Job ID = 6368535 SRX = SRX5020763 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:18:36 prefetch.2.10.7: 1) Downloading 'SRR8201386'... 2020-06-16T00:18:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:21:42 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:21:43 prefetch.2.10.7: 'SRR8201386' is valid 2020-06-16T00:21:43 prefetch.2.10.7: 1) 'SRR8201386' was downloaded successfully Read 14563646 spots for SRR8201386/SRR8201386.sra Written 14563646 spots for SRR8201386/SRR8201386.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: 00:03:20 14563646 reads; of these: 14563646 (100.00%) were unpaired; of these: 1121557 (7.70%) aligned 0 times 11320240 (77.73%) aligned exactly 1 time 2121849 (14.57%) aligned >1 times 92.30% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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] 9365308 / 13442089 = 0.6967 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 09:28:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.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 09:28:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:47: 1000000 INFO @ Tue, 16 Jun 2020 09:28:52: 2000000 INFO @ Tue, 16 Jun 2020 09:28:56: 3000000 INFO @ Tue, 16 Jun 2020 09:29:01: 4000000 INFO @ Tue, 16 Jun 2020 09:29:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:02: #1 total tags in treatment: 4076781 INFO @ Tue, 16 Jun 2020 09:29:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:02: #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 09:29:02: #1 tags after filtering in treatment: 4076781 INFO @ Tue, 16 Jun 2020 09:29:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:02: #2 number of paired peaks: 1012 INFO @ Tue, 16 Jun 2020 09:29:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:02: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 09:29:02: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 16 Jun 2020 09:29:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.05_model.r INFO @ Tue, 16 Jun 2020 09:29:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:02: #3 Pre-compute pvalue-qvalue table... 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 09:29:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.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 09:29:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.05_summits.bed INFO @ Tue, 16 Jun 2020 09:29:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1290 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:17: 1000000 INFO @ Tue, 16 Jun 2020 09:29:23: 2000000 INFO @ Tue, 16 Jun 2020 09:29:28: 3000000 INFO @ Tue, 16 Jun 2020 09:29:34: 4000000 INFO @ Tue, 16 Jun 2020 09:29:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:34: #1 total tags in treatment: 4076781 INFO @ Tue, 16 Jun 2020 09:29:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:34: #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 09:29:34: #1 tags after filtering in treatment: 4076781 INFO @ Tue, 16 Jun 2020 09:29:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:35: #2 number of paired peaks: 1012 INFO @ Tue, 16 Jun 2020 09:29:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:35: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 09:29:35: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 16 Jun 2020 09:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.10_model.r INFO @ Tue, 16 Jun 2020 09:29:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:35: #3 Pre-compute pvalue-qvalue table... 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 09:29:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.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 09:29:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:46: 1000000 INFO @ Tue, 16 Jun 2020 09:29:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (701 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:51: 2000000 INFO @ Tue, 16 Jun 2020 09:29:56: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:30:01: 4000000 INFO @ Tue, 16 Jun 2020 09:30:01: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:01: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:01: #1 total tags in treatment: 4076781 INFO @ Tue, 16 Jun 2020 09:30:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:01: #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 09:30:01: #1 tags after filtering in treatment: 4076781 INFO @ Tue, 16 Jun 2020 09:30:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:30:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:01: #2 number of paired peaks: 1012 INFO @ Tue, 16 Jun 2020 09:30:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:01: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 09:30:01: #2 alternative fragment length(s) may be 120 bps INFO @ Tue, 16 Jun 2020 09:30:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.20_model.r INFO @ Tue, 16 Jun 2020 09:30:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020763/SRX5020763.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 1 millis CompletedMACS2peakCalling