Job ID = 6368708 SRX = SRX5402732 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:37 prefetch.2.10.7: 1) Downloading 'SRR8602966'... 2020-06-16T00:22:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:36 prefetch.2.10.7: 'SRR8602966' is valid 2020-06-16T00:23:36 prefetch.2.10.7: 1) 'SRR8602966' was downloaded successfully 2020-06-16T00:23:36 prefetch.2.10.7: 'SRR8602966' has 0 unresolved dependencies Read 6768843 spots for SRR8602966/SRR8602966.sra Written 6768843 spots for SRR8602966/SRR8602966.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: 00:01:17 6768843 reads; of these: 6768843 (100.00%) were unpaired; of these: 542880 (8.02%) aligned 0 times 5726106 (84.60%) aligned exactly 1 time 499857 (7.38%) aligned >1 times 91.98% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 4447496 / 6225963 = 0.7143 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 09:26:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.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 09:26:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:40: 1000000 INFO @ Tue, 16 Jun 2020 09:26:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:44: #1 total tags in treatment: 1778467 INFO @ Tue, 16 Jun 2020 09:26:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:44: #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 09:26:44: #1 tags after filtering in treatment: 1778467 INFO @ Tue, 16 Jun 2020 09:26:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:44: #2 number of paired peaks: 5256 INFO @ Tue, 16 Jun 2020 09:26:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:44: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:26:44: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 16 Jun 2020 09:26:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.05_model.r INFO @ Tue, 16 Jun 2020 09:26:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.05_summits.bed INFO @ Tue, 16 Jun 2020 09:26:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3897 records, 4 fields): 5 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 09:27:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.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 09:27:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:09: 1000000 INFO @ Tue, 16 Jun 2020 09:27:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:14: #1 total tags in treatment: 1778467 INFO @ Tue, 16 Jun 2020 09:27:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:14: #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 09:27:14: #1 tags after filtering in treatment: 1778467 INFO @ Tue, 16 Jun 2020 09:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:14: #2 number of paired peaks: 5256 INFO @ Tue, 16 Jun 2020 09:27:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:14: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:27:14: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 16 Jun 2020 09:27:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.10_model.r INFO @ Tue, 16 Jun 2020 09:27:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3104 records, 4 fields): 4 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 09:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.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 09:27:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:34: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:27:41: 1000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:46: #1 total tags in treatment: 1778467 INFO @ Tue, 16 Jun 2020 09:27:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:46: #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 09:27:46: #1 tags after filtering in treatment: 1778467 INFO @ Tue, 16 Jun 2020 09:27:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:46: #2 number of paired peaks: 5256 INFO @ Tue, 16 Jun 2020 09:27:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:46: #2 predicted fragment length is 157 bps INFO @ Tue, 16 Jun 2020 09:27:46: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 16 Jun 2020 09:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.20_model.r INFO @ Tue, 16 Jun 2020 09:27:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402732/SRX5402732.20_summits.bed INFO @ Tue, 16 Jun 2020 09:27:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2434 records, 4 fields): 18 millis CompletedMACS2peakCalling