Job ID = 6367616 SRX = SRX341784 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:30:35 prefetch.2.10.7: 1) Downloading 'SRR959925'... 2020-06-15T23:30:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:26 prefetch.2.10.7: 'SRR959925' is valid 2020-06-15T23:32:26 prefetch.2.10.7: 1) 'SRR959925' was downloaded successfully Read 10834267 spots for SRR959925/SRR959925.sra Written 10834267 spots for SRR959925/SRR959925.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: 00:03:08 10834267 reads; of these: 10834267 (100.00%) were unpaired; of these: 934571 (8.63%) aligned 0 times 8745360 (80.72%) aligned exactly 1 time 1154336 (10.65%) aligned >1 times 91.37% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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] 4983571 / 9899696 = 0.5034 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 08:39:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.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 08:39:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:46: 1000000 INFO @ Tue, 16 Jun 2020 08:39:51: 2000000 INFO @ Tue, 16 Jun 2020 08:39:57: 3000000 INFO @ Tue, 16 Jun 2020 08:40:02: 4000000 INFO @ Tue, 16 Jun 2020 08:40:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:07: #1 total tags in treatment: 4916125 INFO @ Tue, 16 Jun 2020 08:40:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:07: #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 08:40:08: #1 tags after filtering in treatment: 4916125 INFO @ Tue, 16 Jun 2020 08:40:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:08: #2 looking for paired plus/minus strand peaks... 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 08:40:08: #2 number of paired peaks: 1149 INFO @ Tue, 16 Jun 2020 08:40:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:08: #2 predicted fragment length is 337 bps INFO @ Tue, 16 Jun 2020 08:40:08: #2 alternative fragment length(s) may be 337 bps INFO @ Tue, 16 Jun 2020 08:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.05_model.r INFO @ Tue, 16 Jun 2020 08:40:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.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 08:40:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:16: 1000000 INFO @ Tue, 16 Jun 2020 08:40:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:21: 2000000 INFO @ Tue, 16 Jun 2020 08:40:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3181 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:27: 3000000 INFO @ Tue, 16 Jun 2020 08:40:33: 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 @ Tue, 16 Jun 2020 08:40:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:38: #1 total tags in treatment: 4916125 INFO @ Tue, 16 Jun 2020 08:40:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:38: #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 08:40:38: #1 tags after filtering in treatment: 4916125 INFO @ Tue, 16 Jun 2020 08:40:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:38: #2 number of paired peaks: 1149 INFO @ Tue, 16 Jun 2020 08:40:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:39: #2 predicted fragment length is 337 bps INFO @ Tue, 16 Jun 2020 08:40:39: #2 alternative fragment length(s) may be 337 bps INFO @ Tue, 16 Jun 2020 08:40:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.10_model.r INFO @ Tue, 16 Jun 2020 08:40:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.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 08:40:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:46: 1000000 INFO @ Tue, 16 Jun 2020 08:40:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:51: 2000000 INFO @ Tue, 16 Jun 2020 08:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2237 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:57: 3000000 INFO @ Tue, 16 Jun 2020 08:41:02: 4000000 INFO @ Tue, 16 Jun 2020 08:41:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:41:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:41:07: #1 total tags in treatment: 4916125 INFO @ Tue, 16 Jun 2020 08:41:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:07: #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 08:41:07: #1 tags after filtering in treatment: 4916125 INFO @ Tue, 16 Jun 2020 08:41:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:08: #2 number of paired peaks: 1149 INFO @ Tue, 16 Jun 2020 08:41:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:08: #2 predicted fragment length is 337 bps INFO @ Tue, 16 Jun 2020 08:41:08: #2 alternative fragment length(s) may be 337 bps INFO @ Tue, 16 Jun 2020 08:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.20_model.r INFO @ Tue, 16 Jun 2020 08:41:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX341784/SRX341784.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:24: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1422 records, 4 fields): 3 millis CompletedMACS2peakCalling