Job ID = 6368705 SRX = SRX5402729 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:27 prefetch.2.10.7: 1) Downloading 'SRR8602963'... 2020-06-16T00:30:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:55 prefetch.2.10.7: 'SRR8602963' is valid 2020-06-16T00:30:55 prefetch.2.10.7: 1) 'SRR8602963' was downloaded successfully 2020-06-16T00:30:55 prefetch.2.10.7: 'SRR8602963' has 0 unresolved dependencies Read 3253636 spots for SRR8602963/SRR8602963.sra Written 3253636 spots for SRR8602963/SRR8602963.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: 00:00:40 3253636 reads; of these: 3253636 (100.00%) were unpaired; of these: 169272 (5.20%) aligned 0 times 2802582 (86.14%) aligned exactly 1 time 281782 (8.66%) aligned >1 times 94.80% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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_rmdupse_core] 1768750 / 3084364 = 0.5735 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 09:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.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 09:32:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:50: 1000000 INFO @ Tue, 16 Jun 2020 09:32:52: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:52: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:52: #1 total tags in treatment: 1315614 INFO @ Tue, 16 Jun 2020 09:32:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:52: #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 09:32:52: #1 tags after filtering in treatment: 1315614 INFO @ Tue, 16 Jun 2020 09:32:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:52: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:52: #2 number of paired peaks: 5425 INFO @ Tue, 16 Jun 2020 09:32:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:52: #2 predicted fragment length is 187 bps INFO @ Tue, 16 Jun 2020 09:32:52: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 16 Jun 2020 09:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.05_model.r INFO @ Tue, 16 Jun 2020 09:32:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4167 records, 4 fields): 6 millis CompletedMACS2peakCalling 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 09:33:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.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 09:33:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:21: 1000000 INFO @ Tue, 16 Jun 2020 09:33:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:22: #1 total tags in treatment: 1315614 INFO @ Tue, 16 Jun 2020 09:33:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:22: #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 09:33:22: #1 tags after filtering in treatment: 1315614 INFO @ Tue, 16 Jun 2020 09:33:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:22: #2 number of paired peaks: 5425 INFO @ Tue, 16 Jun 2020 09:33:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:22: #2 predicted fragment length is 187 bps INFO @ Tue, 16 Jun 2020 09:33:22: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 16 Jun 2020 09:33:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.10_model.r INFO @ Tue, 16 Jun 2020 09:33:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3404 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 09:33:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.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 09:33:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:45: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:51: 1000000 INFO @ Tue, 16 Jun 2020 09:33:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:53: #1 total tags in treatment: 1315614 INFO @ Tue, 16 Jun 2020 09:33:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:53: #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 09:33:53: #1 tags after filtering in treatment: 1315614 INFO @ Tue, 16 Jun 2020 09:33:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:53: #2 number of paired peaks: 5425 INFO @ Tue, 16 Jun 2020 09:33:53: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:53: #2 predicted fragment length is 187 bps INFO @ Tue, 16 Jun 2020 09:33:53: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 16 Jun 2020 09:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.20_model.r INFO @ Tue, 16 Jun 2020 09:33:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402729/SRX5402729.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2524 records, 4 fields): 4 millis CompletedMACS2peakCalling