2 number of paired peaks: 2566 INFO @ Tue, 16 Jun 2020 09:40:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:34: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 09:40:34: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 16 Jun 2020 09:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.05_model.r INFO @ Tue, 16 Jun 2020 09:40:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:35: 2000000 INFO @ Tue, 16 Jun 2020 09:40:42: 3000000 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 09:40:49: 4000000 INFO @ Tue, 16 Jun 2020 09:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.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 09:40:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:56: 5000000 INFO @ Tue, 16 Jun 2020 09:40:58: 1000000 INFO @ Tue, 16 Jun 2020 09:41:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:02: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6017 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:04: 6000000 INFO @ Tue, 16 Jun 2020 09:41:06: 2000000 INFO @ Tue, 16 Jun 2020 09:41:11: 7000000 INFO @ Tue, 16 Jun 2020 09:41:12: 3000000 INFO @ Tue, 16 Jun 2020 09:41:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:15: #1 total tags in treatment: 7653421 INFO @ Tue, 16 Jun 2020 09:41:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:15: #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 09:41:15: #1 tags after filtering in treatment: 7653421 INFO @ Tue, 16 Jun 2020 09:41:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:16: #2 number of paired peaks: 2566 INFO @ Tue, 16 Jun 2020 09:41:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:16: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 09:41:16: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 16 Jun 2020 09:41:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.10_model.r INFO @ Tue, 16 Jun 2020 09:41:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:19: 4000000 INFO @ Tue, 16 Jun 2020 09:41:26: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:41:32: 6000000 INFO @ Tue, 16 Jun 2020 09:41:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:39: 7000000 INFO @ Tue, 16 Jun 2020 09:41:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:44: #1 total tags in treatment: 7653421 INFO @ Tue, 16 Jun 2020 09:41:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:44: #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 09:41:44: #1 tags after filtering in treatment: 7653421 INFO @ Tue, 16 Jun 2020 09:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:45: #2 number of paired peaks: 2566 INFO @ Tue, 16 Jun 2020 09:41:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:45: #2 predicted fragment length is 140 bps INFO @ Tue, 16 Jun 2020 09:41:45: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 16 Jun 2020 09:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.20_model.r INFO @ Tue, 16 Jun 2020 09:41:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3614 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6720161/SRX6720161.20_summits.bed INFO @ Tue, 16 Jun 2020 09:42:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1638 records, 4 fields): 3 millis CompletedMACS2peakCalling