Job ID = 6366334 SRX = SRX113608 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:44 prefetch.2.10.7: 1) Downloading 'SRR393708'... 2020-06-15T22:29:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:16 prefetch.2.10.7: 'SRR393708' is valid 2020-06-15T22:30:16 prefetch.2.10.7: 1) 'SRR393708' was downloaded successfully Read 6956186 spots for SRR393708/SRR393708.sra Written 6956186 spots for SRR393708/SRR393708.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: 00:01:20 6956186 reads; of these: 6956186 (100.00%) were unpaired; of these: 1324749 (19.04%) aligned 0 times 3948630 (56.76%) aligned exactly 1 time 1682807 (24.19%) aligned >1 times 80.96% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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_rmdupse_core] 2733258 / 5631437 = 0.4854 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 07:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.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 07:33:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:33:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:33:39: 1000000 INFO @ Tue, 16 Jun 2020 07:33:46: 2000000 INFO @ Tue, 16 Jun 2020 07:33:52: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:33:52: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:33:52: #1 total tags in treatment: 2898179 INFO @ Tue, 16 Jun 2020 07:33:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:33:52: #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 07:33:52: #1 tags after filtering in treatment: 2898179 INFO @ Tue, 16 Jun 2020 07:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:33:52: #1 finished! INFO @ Tue, 16 Jun 2020 07:33:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:33:53: #2 number of paired peaks: 3674 INFO @ Tue, 16 Jun 2020 07:33:53: start model_add_line... INFO @ Tue, 16 Jun 2020 07:33:53: start X-correlation... INFO @ Tue, 16 Jun 2020 07:33:53: end of X-cor INFO @ Tue, 16 Jun 2020 07:33:53: #2 finished! INFO @ Tue, 16 Jun 2020 07:33:53: #2 predicted fragment length is 191 bps INFO @ Tue, 16 Jun 2020 07:33:53: #2 alternative fragment length(s) may be 2,191 bps INFO @ Tue, 16 Jun 2020 07:33:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.05_model.r INFO @ Tue, 16 Jun 2020 07:33:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:33:53: #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 07:34:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.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 07:34:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.05_summits.bed INFO @ Tue, 16 Jun 2020 07:34:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1847 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:34:08: 1000000 INFO @ Tue, 16 Jun 2020 07:34:14: 2000000 INFO @ Tue, 16 Jun 2020 07:34:19: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:34:19: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:34:19: #1 total tags in treatment: 2898179 INFO @ Tue, 16 Jun 2020 07:34:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:19: #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 07:34:19: #1 tags after filtering in treatment: 2898179 INFO @ Tue, 16 Jun 2020 07:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:20: #2 number of paired peaks: 3674 INFO @ Tue, 16 Jun 2020 07:34:20: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:20: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:20: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:20: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:20: #2 predicted fragment length is 191 bps INFO @ Tue, 16 Jun 2020 07:34:20: #2 alternative fragment length(s) may be 2,191 bps INFO @ Tue, 16 Jun 2020 07:34:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.10_model.r INFO @ Tue, 16 Jun 2020 07:34:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:34:28: #3 Call peaks for each chromosome... 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 07:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.10_summits.bed INFO @ Tue, 16 Jun 2020 07:34:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (543 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:34:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.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 07:34:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:34:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:34:38: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:34:44: 2000000 INFO @ Tue, 16 Jun 2020 07:34:49: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:34:49: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:34:49: #1 total tags in treatment: 2898179 INFO @ Tue, 16 Jun 2020 07:34:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:34:49: #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 07:34:49: #1 tags after filtering in treatment: 2898179 INFO @ Tue, 16 Jun 2020 07:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:34:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:34:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:34:49: #2 number of paired peaks: 3674 INFO @ Tue, 16 Jun 2020 07:34:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:34:49: start X-correlation... INFO @ Tue, 16 Jun 2020 07:34:49: end of X-cor INFO @ Tue, 16 Jun 2020 07:34:49: #2 finished! INFO @ Tue, 16 Jun 2020 07:34:49: #2 predicted fragment length is 191 bps INFO @ Tue, 16 Jun 2020 07:34:49: #2 alternative fragment length(s) may be 2,191 bps INFO @ Tue, 16 Jun 2020 07:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.20_model.r INFO @ Tue, 16 Jun 2020 07:34:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:34:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:34:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:35:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:35:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:35:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX113608/SRX113608.20_summits.bed INFO @ Tue, 16 Jun 2020 07:35:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling