Job ID = 6507896 SRX = SRX494981 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:22:33 prefetch.2.10.7: 1) Downloading 'SRR1198513'... 2020-06-26T13:22:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:23:29 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:23:30 prefetch.2.10.7: 'SRR1198513' is valid 2020-06-26T13:23:30 prefetch.2.10.7: 1) 'SRR1198513' was downloaded successfully Read 11474202 spots for SRR1198513/SRR1198513.sra Written 11474202 spots for SRR1198513/SRR1198513.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: 00:01:39 11474202 reads; of these: 11474202 (100.00%) were unpaired; of these: 2186386 (19.05%) aligned 0 times 6611733 (57.62%) aligned exactly 1 time 2676083 (23.32%) aligned >1 times 80.95% overall alignment rate Time searching: 00:01:39 Overall time: 00:01:39 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] 1306050 / 9287816 = 0.1406 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 @ Fri, 26 Jun 2020 22:27:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.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 @ Fri, 26 Jun 2020 22:27:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:27:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:28:05: 1000000 INFO @ Fri, 26 Jun 2020 22:28:11: 2000000 INFO @ Fri, 26 Jun 2020 22:28:16: 3000000 INFO @ Fri, 26 Jun 2020 22:28:21: 4000000 INFO @ Fri, 26 Jun 2020 22:28:27: 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 @ Fri, 26 Jun 2020 22:28:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.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 @ Fri, 26 Jun 2020 22:28:29: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:28:29: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:28:33: 6000000 INFO @ Fri, 26 Jun 2020 22:28:37: 1000000 INFO @ Fri, 26 Jun 2020 22:28:39: 7000000 INFO @ Fri, 26 Jun 2020 22:28:44: 2000000 INFO @ Fri, 26 Jun 2020 22:28:46: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 22:28:46: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 22:28:46: #1 total tags in treatment: 7981766 INFO @ Fri, 26 Jun 2020 22:28:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:28:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:28:46: #1 tags after filtering in treatment: 7981766 INFO @ Fri, 26 Jun 2020 22:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:28:46: #1 finished! INFO @ Fri, 26 Jun 2020 22:28:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:28:47: #2 number of paired peaks: 1848 INFO @ Fri, 26 Jun 2020 22:28:47: start model_add_line... INFO @ Fri, 26 Jun 2020 22:28:47: start X-correlation... INFO @ Fri, 26 Jun 2020 22:28:47: end of X-cor INFO @ Fri, 26 Jun 2020 22:28:47: #2 finished! INFO @ Fri, 26 Jun 2020 22:28:47: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 22:28:47: #2 alternative fragment length(s) may be 2,133,155 bps INFO @ Fri, 26 Jun 2020 22:28:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.05_model.r INFO @ Fri, 26 Jun 2020 22:28:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:28:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:28:50: 3000000 INFO @ Fri, 26 Jun 2020 22:28:57: 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 @ Fri, 26 Jun 2020 22:28:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.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 @ Fri, 26 Jun 2020 22:28:59: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:28:59: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:29:03: 5000000 INFO @ Fri, 26 Jun 2020 22:29:06: 1000000 INFO @ Fri, 26 Jun 2020 22:29:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:29:10: 6000000 INFO @ Fri, 26 Jun 2020 22:29:13: 2000000 INFO @ Fri, 26 Jun 2020 22:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.05_summits.bed INFO @ Fri, 26 Jun 2020 22:29:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2562 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:29:17: 7000000 INFO @ Fri, 26 Jun 2020 22:29:19: 3000000 INFO @ Fri, 26 Jun 2020 22:29:23: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 22:29:23: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 22:29:23: #1 total tags in treatment: 7981766 INFO @ Fri, 26 Jun 2020 22:29:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:29:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:29:23: #1 tags after filtering in treatment: 7981766 INFO @ Fri, 26 Jun 2020 22:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:23: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:24: #2 number of paired peaks: 1848 INFO @ Fri, 26 Jun 2020 22:29:24: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:24: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:24: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:24: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:24: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 22:29:24: #2 alternative fragment length(s) may be 2,133,155 bps INFO @ Fri, 26 Jun 2020 22:29:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.10_model.r INFO @ Fri, 26 Jun 2020 22:29:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:29:25: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:29:31: 5000000 INFO @ Fri, 26 Jun 2020 22:29:37: 6000000 INFO @ Fri, 26 Jun 2020 22:29:42: 7000000 INFO @ Fri, 26 Jun 2020 22:29:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:29:47: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 22:29:47: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 22:29:47: #1 total tags in treatment: 7981766 INFO @ Fri, 26 Jun 2020 22:29:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:29:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:29:47: #1 tags after filtering in treatment: 7981766 INFO @ Fri, 26 Jun 2020 22:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:29:47: #1 finished! INFO @ Fri, 26 Jun 2020 22:29:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:29:48: #2 number of paired peaks: 1848 INFO @ Fri, 26 Jun 2020 22:29:48: start model_add_line... INFO @ Fri, 26 Jun 2020 22:29:48: start X-correlation... INFO @ Fri, 26 Jun 2020 22:29:48: end of X-cor INFO @ Fri, 26 Jun 2020 22:29:48: #2 finished! INFO @ Fri, 26 Jun 2020 22:29:48: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 22:29:48: #2 alternative fragment length(s) may be 2,133,155 bps INFO @ Fri, 26 Jun 2020 22:29:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.20_model.r INFO @ Fri, 26 Jun 2020 22:29:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:29:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.10_summits.bed INFO @ Fri, 26 Jun 2020 22:29:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (906 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:30:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494981/SRX494981.20_summits.bed INFO @ Fri, 26 Jun 2020 22:30:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (287 records, 4 fields): 2 millis CompletedMACS2peakCalling